The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces.

Many fungi require specific growth conditions before they can be identified. Direct environmental DNA sequencing is advantageous, although for some taxa, specific primers need to be used for successful amplification of molecular markers. The internal transcribed spacer region is the preferred DNA barcode for fungi. However, inter- and intra-specific distances in ITS sequences highly vary among some fungal groups; consequently, it is not a solely reliable tool for species delineation. Ampelomyces, mycoparasites of the fungal phytopathogen order Erysiphales, can have ITS genetic differences up to 15%; this may lead to misidentification with other closely related unknown fungi. Indeed, Ampelomyces were initially misidentified as other pycnidial mycoparasites, but subsequent research showed that they differ in pycnidia morphology and culture characteristics. We investigated whether the ITS2 nucleotide content and secondary structure was different between Ampelomyces ITS2 sequences and those unrelated to this genus. To this end, we retrieved all ITS sequences referred to as Ampelomyces from the GenBank database. This analysis revealed that fungal ITS environmental DNA sequences are still being deposited in the database under the name Ampelomyces, but they do not belong to this genus. We also detected variations in the conserved hybridization model of the ITS2 proximal 5.8S and 28S stem from two Ampelomyces strains. Moreover, we suggested for the first time that pseudogenes form in the ITS region of this mycoparasite. A phylogenetic analysis based on ITS2 sequences-structures grouped the environmental sequences of putative Ampelomyces into a different clade from the Ampelomyces-containing clades. Indeed, when conducting ITS2 analysis, resolution of genetic distances between Ampelomyces and those putative Ampelomyces improved. Each clade represented a distinct consensus ITS2 S2, which suggested that different pre-ribosomal RNA (pre-rRNA) processes occur across different lineages. This study recommends the use of ITS2 S2s as an important tool to analyse environmental sequencing and unveiling the underlying evolutionary processes.

Introduction

Ribosomes are RNA-protein complexes that are responsible for translating messenger RNA (mRNA) into protein. The eukaryotic nuclear ribosomal DNA (nrDNA) cistron encodes the rRNAs for the small (18S rRNA) and large (5.8S and 28S rRNA) ribosomal subunits. The nrDNA region also contains two spacers. The 1 internal transcribed spacer, ITS1, is located between the 18S and the 5.8S genes and the 2 internal transcribed spacer, ITS2, resides between the 5.8S and the 28S genes [1,2]. In order to fulfill the demand of protein production for various cellular processes, the nrDNA cistrons are transcribed at a high rate by the enzyme polymerase I [3], which generates pre-rRNA. Subsequently, this pre-rRNA undergoes multiple posttranscriptional processing events as well as ribosome biogenesis, which generates functional rRNAs comprising 5.8S, 18S and 28S units. During processing both spacers are removed [1,2].

rRNA genes are highly similar within and between individuals of the same species. Nevertheless, rRNA sequence variations are sufficiently divergent to differentiate one species from another. Consequently, the ITS1, 5.8S and ITS2, named the internal transcribed spacer (ITS) region, have been widely used for molecular identification and phylogenetic studies [4]. Indeed, the nrDNA ITS region is the preferred barcode in fungi classification [5]. However, the identification of fungal DNA environmental samples is challenging. Several taxonomical and phylogenetic fungal groups require appropriate cultural conditions before identification although many fungi are unculturable [6]. Furthermore, for some fungal groups, specific primers are required for successful amplification of other appropriate molecular markers [5,7]. In accordance with the taxonomy and phylogeny of the fungal group under study, the use of only one molecular marker can result in poor species discrimination resolution [8]. For a barcode gap, the interspecific genetic variability needs to be higher than the intraspecific variability. In fungi, the nrDNA ITS region has been widely used as a DNA barcode [8] as it has enough genetic variability to the species level, but sometimes it does not resolve closely phylogenetic related species and some fungi require extra identifiers for species delimitation within a determined genus or family [9]. For example, if some taxa have low ITS interspecific variability other molecular markers need to be used to precisely report genetic diversity [9]. Conversely, intragenomic variation of the ITS can result in overestimate the intraspecific variability in some fungi [9-12]. Thus, relying in the use of only one molecular marker in some fungi can result in poor species discrimination resolution and other molecular barcodes may be required as the accuracy of the identification can be compromised. Therefore, it is crucial to have an optimum barcode gap.

In addition, the ITS1 and ITS2 are assumed to evolve neutrally. However, it has been probed that they are subjected to secondary structural constraints [13,14], which may have an impact on phylogenetic inferences. For instance, the phylogeny of the species from the genus Ampelomyces are primarily based on the ITS region, where some contrasting results have been obtained. Interesting, the utility of Ampelomyces ITS2 secondary structures (S2s) to study its phylogeny has not been investigated even when several works have demonstrated ITS2 S2s can provide with important features to improve phylogenetic analyses [13,15].

Ampelomyces spp. are mycoparasites of the Erysiphaceae fungi [16], which are devastating plant pathogens [17,18] that are responsible for powdery mildew (PM) diseases that afflict important agricultural and ornamental crops worldwide [19]. Despite environmental and health risks [20], agrochemicals are mainly used to control and prevent these PM infections [21]. The potential use of Ampelomyces strains as biocontrol agents against PM fungi have been tested in both field [22-24] and laboratory environments [25,26]. Two different strains [25,27] have been commercialized as biofungicides with some degree of effectiveness [22]. In order to advance the development of potent pest control products based on Ampelomyces strains, it is important to fully characterize their intra- and inter-population genetic diversity over space and time. Some studies suggest that the Ampelomyces mycoparasites are complex organisms that lack host specificity [28,29]. Nevertheless, temporal isolation can lead to genetic variability within populations [23]. Ampelomyces strains that infect apple powdery mildew (APM, caused by Podosphaera leucotricha) were found to be cryptic species of non-apple powdery mildew (non-APM) that resulted from an effective allopatric process. Furthermore, recombination events between APM and non-APM Ampelomyces were also detected, although their sexual reproductive stage was not observed [23].

Undoubtedly, population genetic studies in Ampelomyces are difficult to carry out. For example, some nucleotide sequences deposited in public databases under the name of Ampelomyces are not related to the mycoparasites by comparing their phylogeny and growth rates in culture [30,31]. In addition, most phylogenetic studies have been based on the ITS region [28-30,32-34] and other molecular markers may be required for species identification due to the high genetic divergence of ITS sequences from some Ampelomyces lineages that can reach up to 15% [24,30]. Nevertheless, the successful design of primers for other markers are difficult to obtain, which often occurs for other fungi. In order to resolve these issues and contribute to knowledge and future research in this area, we have investigated whether ITS2 S2s contain specific features that may be incorporated into phylogenetic analysis and provide with novel important information regarding evolutive processes occurring in Ampelomyces. Indeed, the utility of the ITS2 S2 to study the phylogeny of several organisms have been demonstrated [15,35] but it has not been investigated in Ampelomyces.

This study also has investigated whether the nucleotide sequences of the ITS region from fungi sampled in PM-free environments are still being deposited in the GenBank database as species of the genus Ampelomyces. Here, we also evaluated the potential use of the ITS2 S2 as an additional identifier of Ampelomyces against the related fungus Didymella glomerata (previously known as Phoma glomerata) [36] and other putative Ampelomyces fungi isolated from non-PM hosts [37-40]. This analysis included all of the nucleotide sequences comprising the ITS region from Ampelomyces spp. sensu stricto deposited in GenBank until the May 2020 period.

Lastly, we propose that the predicted S2 of ITS2 from Ampelomyces spp. obtained from the ITS2 Database (ITS2-DB) web server [41-45] can be utilized as a new guideline for future molecular identification of ITS sequences extracted from environmental DNA samples.

Materials and methods

Sequence acquisition from the GenBank database

The nucleotide sequences of the nrDNA ITS region of all species identified with the name of Ampelomyces were searched in the GenBank database using the query: Ampelomyces (in plain text). Partial sequences of the ITS region were not included in this analysis. In Table 1 in shows the details of all the 376 nucleotide sequences used in this study, which were derived from 376 Ampelomyces spp. sensu stricto. The former sequences were compared to the following sequences: (1) 10 sequences derived from putative Ampelomyces species (Groups 1 and 2), (2) four sequences belonging to Didymella species and (3) one sequence from Phoma species formed the outgroup taxa (Tables 2–4 in ).

Group 1 contains two sequences of fungi identified as Ampelomyces humuli, which was derived from plant tissues of Picea abies decayed root [46] and from Zea mays [40]. Group 1 also contains three sequences from fungi known to form a different phylogenetic group from the ‘true’ species of the genus Ampelomyces [30,31] and are referred to as A. humuli (GenBank sequence identifier (GI) AF035779), Ampelomyces quercinus (GI: AF035778) and Ampelomyces sp. (GI: U82452). Ampelomyces quercinus is currently known as Nothophoma quercina [36], Table 2 in .

Group 2 has five nucleotide sequences belonging to three fungi identified as A. humuli isolated from human nasal mucus [39] and soil [37], as well as two fungi identified as Ampelomyces spp. derived from creosote-treated crosstie waste [38] and air samples [47], Table 3 in . Finally, the outgroup is formed by ITS sequences belonging to four Didymella species [31,48-50] and one Phoma species [51], Table 4 in .

These groups were established in order to differentiate ITS sequences extracted from PMs that were unrelated to the genus Ampelomyces by cultural growth and phylogeny [30,31] from those sequences extracted from plant material and PM; and no plant material and human mucus, which were defined as groups 1 and 2, respectively.

Selection and extraction of complete nrDNA ITS sequences from Ampelomyces spp. sensu stricto

Complete nucleotide sequences of ITS regions belonging to the Ampelomyces mycoparasites were selected as ‘true’ if their original references indicated that isolates or strains were derived from PM environments and if their cultural growth characteristics were also indicated. Any other relevant information such as photographs of fruiting bodies (pycnidia) and the type of phylogenetic analysis were considered important for the preliminary selection of key sequences.

We did not include partial sequences of ITS regions even when these were extracted from Ampelomyces species infecting PM fungi that had a phylogenetic analysis that correctly identified the mycoparasites from the outgroup taxa. This approach was required to correctly model their ITS2 S2s and to visualize the hybridization model of its proximal stem. All complete ITS sequences were retrieved directly from GenBank in the FASTA format. Redundant or partial sequences that were deposited by different authors that corresponded to the same type of culture were not selected even if they belonged to the genus Ampelomyces. We confirmed that these sequences belonged to the Ampelomyces mycoparasites by manually checking their original references.

Comparison of ITS sequence length and nucleotide content between species of the genus Ampelomyces and to those Ampelomyces identified from PM-free environments

In this report, a total of 376 ITS sequences that correspond to the ‘true’ Ampelomyces species (Table 1 in ) were compared to those from fungal species identified with the generic name of Ampelomyces and comprised by (1) putative Ampelomyces groups 1 and 2 and (2) outgroup taxa, (Tables 2–4 in

Sequence statistics of the nrDNA ITS region and its individual components (ITS1, 5.8S and ITS2)

Statistics of the nucleotide pair bases (G/C) and (A/T) expressed as total percentages from the ITS region and its components (ITS1, 5.8S and ITS2) were calculated for all groups using the Sequence Manipulation Suite at https://www.bioinformatics.org/sms2/dna_stats.html [52]. In order to determine the statistical significance of the sequence lengths and nucleotide contents of the ITS regions among fungal groups, the Kruskal-Wallis rank sum test for multiple independent samples was performed with the web server https://astatsa.com/KruskalWallisTest/ [53]. In brief, the differences among groups were evaluated by the Dunn post-hoc pairwise multiple comparison test after confirming that at least one group was different using the Kruskal-Wallis test. Values were statistically significant with a p < 0.05. The Dunn p-values were calculated without p-value adjustment.

Partial 18S and 28S sequences that flank the ITS region were deleted before the analysis. Nevertheless, some DNA environmental sequences do not contain the common sequence motifs at the borders of the ITS region (partial 18S and 28S sequences) despite being deposited as complete ITS region sequences; and it is difficult to delimitate them. Thus, the total nucleotide length of the complete ITS region for each fungus was normalized to the maximum length (697 base pairs) expected from ITS region sequences belonging to ascomycetes fungi that were amplified using the primers ITS1f and ITS4 as previously reported [54]; and statistical significance was determine by the Kruskal-Wallis rank sum test as described above.

Insertion-deletion polymorphic analysis of the ITS1 among Ampelomyces groups and between unrelated groups

We investigate the distribution of insertion-deletion polymorphisms in ITS1 sequences that could cause sequence length variations. Multiple sequence alignment (MSA) of Ampelomyces ITS sequences extracted from each genus of PM were aligned independently, while those from putative Ampelomyces Groups 1 and 2 together with the outgroup were conducted with the ‘multiple alignment using fast Fourier transform’ (MAFFT) web service tool available at https://mafft.cbrc.jp/alignment/server/ [55-57]. The following parameters were used: (1) a scoring matrix 200 PAM/k = 2 and (2) a gap opening penalty of 1.53. The plots and alignments were executed with a threshold score of 39 (E = 8.4e-11). The sequences were aligned using the program MAFFTWS v7 and through the iterative refinement method L-INS-i (accuracy orientated) that includes local pairwise alignment. Resulting multiple alignments were saved in the FASTA format. All ITS1 sequences were extracted from the ITS alignment with MEGA-X V10.1.8 software [58]. Nucleotide polymorphism analysis was conducted with the DnaSP 6.0 software [59,60].

ITS2 structure prediction

To evaluate the utility of ITS2 S2s, the ITS2 sequences from each Ampelomyces spp. sensu stricto and those from the putative Ampelomyces groups were extracted from the alignment between the 5.8S and 28S gene proximal stem motifs using the new version of the web interface Internal Transcribed Spacer 2 Ribosomal RNA Database, ITS2-DB, at http://its2.bioapps.biozentrum.uni-wuerzburg.de/ [41]. The complementary hybridization of both regions was observed using the ITS2-DB together with its ‘Annotate’ tool, which functions based on the hidden Markov models (HMMs), [61]. In order to predict the folding of the ITS2 S2, we used an expected value for detection of significant hits below 0.001 (E-value < 0.001) and HMMs for fungal organisms with a minimum size of 150 nucleotides. Visualization of the ITS2 S2 was conducted using the program PseudoViewer v3.0 at http://pseudoviewer.inha.ac.kr/ [62]. We selected only those S2s that were obtained by direct folding and preferred over other modelled S2s.

We also obtained minimum free energy structures of the ITS2 using the RNAfold online tool, which were visualized using a force directed graph layout (forna) [63] via the web application from ViennaRNA Web Services [64].

Multiple ITS2 sequence-structure alignment and phylogenetic tree of Ampelomyces strains

To determine Ampelomyces lineages based on its ITS2 S2s, a simultaneous multiple sequence alignment of ITS2 S2s was firstly estimated. We used the online tool LocARNA v4.8.3 at http://rna.informatik.uni-freiburg.de [65] for multiple alignment of RNA molecules. The input data were extracted from the ITS2-DB and comprised 25 ITS2 sequences and structures, which were obtained from the following sources: (1) 21 Ampelomyces spp., (2) two putative Ampelomyces Group 1 extracted from Golovinomyces cichoracearum (GI: U82452) and P. abies decayed root (GI: DQ093657), (3) one Putative Ampelomyces Group 2 extracted from creosote-treated crosstie waste (GI:GQ241274) and (4) one outgroup member from Phoma herbarum (GI: JF810528), (Table 5 in ). The selected parameters consisted of a global alignment in LocARNA-P (probabilistic) mode where the complete input ITS2 sequences were aligned. For the alignment scoring, the default values were used. Thus, the values for structure weight, insertion-deletion (indel) opening score and indel score were 200, -800 and -50, respectively. The match score for the alignment of two identical sequences was 50, while the mismatch score for the alignment of two different sequences was 0. The RIBOSUM matrix was used to score sequence match/mismatch. The parameters of RNA folding energy were used with a temperature of 37°C. The energy parameter settings were described by the Turner model 2004 [66].

The resulting multiple ITS2 sequence-structure alignment was analysed by the molecular evolutionary genetics analysis (MEGA)-X v10.1.8 software in order to calculate a maximum likelihood tree based on the Kimura two-parameter DNA model of evolution [67]. This analysis was conducted with a gamma distribution for the evolutionary rate among sites. The branches of the inferred unrooted tree were assayed using the bootstrap analysis with 1 000 replicates. The phylogram of 21 Ampelomyces sequence structure pairs was visualized using FigTree v1.4.4 software [68].

A second phylogenetic tree based on ITS sequences was built to compare the distribution of Ampelomyces clades and not related fungi with those obtained using ITS2 S2s, but the dataset consisted of 21 ITS from Ampelomyces spp. sensu stricto extracted from seven powdery mildew genera and four from the following sources: (1) two putative Ampelomyces Group 1extracted from Golovinomyces cichoracearum (GI: U82452) and P. abies decayed root (GI: DQ093657), (2) one Putative Ampelomyces Group 2 extracted from creosote-treated crosstie waste (GI: GQ241274) and (3) one outgroup member from Phoma herbarum (GI: JF810528), (Table 5.1 in ) were utilized as the input dataset to conduct a MSA via the MAFFT web server at https://mafft.cbrc.jp/alignment/server/ [57] under the previous conditions. Next, phylogenetic analysis was performed with MEGA-X software [58] using the maximum likelihood method and the Tamura-Nei model [69] with gamma distribution among the sites. The branches of the inferred unrooted tree were assayed using bootstrap analysis with 1 000 replicates. The phylogram was visualized using FigTree v1.4.4 software [68].

For a comprehensible analysis, a second phylogenetic tree was constructed as described above, but the input data consisted of 26 ITS2 S2s from Ampelomyces spp. sensu stricto extracted from seven powdery mildew genera and four from the following sources: (1) Group 1, putative Ampelomyces extracted from P. abies (GI: DQ093657); (2) Group 2 that consisted of creosote-treated crosstie waste (GI: GQ241274) and (3) two of the outgroup members, D. glomerata (GI: MH864401) from soil and Malus sylvestris (GI: JF810528), (Table 5.2 in ).

Evolutionary distance estimation among Ampelomyces lineages and putative Ampelomyces

The resolution power of the phylogeny based on the ITS2 S2s to distinguish the ‘true’ Ampelomyces from putative Ampelomyces was evaluated by comparing the genetic divergences obtained among groups based on the simultaneous ITS2 sequences and structures alignment, and on the MSA of complete ITS sequences. The input data was the 25 ITS2 sequences consisted of 21 from Ampelomyces spp., three from putative Ampelomyces and one from the outgroup taxa as described in the previous section, Table 5 and 5.1 in .

The mean sequence divergence values among the major clades were estimated using MEGA-X software with the log-determinant (log-det) method and the Tamura-Kumar model [70]. The rate variation among sites was modelled using a gamma distribution (with the shape parameter = 5) and standard errors of the estimate distances were calculated with MEGA-X software using the bootstrap method.

Prediction of consensus ITS2 S2s from Ampelomyces

For comparative purposes of sequence-structure motifs among fungal groups, the resulting simultaneous alignment of ITS2 sequences and structures obtained via the ITS2-DB was used as input into the 4SALE v1.7.1 software [71,72] to obtain consensus ITS2 S2s from the following sources: (1) five from Ampelomyces spp. extracted from Arthrocladiella mougeotii; (2) four from P. leucotricha; (3) one from Podosphaera ferruginea; (4) four from Erysiphe necator; (5) one from Uncinula necator; (6) four from Podosphaera fusca (GI: DQ490745, DQ490747, DQ490754 and DQ490757); (7) one from Podosphaera xanthii (GI: DQ490759) and (8) four from putative Ampelomyces (GI: DQ093657, GQ241274, JF810528 and U82452).

Results

The first aim of this study was to verify the authenticity of the nucleotide sequences of the ITS regions that were deposited in GenBank under the name Ampelomyces. Until May 2020, 808 sequences were retrieved and 19% were derived from environmental sampling of fungi or plant tissues. Amongst all nucleotide sequences belonging to Ampelomyces spp. sensu stricto, 68% corresponded to the ITS region (complete and partial sequences), 27% were from the actin1 gene, 2.97% corresponded to nucleotide sequences from the small subunit ribosomal (18S) and the large subunit ribosomal (28S) genes (complete and partial sequences) and 0.98% corresponded to those from microsatellites and the sequence of the complete genome of Ampelomyces quisqualis strain MHLAC05119 [8], (Table 1 in ). Since most of the sequences corresponded to the nrDNA ITS region, we focused our analysis on complete sequences of this molecular marker that reduced the dataset to 376 sequences.

Ampelomyces spp. ITS nucleotide content and sequence length do not resemble those extracted from environmental DNA and human mucus samples

From the dataset of Ampelomyces spp. sensu stricto extracted from seven genera of PM fungi (Arthrocladiella, Erysiphe, Golovinomyces, Neoerysiphe, Oidium sp. subgenus Pseudoidium, Phyllactinia and Podosphaera), we found that the sequence lengths of the complete ITS regions (492–502 bp) and their constituents, the ITS1 (182–193 bp), and ITS2 (149–155 bp) varied across the whole population, Table 2 in .

In contrast, the sequence length from the 5.8S ribosomal gene (157 bp) remained constant. The A/T and G/C content for both spacers and the 5.8S ribosomal gene were above and below 50%, respectively. The lowest G/C content value (39.25%) was observed for the ITS1 (), Table 3 in .

In order to verify if the complete fungal ITS sequences from environmental DNA are related to those from Ampelomyces lineages, we have investigated whether they can be differentiated by comparing nucleotide content and sequence length of their complete nrDNA ITS regions. In addition, we used five ITS sequences retrieved from species of the Didymella and Phoma genera, as a reference outgroup. These species are commonly used as outgroup taxa in phylogenetic studies of the Ampelomyces mycoparasites [23,33]. Thus, we compared the sequence length and nucleotide content of the ITS sequences from Ampelomyces spp. sensu stricto to ITS sequences belonging to two groups of putative Ampelomyces. Group 1 contains sequences from Ampelomyces heraclei, A. humuli, and Ampelomyces sp. that were previously shown to be unrelated to the genus Ampelomyces [30,31]. It also contains two other sequences of fungi classified as A. humuli, which were isolated from plant material (P. abies and Zea mays) (Table 4 in ).

On the other hand, Group 2 contains sequences extracted from human and environmental DNA samples, which were classified under the generic name of Ampelomyces (Table 5 in ). We found that the average ITS sequence length for Groups 1 (453.6 bp ± 0.92) and 2 (453 bp ± 1.84), , differed significantly (p-values: < 0.001) by 50 bp when compared to those extracted from the entire Ampelomyces population (498 bp ± 0.004). Indeed, the average sequence lengths of the putative Ampelomyces ITSs were similar to those extracted from species of the Didymella and Phoma genera (452 bp ±0.0), (Table 6 in ).

Several fungal environmental DNA ITS samples from GenBank do not contain nucleotide sequence information at the borders flanking the complete ITS region. Thus, all of the sequence lengths were normalized to the maximum sequence length that can be obtained for fungal species ascomycetes using the primers ITS1f and ITS4 as previously described [54]. After normalizing the sequence lengths, we observed the same differences in length variation of ITS sequences among all fungal groups () as described above. In addition, the normalized sequence length of the complete ITS region from the Ampelomyces lineages is significantly (p-values: < 0.001) higher than those from the putative Ampelomyces (), .

Normalized nrDNA ITS sequence lengths from environmental fungi are similar to those from the outgroup.

The graph shows the normalized sequence length (%) of the ITS region from Ampelomyces strains (n = 376), putative Ampelomyces Groups 1 (n = 5) and 2 (n = 5) as well as the outgroup (n = 5). The normalized ITS sequence length of the Ampelomyces strains was significantly higher than those from putative Ampelomyces Groups 1 and 2 as well as from fungi belonging to the outgroup taxa, with a Kruskal-Wallis chi-squared statistic value of 53.27, a p-value of 1.59e-11 and 3 degrees of freedom. The error bars indicate the S.E.M. and the * indicates the statistical significance at the 5% confidence level.

On the other hand, the normalized sequence lengths of the 5.8S gene and the ITS2 were similar across all the fungal groups. Conversely, the normalized sequence lengths of the ITS1 from Ampelomyces spp. were significantly (p-values: < 0.001) higher than those from Groups 1 and 2 as well as the outgroup taxa ().

In addition, the A/T content of the ITS sequences from Ampelomyces spp. () were significantly (p-values: < 0.001) higher than those from putative Ampelomyces Groups 1 and 2 as well as the outgroup taxa based on the Kruskal-Wallis test and Dunn’s post-hoc test for multiple comparisons. Conversely, the C/G content () around the median of the ITS sequences from Ampelomyces spp. were significantly (p-values: < 0.001) lower than those from putative Ampelomyces groups and the outgroup taxa based on the Kruskal-Wallis test and Dunn’s post-hoc test for multiple comparisons.

Differences in ITS nucleotide contents help in distinguishing putative Ampelomyces from the ‘true’ Ampelomyces.

(A) The A/T and (B) C/G content values around the median for ITS sequences from Ampelomyces spp. (1; n = 376), putative Ampelomyces Groups 1 (2; n = 5) and 2 (3; n = 5) as well as the outgroup (4; n = 5). For each box plot, the central line as well as the top and bottom of each box represent the median, the third and first quartile, respectively. The whiskers indicate the maximum and minimum values, while circles above each box plot represent the outliers of each dataset. The statistical significance of the results was assessed using the Kruskal-Wallis test with Dunn’s post-hoc test for multiple comparisons (p-values< 0.05) with 3 degrees of freedom. The differences were statistically significant at the 5% confidence level.

Even though this study was not focused on identifying the ITS sequences from PM-free environments, we have found that the A/T and C/G median values of fungal Group 1 overlapped the median value from the outgroup. This indicated that the putative Ampelomyces from Group 1 are likely related to the outgroup taxa. We also observed that the nucleotide content values from fungal Group 2 were more varied, but not statistically different from fungal Group 1 (p-value: 0.98 and significance at 5%) and the outgroup taxa (p-value: 0.95 and significance at 5%). In summary, no statistically significant differences in the A/T and C/G content were found between putative Ampelomyces and the outgroup taxa.

Analysis of deletion/insertion polymorphisms in Ampelomyces ITS1 sequences and unrelated sequences

We found that the total number of indels (I = 8) between groups of Ampelomyces isolated from the same PM genera varied as assessed with DnaSP software [59,60]. Visualization of the MSA comprised of 376 ITS1 sequences, revealed that Ampelomyces ITS1 sequences extracted from PM of the genera Erysiphe, Golovinomyces and Podosphaera have indels that are evenly distributed along the sequence. In contrast, the ITS1s from Ampelomyces extracted from Podosphaera fusca in Korea, contained indels, which are more distributed at the beginning of the ITS1 sequence (first 100 nucleotides), while the same Ampelomyces sampled in China harboured indels at the end of the sequence. Conversely, Ampelomyces extracted from the genera Arthrocladiella, Oidium and the subgenus Pseudoidium had indels at the beginning and at the end of the sequence, while Ampelomyces derived from Phyllactinia contained indels localized at the end of the sequence. We also compared the number of indels (I = 8) for all Ampelomyces ITS1 sequences with those from putative Ampelomyces Groups 1 and 2 as well as the outgroup taxa (I = 6) where the ITS1 sequences for all outgroup samples contained indels at various positions across the sequence.

Variations in the hybridization model of a proximal stem containing the 5.8S and 28S motifs were found in two Ampelomyces strains

We further characterized the ITS sequences by modelling the hybridization of a proximal stem containing the 5.8S and 28S motifs that delimitate the S2 of the ITS2 (Table 8 in ). Among the 376 ITS sequences from the ‘true’ Ampelomyces spp., 257 were not amenable for modelling with the ITS2-DB web server because these sequences contained a short 28S motif. Nevertheless, 120 ITS2 sequences were modelled and 118 exhibited the typical hybridization of the proximal stem containing 5.8S and 28S motifs with a Gibbs free energy (dG) of -19 and enthalpy (dH) of -147.1 for the ensemble (Table 8 in ). This S2 is formed by an imperfect stem that harbors one free nucleotide on the 5.8S strand and one free nucleotide on the 28S strand. Interestingly, variations in the dG and dH were detected from three other sequences. For example, DQ490759 had a dG and dH of -15 and -133, respectively, but the assembly of the typical proximal stem was not modified ().

Two variations in the hybridization model of the proximal stem region were found in Ampelomyces.

(A) The typical 5.8S and 28S hybridization model was obtained from an ITS2 sequence extracted from Ampelomyces conidia infecting P. xanthii. (B) A variation in the 5.8S and 28S hybridization model detected in Ampelomyces sp. infecting P. xanthii. (C) Another variation in the 5.8S and 28S hybridization model obtained from Ampelomyces sp. infecting E. necator (Section Uncinula) chasmothecia. The blue nucleotides denote the 5.8S strand, the red nucleotides indicate the 28S strand and the black nucleotides comprise the flanking regions of the ITS2 spacer. The formation of an internal loop is indicated by the two black arrows. The typical free nucleotides found in the 5.8S and 28S strands are indicated with blue and red arrows, respectively. The GenBank accession number is shown below each structure. The Gibbs free energy (dG) and enthalpy (dH) values are shown after the taxon name.

Conversely, the DQ490752 and HM125018 sequences exhibited variations in the model along with thermodynamic changes in energies -13.7 and -16.9, respectively. DQ490752 () corresponded to Ampelomyces sp. isolated from the conidia of P. xanthii infecting Cucurbita. The typical single free nucleotide in the 5.8S motif is absent and it is directly substituted with unaligned nucleotides from both strands that terminate in three free nucleotides. Another variation of the model was identified in the Ampelomyces ITS sequence extracted from the chasmothecia of Erysiphe necator (Section Uncinula) on grapevine bark (). In this model variant, the typical single free nucleotide from the 5.8S motif is absent and it is directly substituted with unaligned nucleotides from both strands that terminate in three free nucleotides. In addition, the dG and dH values for the ensemble of the typical hybridization model of the proximal stem from 118 Ampelomyces ITS2 sequences was -19 and -147.1, respectively. Even though we modelled a small sample of predicted hybridized stems, it appeared that stems with dGs less than -13.7 destabilized this secondary structure while values energy between -15 and -19 confer to the structure with some flexibility.

One common ITS2 S2 was found across Ampelomyces spp. extracted from seven PM genera

From the dataset comprised of 120 ITS2 sequences, only 87 were directly folded and modelled (Table 8 in ). We obtained seven different models. All contained a core structure with four helices (I–IV) and helix III was the longest (). All helices III contained a motif that varied across the Ampelomyces lineages ().

Common features of the ITS2 S2 from Ampelomyces.

(A) The ITS2 S2 from Ampelomyces extracted from seven PM genera. The ITS2 contained a core structure with four helices (I–IV), a U-U mismatch on helix II and a large helix III containing a UGG motif. (B) This ITS2 S2 was found in Ampelomyces sampled in China (GI: DQ490752). The UGGU and UU motifs were located in helix III. The minimum free energy structures were calculated with RNAfold and visualized using a force directed graph layout with the Vienna RNA Web Services [64]. The helices are indicated with Roman numerals (I–IV). The U-U mismatch on helix II and the UGG, UGGU and UU motifs are indicated with arrows.

The most common S2 (Model 1) found in the Ampelomyces population is represented by a four-fingered model with a single-stranded ring rich in pyrimidines situated between helices I and IV. Model 1 also contains the conserved sequence, GTACCC (). In addition, between helices II and III there is another single-stranded ring of two nucleotides (A and T). Helix III comprises the largest helix with five internal loops that terminates in a single-stranded loop of six unpaired nucleotides.

The most common ITS2 S2 (Model 1) found in the Ampelomyces population.

(A) The ITS2 S2 Model 1 derived from Ampelomyces extracted from seven PM genera. (B) The ITS2 S2 Model 7 derived from Ampelomyces extracted from A. mougeotii. Compared to Model 1, Model 7 contains several nucleotide substitutions. Specifically, nucleotides cytosine and uracil in helices III and IV, respectively of Model 1 are present as uracil and thymine in the helices III and IV, respectively of Model 7; (red arrows indicate nucleotide substitutions). The helices are indicated by Roman numerals (I–IV). The following shared ITS2 features are shown in black arrows and circles: (1) a U-U mismatch on helix II and (2) the UGG motif on helix III. A single-stranded ring between helices I and IV is indicated with red left right arrows. It comprises the sequence GTACCC or *UACCC when T is substituted with U. The structures were directly folded and modelled using the ITS2-DB.

Variations of Model 1, referred to as 1–2 and 1–3, were observed in two Ampelomyces sequences extracted from A. mougeotii (Slides 1–3 in ). The variations included a deletion of a pyrimidine in an internal loop of helix II and pyrimidine additions in the single-stranded rings between helices II and III as well as III and IV (slide 3 in ). Model 1 was found in those Ampelomyces spp. infecting several PM species representing seven genera, specifically from A. mougeotii on Lycium hamilifolium, Erysiphe alni, Erysiphe berberidis, Erysiphe convolvuli, Erysiphe cruciferarum, Erysiphe euonymi, Erysiphe heraclei, Erysiphe polygoni, Erysiphe sordida, Erysiphe sp., Erysiphe trifolii, Golovinomyces cichoracearum on Aster salignus and on Lactuca sp., Golovinomyces orontii, Neoerysiphe galeopsidis, Oidium sp., Phyllactinia fraxini, and Podosphaera pannosa (slides 4–13 in ).

A major variation of Model 1 referred to as Model 7 was found from an ITS2 S2 from Ampelomyces sp. extracted from A. mougeotii infecting L. hamilifolium and sampled in Biatorbágy, Hungary (, slide 14 in ). Model 7 contained transition and transversion mutations on helices III and IV, respectively. The common features of Models 1 and 7 are the presence of the U-U mismatch on helix II and the UGG motif on helix III.

The second most common S2, Model 2, () contains a distinctive helix II that has two bulges ending in a large single-stranded loop of 12 unpaired nucleotides (slide 14 in ). Between helices II and III there is a single ring with one nucleotide (A). In addition, helix III has three internal loops, and two bulges with one unpaired nucleotide on each strand. A single-stranded ring with two nucleotides (A-A) is located between helices III and IV. In addition, Model 2 contains a single-stranded ring between helices I and IV that contains the highly conserved sequence, GTCTCC.

The second most common ITS2 S2 (Model 2) found in the Ampelomyces population.

(A) The ITS2 S2 Model 2 derived from mycoparasites extracted from the three PM genera Arthrocladiella, Golovinomyces and Podosphaera. (B) The ITS2 S2 Model 3 was only found in one ITS2 sequence (GenBank accession number DQ490754) from Ampelomyces sp. extracted from P. fusca. The helices are indicated by Roman numerals (I–IV). Single-stranded rings (between helices I and IV) for Models 2 and 3 with the sequence GTGTCC are indicated with blue left right arrows. The following shared ITS2 features are indicated by black arrows and circles: (1) a U-U mismatch on helix II and (2) the UGGU and UU motifs on helix III. The structures were directly folded and modelled with the ITS2-DB.

A Model 2 variant, referred to as Model 3, contains a major variation () in helix III, which comprises four internal bulges. Model 3 is derived from an Ampelomyces ITS2 sequence (GI: DQ490754) extracted from Podosphaera fusca infecting Xanthium sibiricum, which was sampled in China. Model 2 was found in Ampelomyces ITS2 sequences isolated from the three PM genera, Arthrocladiella, Golovinomyces and Podosphaera (slides 14–19 in ).

In addition, models 2 and 3 contain the U-U mismatch in helix II and the UGGU and UU motifs in helix III ().

On the other hand, the three ITS2 S2 Models 4–6 (–7C) were only found in Ampelomyces ITS2 sequences isolated from P. leucotricha, Podosphaera ferruginea and E. necator (section Uncinula), respectively (slides 20–22 in ). Models 4–6 contain an internal loop in helix I and a single-stranded ring between helices II and III that is rich in purines (–7C). Between Models 4 and 5 (), major variations were observed in the internal loops and bulges of helix III. Model 6 was only found in Ampelomyces extracted from E. necator. The helix IV in Model 6 contains a stack of three paired nucleotides and terminates in a single-stranded loop of three unpaired Cs (). Unlike Models 1–3 and 7, Models 4–6 contain a single-stranded ring between helices II and III that is rich in As and a large helix III with a UGGU motif.

Fig 7

Predicted ITS2 S2 found in the Ampelomyces population isolated from two PM genera, Podosphaera and Erysiphe.

(A) The ITS2 S2 Model 4 predicted from Ampelomyces spp. strains extracted from P. leucotricha on Malus domestica. (B) The ITS2 S2 Model 5 from P. ferruginea on Sanguisorba officinalis. (C) The ITS2 S2 Model 6 from E. necator infecting Vitis sp.. M. domestica and S. officinalis are plants from the family Rosaceae, whereas Vitis sp. is a plant from the family Vitaceae. The U-U mismatch motifs, a single-stranded ring rich in adenine nucleotides between helices II and III and a large helix III with a UGGU motif are indicated with black arrows and circles. The structures were directly folded and modelled with the ITS2-DB. The helices are indicated with Roman numerals (I–IV). The single-stranded ring between helices I and IV is indicated with green left right arrows. However, the one from Model 4 is not complete and the green arrow is not shown.

Conversely, most of the ITS2 sequences from Ampelomyces strains extracted from the PM Erysiphe genus had an ITS2 S2 represented by Model 1, except for those mycoparasitic strains extracted from E. necator, which comprise the distinctive ITS2 S2 Model 6 (). Minor changes in Model 6 were observed for Ampelomyces strains extracted from E. necator. These changes included transition mutations (C ↔ T) in the internal loop and hairpin of helix II and in the single-stranded ring between helices II and III (slides 23–26 in ).

Characterization of the ITS2 S2 improved environmental sequencing analysis

The predicted S2 of the putative Ampelomyces spp. from Groups 1 and 2 had the same four-fingered model, but the largest helix (helix III) contains between three and four internal loops and four or six bulges (–8E). In addition, all these S2s only contain the U-U mismatch motif on helix II. Unlike the ITS2 S2 from Ampelomyces spp. sensu stricto, S2 models from putative Ampelomyces contain a single-stranded ring between helices I and IV with the sequence, TCCATG. No variations in the hybridization model of the proximal stem were observed in fungal Group 1, Table 4.1 in . The ITS2 sequences from the putative Ampelomyces Group 1 isolated from plant material or from PM fungi were correctly annotated using both the ITS2-DB and homology modelling (Table 4.2 in .

Fig 8

Predicted putative Ampelomyces ITS2 S2s were modelled to those from Didymella, Epicoccum and Phoma.

(A) The ITS2 S2 from A. quercinus was homology modelled based on the ITS2 S2 from D. pomorum (FJ839851). (B) The ITS2 S2 from A. humuli were modelled according to the ITS2 S2 from Epiccocum sp. (GU973791) and (C) from the ITS2 S2 from D. glomerata (FJ839851). (D) The ITS2 S2 from putative Ampelomyces sp. (Group 1) was homology modelled based on the structure of P. labilis (GU237868). (E) The ITS2 S2 from putative Ampelomyces sp. (Group 2) extracted from crosstie waste was directly folded and modelled. The helices are indicated with Roman numerals (I–IV). The single-stranded ring between helices I and IV is indicated by orange left right arrows. The U-U mismatch on helix II is indicated with red arrows and circles. The S2s were obtained with the ITS2-DB.

The sequences from A. humuli (AF035779) and A. quercinus (AF035778) () were homology modelled with the S2 of D. glomerata [GenInfo Identifier (GI) model: 332002412] and exhibited 99.4% similarity. Another sequence from an endophytic fungi referred to as A. humuli DQ093657 () was homology modelled based on the GI model 226933708 of the ITS2 from Didymella pomorum formerly known as Peyronellaea pomorum [36]. This analysis revealed 98.8% identity between ITS2 sequences of A. humuli and D. pomorum. In addition, the homology modelling of A. humuli (KU204751), , based on the GI model 296840485 of the ITS2 from Epicoccum sp. ASR-245 revealed a 98.8% identity.

The last ITS2 sequences from Group 1 belonged to an Ampelomyces strain (U82452) extracted from G. cichoracearum infecting Cucurbita pepo ().This sequence was modelled with the structure of Phoma labilis (GI model: 294346519) and exhibited 98.8% identity. These results indicated that the Group 1 fungi are not related to the Ampelomyces lineages, but are related to the genera Didymella, Epicoccum and Phoma.

For Group 2 fungi (Table 5.1 in ), only three ITS2 sequences were amenable for predicting the hybridization model of the proximal stem. These sequences are from putative A. humuli (AF455498, AF455518 and KT363070) and no variations in the hybridization model of their proximal 5.8S and 28S stem were detected. In addition, their S2s were not amenable to direct folding and instead a Basic Local Alignment Search Tool (BLAST) was conducted to search for their homologous sequences and S2s. This analysis demonstrated that fungi identified as A. humuli (AF455518 and AF455498) from human nasal mucus were amenable for modelling of their S2 based on the structure of the fungus Cumuliphoma omnivirens. In contrast, the S2 from A. humuli (KT363070) derived from soil could be predicted using a model of the ITS2 S2 from the species D. glomerata with 99.4% of identity (Table 5.2 in ). Two other ITS2 sequences (GQ241274 and LN80895) from putative Ampelomyces spp., which were extracted from environmental DNA samples (treated crosstie waste and air, respectively), were not amenable to verification of the hybridization of the proximal 5.8S and 28S stem due to the short length of the 28S strand. Nevertheless, the S2 from the fungus named Ampelomyces sp. (GQ241274) and isolated from creosote-treated crosstie waste could be folded directly (). It has a distinct S2; helix III has only four internal loops and a large hairpin formed by 10 unpaired nucleotides.

On the other hand, in order to predict the ITS2 S2 of the fungus identified as A. humuli from air samples, we conducted a BLAST search. This ITS2 S2 could only be partially modelled using the ITS2 S2 from species of the Phoma genus as a template with 32.5% of coverage. In addition, the ITS2 S2 of Group 2 were homology modelled using the ITS2 S2 models from the two fungal genera, Cumuliphoma and Phoma. These results support the hypothesis that these fungi are not related to the genus Ampelomyces. In summary, the ITS2 S2 from putative Ampelomyces sp. were homology modelled or directly folded and exhibited lower negative energy values between -25.8 and -35.9 than those from Ampelomyces spp. sensu stricto, which were obtained by direct folding and exhibited energy values between -47.3 and -36.8. This was another difference found between the ITS2 S2s of both fungal groups. The ITS2 S2 of fungi from the outgroup taxa were modelled using the structures from species of the Didymella and Phoma genera. This suggested that these sequences belonged to fungi from the genera Didymella and Phoma (Table 6.1 and 6.2 in ).

The ITS2 sequence-structure from PM-free environments did not cluster with those from Ampelomyces lineages

We aligned a sample of 21 directly predicted ITS2 S2s from Ampelomyces spp. sensu stricto together with those extracted from plant tissues and creosote-treated crosstie waste. The ITS2 sequence U82452, included in this analysis, was originally identified as belonging to Ampelomyces and was isolated from G. cichoracearum. Even though this mycoparasite co-infects the same PM host, this sequence was identified in early studies as belonging to fungi of the genus Phoma.

The evolutionary relationship of these fungi was estimated using the maximum likelihood method. The highest log likelihood of the ITS2 S2-based tree was -866.33 () and the Ampelomyces population was grouped into three main clades. The first clade 1a contains all Ampelomyces sequences extracted from PM of the genus Podosphaera and it is represented by the ITS2 S2 Model 2 as well as its variations. Clade 1b contains Ampelomyces sequences extracted from E. necator on grapes and it is represented by the ITS2 S2 Model 6 and its variations. All clade 1b samples were collected in the USA. A very well-supported and independent clade 2 was formed by Ampelomyces sequences extracted from P. leucotricha from several parts of Europe and from P. ferruginea sampled in China. This clade 2 is represented by the ITS2 S2 Models 4 and 5. Clade 3 consists of Ampelomyces sequences that were isolated from A. mougeotii in different locales in Hungary and it is represented by the ITS2 S2 Models 1 and its variations as well as Model 7. Conversely, similar to the ITS2 S2 sequence from P. herbarum (GI JF810528), fungi strains isolated from G. cichoracearum, P. abies decayed root and creosote-treated crosstie waste were not grouped into clades 1–3. This result is in agreement with our previous findings, which confirm that these environmental DNA sequences are not related to the Ampelomyces genus.

Phylogram based on ITS2 S2s enhance the discrimination between fungal DNA environmental samples and the ‘true’ Ampelomyces.

(A) The phylogram with the highest log likelihood (-866.33) was based on the ITS2 S2s and inferred via the maximum likelihood (ML) method and the Kimura two-parameter model. An evolutionary rate among sites was modelled with a discrete gamma distribution (+G) parameter = 0.99. (B) The phylogenetic tree with the highest log likelihood (-2040.24) was based on the ITS region and estimated with the maximum likelihood method and the Tamura-Nei model with a discrete gamma distribution (+G) parameter = 0.48. The ML bootstrap values >60% are indicated over the branches and are expressed as percentages. The scale bar represents the nucleotide substitutions per site. The tree was edited with FigTree v1.4.4 software. The GenBank accession numbers are indicated before the taxa names. Abbreviations: ITS2 S2 variations of main Models 1 (M1, M1-2 and M1-3); Models 2 (M2, M2-1, M2-2 and M2-3); Model 3 (M3); Model 4 (M4); Model 5 (M5); Models 6 (M6-1 and M6-2); and Model 7 (M7).

We also compared the previous tree () with the one based on the complete ITS region (). We found similar results. However, clade 2a emerged as a sister clade of clade 2b. Among the outgroup taxa samples, the ITS region resolved better than the ITS2 S2. Part of this could be due to the small number of samples used in the ITS2 S2 analysis. Even though clades 1a and 3 were represented by Ampelomyces extracted from PMs of the genera Podosphaera and Arthrocladiella, respectively, it does not indicate that these S2s are mycohost-associated. Indeed, in the clade of Podosphaera, other Model 2 sequences from Ampelomyces extracted from other PMs such as Arthrocladiella and Golovinomyces were grouped together (). Nevertheless, no additional S2 Models (2 nor 3) were found in those samples from Europe. Instead, they were only found in China. Conversely, the ITS2 S2 Model 1 was grouped with others from Ampelomyces extracted from seven PM genera.

Phylogram based on 26 Ampelomyces ITS2 S2s shows that the S2s are not associated with PM hosts.

The phylogram with the highest log likelihood (-829.62) is shown based on the Kimura two-parameter DNA model and an evolutionary rate among sites modelled with a discrete gamma distribution (+G) parameter = 0.90. The ML bootstrap values >60% are indicated over the branches and are expressed as percentages. The scale bar represents the nucleotide substitutions per site. The tree was edited with FigTree v1.4.4 software. The GenBank accession numbers are indicated before the taxa names. Abbreviations: ITS2 S2 variations of main Models 1 (M1, and M1-3); Models 2 (M2, M2-1 and M2-3); Model 3 (M3); Model 4 (M4); Model 5 (M5); Models 6 (M6-1 and M6-2); and Model 7 (M7).

In order to support our hypothesis that the ITS2 S2 analysis can improve the differentiation between the ‘true’ Ampelomyces and unrelated fungi, we determined the genetic divergence distances among groups between the phylogenies. These distance calculations were based on the simultaneous alignment of the ITS2 S2 () and the complete ITS region (). For the ITS2 S2 analysis, the maximum distance observed between clades 1a and 3 was 0.298 ± 0.056 standard error (S.E.) while those between the outgroup taxa and clade 3 was 0.403 ± 0.073 (S.E.), ().

In contrast, by using the ITS-like DNA barcode, we found that the maximum distance between closed related Ampelomyces clades 1a and 2b was 0.186 ± 0.021 (S.E.), while the minimum distance between the outgroup and an Ampelomyces clade (clade 2a) was 0.195 ± 0.021 (S.E.), (). These findings suggested that the ITS could not distinguish Ampelomyces from other closely related fungal genera, while the ITS2 S2 exhibited greater discrimination between the outgroup taxa and the closely related Ampelomyces clade 3.

Other differences were observed when comparing all consensus ITS2 S2s belonging to each clade (). All Ampelomyces consensus structures contain the U-U unpaired motif in helix II. In helix III, the UGG and UU motifs in Models 2 and 3 (), the UGGU motif in Models 6 (), 4 and 5 () and the UGG motif in Models 1 and 7 () formed the clades 1a, 1b, 2 and 3, respectively. The AAA motif between helices II and III was only present in Ampelomyces extracted from E. necator in clade 1b () and in Ampelomyces extracted from P. leucotricha and P. ferruginea in clade 2 ().

Four major consensus ITS2 S2s from Ampelomyces are represented in three main clades.

(A) Consensus ITS2 S2 of Models 2 and 3, which are grouped in clade 1a. (B) Consensus ITS2 S2 belonging to clade 1b are represented by Model 6. (C) Consensus ITS2 S2 of Models 4 and 5 that belong to clade 2. (D) Consensus ITS2 S2 of Models 1 and 7 that belong to clade 3. All consensus ITS2 S2s have gaps and were obtained with the 4SALE v1.7.1 software. Yellow nucleotides indicate conserved motifs (U-U mismatch and AAA motifs) known to be found in yeasts and vertebrates [73]. UGG, UGGU and GGUU motifs on helix III are indicated with black circles. The bar on the upper right side indicates the level of nucleotide conservation, with the most conserved nucleotides in green. The gaps are depicted in red. The GenBank IDs used to build each consensus are indicated below each S2.

Conversely, the consensus structure from the outgroup taxa do not contain the AAA motif between helices II and III but it does harbor the unpaired U-U motif in helix II (). When the predicted consensus ITS2 S2 from the outgroup was built based on the alignment of the four ITS2 sequences and structures including the gaps (), the consensus S2 was highly modified, indicating that these sequences belong to diverse fungi.

Highly diverse consensus ITS2 S2s from the outgroup taxa.

(A) The consensus ITS2 S2 was elaborated without gaps. The GenBank ID numbers of four ITS2 sequences used to predict the ITS2 S2 are indicated. (B) The consensus ITS2 S2 build with gaps. The consensus ITS2 S2s were obtained using the 4SALE v1.7.1 software. The helices are indicated by Roman numerals (I–IV). Nucleotides in yellow indicate the U-U mismatch motifs in helix II. The bar on the upper right side indicates the nucleotide conservation across the four ITS2 sequences used to obtain the consensus structure. Gaps in the structure are indicated in red.

After this comprehensive analysis, the selected nucleotide sequences belonging to Ampelomyces spp. sensu stricto were included in the

Discussion

Improving the accuracy in identifying the ITS sequences derived from environmental DNA sampling of fungi is expected to benefit future fungal genetic population studies including those for Ampelomyces. In addition, it may also provide insight into the mechanisms of parasitism, which may improve the use of biocontrol agents against PMs. Previous researches have shown that fungi identified as A. humuli or A. quercinus were not related to the mycoparasites Ampelomyces based on their culture characteristics and phylogeny [30,31]. Indeed, this research shows ITS sequences from plant tissues, environmental DNA samples and human mucus do not belong to species of the genus Ampelomyces. This classification is based on their ITS sequence length and nucleotide content, their ITS2 S2 together with simultaneous ITS2 sequence-structure alignment and its corresponding maximum likelihood tree.

On the other hand, S2 analysis has provided insight into the regulatory mechanisms of mycoparasite pre-RNA S2. Based on the phylogenetic tree of ITS2 sequences and structures, we propose that a basic ribosomal regulatory mechanism exists across the entire mycoparasite population since the S2 Model 1 was observed in strains extracted from seven PM genera. Moreover, major differences in S2 were found in the internal loops of hairpins that are essential for alternative splicing during pre-RNA processing [74]. Indeed, mutations occurring adjacent to these areas are known to stop the rRNA maturation process [75]. Interestingly, only ITS2 S2 Models 4–6 from Ampelomyces strains isolated from P. leucotricha, P. ferruginea and E. necator, respectively, share conserved motifs i.e., poly adenine nucleotides in the single-stranded ring between helices II and III, that were previously reported in yeasts and vertebrates [73]. This suggests that in some Ampelomyces mycoparasites, post-transcriptional processes for ribosomal biogenesis may be similar across higher organisms, such as fish and mammals [73]. Conversely, ITS2 S2 models 1–3 and 7 that do not have this conserved motif may have different regulatory mechanisms.

Early studies demonstrated that when using ITS sequences and microsatellites as DNA barcodes, the only haplotype found in Ampelomyces extracted from P. leucotricha on apples (APM Ampelomyces), which caused epidemics in the spring, may be the result of its PM host phenology [23]. However, there was an exception to this finding; APM Ampelomyces grouped with non-APM Ampelomyces (isolated from P. ferruginea and P. pannosa). Moreover, isolation date of one of the strains was unknown, thus the impact of mycohost phenology on the evolution of the only Ampelomyces ITS haplotype remains unclear. In our phylogenetic study based on ITS2 sequence and structure, we obtained clustering patterns similar to those reported previously, but in our case each clade indicated that Ampelomyces can be grouped into four major S2s. This also explains why non-APM Ampelomyces clustered with APM Ampelomyces. These different structures also imply that different mechanisms of ribosomal regulation may occur.

These results beg the question: how did these different ITS2 S2s originate? In a previous study, it was proposed that the four major ITS2 S2s found in the ITS sequences of the hyperparasitic fungus Sphaeropsis visci may be due to sexual recombination, although no teleomorphs were found [35]. Microsatellite analysis of APM Ampelomyces [23] showed that they undergo frequent asexual reproduction and regular recombination, and an Ampelomyces sexual reproductive state was not observed. Interestingly, unequal crossing over occurs during mitosis in other fungi such as Saccharomyces cerevisiae [76] and Ceratocystis manginecans [77]; we cannot discount its occurrence in Ampelomyces, whose sexual reproductive stages were not detected in the early studies. It is also possible that the ITS2 S2 found in APM Ampelomyces in Europe is the result of a recombination process with other non-APM Ampelomyces. However, this S2 was also observed in Ampelomyces extracted from other PMs, such as P. ferruginea and was found in other locales, such as China. Another explanation is derived from a previous report [78], which demonstrated that specific regions of the rRNA cistron in humans and several primates maintain polymorphic sites by natural selection. Since the ITS2 C/G content and minimum free energy values of ITS2 structure formation were not significantly different to those from the rest of the population (data not shown), we hypothesize that the variations observed in the proximal 5.8S and 28S stem indicate an early stage of pseudogene formation in two Ampelomyces ITS sequences extracted from U. necator and P. xanthii. The polymorphisms observed in the proximal 5.8S and 28S stem and the ITS2 can be either homogenized across the cistrons by unequal crossing over [76] or gene conversion through concerted evolution, and their fate determined by genetic drift. Nevertheless, the modifications observed in the proximal 5.8S and 28S stem may affect positively or negatively ITS2 processing. For example, the first variation of the hybridization model, an ITS2 derived from an Ampelomyces strain extracted from P. xanthii contains a short proximal 5.8S and 28S stem. This short stem may affect the enzymatic machinery that processes the ITS2 because the length of the stem is important for processing [75]. Consequently, the mutations observed in both strands 5.8S and 28S may be eliminated by genetic drift through concerted evolution [77,79]. On the other hand, the second variation of the hybridization model, an ITS2 derived from an Ampelomyces isolated from U. necator, may have a more relaxed structure that is still functional. The function of the secondary molecules resulting from the processing of the ITS2 remains to be elucidated. In addition, it remains to be determined whether these secondary molecules provide a specific trait to the fungus. Indeed, it has recently been shown that ribosomes containing rRNA variants have altered gene expression and physiology [80]. If the ITS sequence becomes a ghost pseudogene that favours the synthesis of proteins via ribosomal regulation, then it may be naturally selected by inhabiting a new environment under different biotic or abiotic pressures. Based on this, we think that the random appearance of a ghost pseudogene may lead to the formation of new individuals that form sister clades. For instance, in the phylogram of ITS2 S2s, clade 2 will be divided into two sister clades where each is formed by APM Ampelomyces and non-APM Ampelomyces ITS2 S2s. This evolutionary process may be initiated by the random appearance of a ghost pseudogene in ITS sequences of APM Ampelomyces that was selected by phenology of its powdery mildew host. Nevertheless, no additional samples were available from Ampelomyces isolated from P. ferruginea in China; and this needs to be addressed in the future.

On the other hand, the interspecific genetic distances between the ‘true’ Ampelomyces -containing clades and the whole outgroup taxa were higher than the intraspecific genetic divergences among the ‘true’ Ampelomyces clades calculated by using either the ITS2 S2s alignment or the ITS alignment. However, the barcode gap was notably enhanced by using the ITS2 S2s. This demonstrates that ITS2 S2s are an important tool to enhance the identification of Ampelomyces mycoparasites from DNA environmental samples.

Further research is required in this area together with sampling across different crops, countries and seasons. Partial sequences of the ITS region deposited in GenBank and belonging to Ampelomyces spp. are valuable, but we can obtain more information when whole sequences are used. We propose that future studies publish complete Ampelomyces ITS sequences and sample the same host at least two times.

In summary, we found that ITS sequences from fungi derived from PM-free environments are still being deposited in the GenBank database under the generic name of Ampelomyces. We also showed that these sequences are not related to the genus Ampelomyces based on their ITS sequence length, nucleotide composition and the simultaneous alignment of their ITS2 sequences and structures. Finally, we detected for the first time that pseudogene formation could occur in the nrDNA ITS region of Ampelomyces mycoparasites. Our study suggested that complete ITS2 sequences are crucial for understanding the phylogeny of these understudied Ampelomyces mycoparasites.

Conclusions

In this study, we demonstrated the utility of ITS2 S2 analysis to unveil underlying evolutionary processes in the Ampelomyces mycoparasites. Furthermore, the predicted S2s represent a valuable source of information that enhanced the analysis of environmental sequencing and advanced our knowledge in the field of fungal genetic population biodiversity. We highly recommend using the ITS2-DB for this purpose. On the other hand, the controversy surrounding whether the ITS region alone is suitable to discriminate between closely related species may be ameliorated by analysing S2 together with phylogenetic studies based on simultaneous sequence-structure alignment of the ITS2s. Our results support the utility of this strategy as well as the view that the ITS region is an excellent primary fungal barcode marker, and we are beginning to uncover its real potential.

DNA ITS and ITS2 secondary structures sequence analyses.

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ITS2 secondary structures from Ampelomyces spp. sensu stricto and putative Ampelomyces spp.

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Datasets.

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7 Jan 2021

PONE-D-20-39142

ITS2 Secondary Structures in Mycoparasitic Ampelomyces: Evolution and Environmental DNA Analysis

PLOS ONE

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Reviewer #1: Partly

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Reviewer #1: Yes

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Reviewer #1: Yes

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Reviewer #1: No

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5. Review Comments to the Author

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Reviewer #1: The manuscript by Rosa Prahl and co-authors describe a computational study of the importance of the secondary structure of ITS2 for identification of Ampelomyces strains in environmental samples. Overall, the work is relevant and performed with appropriate methods. However, it lacks in clarity of the presentation and in the interpretation and discussion of parts of the results.

1. The abstract is not providing enough information to understand the significance of the work. Why is molecular identification of fungi based on environmental DNA challenging? Due to low levels of polymorphisms in different markers, or too much variation etc., please be specific. Why did you predict ITS2 secondary structures? No explanation of the significance is provided. It is too bold to state that the polymorphisms identified are key drivers of ITS evolution, the mutations are the result from an evolutionary process, hardly the drivers.

2. It is difficult to follow the significance and purpose of the different steps in the Result section. This may partly be due to the format where materials and methods comes after the discussion, but it may help to provide a little more info regarding this in the beginning of the different sections in the results.

3. The discussion concerning pseudogenes (lines 459-472) is vague and is some aspects problematic. The provided reference for pseudogenes (Harpke and Peterson) merely discuss this in the context of the 5.8S gene, not the ITS. This is understandable, as the term pseudogene is usually related with expression, and Harpke and Peterson indeed takes this into account by comparing 5.8S sequences from genomic DNA verses cDNA. It is however clear that the secondary structure of ITS is important for the splicing but whether the observed polymorphisms are enough to discuss loss-of-function paralogs is not clear to me. This part of the discussion needs to be made more specific. The last part of this section (line 466 onwards) is difficult to understand. Why would these pseudogenes be naturally selected? It would be more reasonable to assume release of selective constraints, leading to continuous accumulation of mutations, with the ultimate fate determined by genetic drift. Also, the evolution of the rRNA repeat is very much depending on concerted evolution, but this is not even mentioned nor discussed. In fact, as concerted evolution at least partially can be connected with meiosis and sexual reproduction, it would make sense to discuss this in the current manuscript.

4. The comparison of the secondary structure prediction and the phylogenetic analysis is lacking from the discussion. The authors repeatedly state that the secondary structure prediction of ITS is a valuable tool for identifying Ampelomyces sequences from the environment. This may indeed be the case, but it seems to me that the phylogenetic analysis provides exactly the same result and resolution. What exactly is the gain from using secondary structure prediction? I am lacking a critical discussion of this in the manuscript.

5. The analysis of length variation. First, it would be useful to provide a statement regarding the distribution of the ITS1 length variation between Ampelomyces and the other groups, is it due to specific indels or more evenly spread out over the sequence? Secondly, what was the basis for defining groups 1 and 2? This was not clear to me. Third, why is the normalization of the length even necessary? The authors argue that it was necessary due to the use of different primers, but if all used sequences were complete full-length (ITS1-5.8S-ITS2) as stated, the primers should not matter. I assume that partial 18S and 28S sequences should be deleted before the analysis. This is not clear to me.

Minor issues:

1. Lines 41-43. The 5.8S gene is not assumed to evolve neutrally. Probably an error in the sentence.

2. Line 53. I would exchange “although only” with “and” in order to be a bit more positive concerning the application aspects. Commercialization is a complicated process, so it is great that two strains have gone the whole way to products.

3. Line 55. Delete “conidia, fruiting bodies”.

4. Line 97. Table 3 comes before Table 2.

5. Line 109. Replace “extracted” with “retrieved”.

6. Line 110. Replace “the mycoparasites” with “Ampelomyces mycoparasites”.

7. The figures were of poor quality, but it may be related with the review versions.

8. Line 274. “Major” should be “major”.

9. Line 282. “helices IIII” should be “helices III”, I guess.

10. Line 369. What is the significance of mentioning the free energy value for this structure but not for the others?

11. Line 410. Replace “from” with “with”.

12. Figure 9 + legend. Bootstrap support values are typically reported as the percentage, e.g. 53 instead of 0.53.

13. Line 446. “neighbor-joining” should be “maximum likelihood”, right?

14. Lines 450-452. Is the Bartys et al reference really appropriate here? The reference seems to deal with hairpin structures in mRNA, while the importance in non-coding RNA may be different.

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Reviewer #1: No

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2 Mar 2021

Detailed Response to Reviewer 1

The authors would like to thank the Editor in Chief and Reviewer 1 for taking their time to read our manuscript, provide constructive criticisms and helpful comments. We have revised the manuscript accordingly. The point by point response to the comments of the Reviewer 1 are provided below. The subsequent changes in the manuscript are also highlighted to demonstrate the changes that were made in revised version.

Reviewer #1: The manuscript by Rosa Prahl and co-authors describe a computational study of the importance of the secondary structure of ITS2 for identification of Ampelomyces strains in environmental samples. Overall, the work is relevant and performed with appropriate methods. However, it lacks in clarity of the presentation and in the interpretation and discussion of parts of the results.

1. The abstract is not providing enough information to understand the significance of the work (1.1-1.4).

A new abstract has been written (Lines 27-49).

1.1 Why is molecular identification of fungi based on environmental DNA challenging?

Answer: Accurate fungal identification depends on the method used to classify the fungus. Several taxonomical and phylogenetic fungal groups require appropriate cultural conditions before identification and specific primers for successful amplification of molecular markers. This has been clarified in the revised version. Please see Lines 67-71.

1.2 Due to low levels of polymorphisms in different markers, or too much variation etc., please be specific.

Answer: In accordance with the taxonomy and phylogeny of the fungal group under study, the use of only one molecular marker can result in poor species discrimination resolution (Schoch et al., 2012). For a barcode gap, the interspecific genetic variability needs to be higher than the intraspecific variability. In fungi, the nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) region has been widely used as a DNA barcode (Schoch et al., 2012). For fungal identification, the ITS region has enough genetic variability to the species level, but sometimes it does not resolve closely phylogenetic related species (Bruns, 2001) and some fungi require extra identifiers for species delimitation within a determined genus or family. The nrDNA ITS region is the preferred DNA barcode for fungi (Schoch et al., 2012). However, it can have some limitations. If some taxa have low ITS interspecific variability other molecular markers need to be used to precisely report genetic diversity (Gazis et al., 2011). Conversely, intragenomic variation caused by the presence of several nonorthologous and paralogous copies in a single conidium (Lindner and Banik, 2001; and Kovács et al., 2011) can result in overestimate the intraspecific variability in some fungi (Gomes et al., 2002 and Simon et al., 2008). For instance, in Glomeromycota, the upper range of this variability in the ITS region can reach up to 20% within a single spore (Krüger et al., 2012). This has been added to the revised manuscript. Please see Lines 71-86).

1.3 Why did you predict ITS2 secondary structures? No explanation of the significance is provided.

Answer: This is a useful point to further increase the clarity of the revised manuscript. The following rationale has prompted us to predict Ampelomyces secondary structures (S2): (1) Interspecific divergences among some Ampelomyces groups have reach up to 15%; and extra markers may be used to accurate identify these species (2) most of the phylogenetic studies conducted on Ampelomyces were based on the nrDNA ITS region and the successful design of primers for other markers are difficult to obtain, which often occurs for other fungi and (3) the utility of ITS2 secondary structures (S2) of Ampelomyces have not been evaluated.

In order to resolve these issues and contribute to knowledge and future research in this area, we have investigated whether ITS2 secondary structures (S2) contains specific features that may be incorporated into phylogenetic analysis and provide with novel important information regarding evolutive processes occurring in Ampelomyces. Indeed, the utility of the ITS2 S2 to study the phylogeny of several organisms have been demonstrated (Gottschling et al. 2004 and Poczai et al. 2015) but it has not been investigated in Ampelomyces.

This has been added to the revised manuscript. Please see lines 110-122.

1.4 It is too bold to state that the polymorphisms identified are key drivers of ITS evolution, the mutations are the result from an evolutionary process, hardly the drivers.

Answer: Thank you for this comment. We agree with your comment and we wish to clarify some points. We focus on the polymorphisms found in the hybridization model of the proximal 5.8S and 28S stem and not on other polymorphic sites that occurred mainly in the bulges and single-stranded rings of the ITS2 S2.

According to the classification introduced by Zheng and Gerstein, some pseudogenes may have some functionality in RNA coding regions; and classified them as ‘ghost pseudogenes’. These ghost pseudogenes may regulate responses to environmental stresses in yeasts, while ‘dead pseudogenes’ do not have any function and may be subjected to evolutionary genetic drift. Variations in the hybridization model of the proximal 5.8S and 28S stem suggested that the formation of pseudogenes occurs in the nrDNA ITS region of Ampelomyces strains. Thus, our study, adding new knowledge to the body of research, has indicated for the first time that the formation of pseudogenes can occur in the nrDNA ITS region from two distinct Ampelomyces infecting cucumber and grape powdery mildews (PMs). Since the correct structure and assembly of the proximal 5.8S and 28S stem determines whether the enzymatic ribosomal machinery will continue to form mature 5.8S and 28S rRNAs (Côté et al. 2001), we hypothesize, that the modification observed in the proximal 5.8S and 28S stem from two Ampelomyces spp. may decrease the efficiency of ribosomal maturation or alternatively, it may lead to the production of other molecules that favour the maturation of rRNA for protein synthesis. In detail, the variations observed in the proximal 5.8S and 28S stem from Ampelomyces sampled from Podosphaera xanthii, indicated that the short length of the stem may impede the maturation of the pre-rRNA as previously shown (Côté et al. 2001) and consequently the mutations observed in both strands 5.8S and 28S may be eliminated by genetic drift through concerted evolution (Elder and Turner, 1995 and Naidoo et al., 2013). However, the second modification detected in the sequence from Ampelomyces extracted from Erysiphe necator (Section Uncinula) may provide some flexibility in the stem as reported by Côté et al. 2001. and could lead to the production of secondary molecules that positively affect ribosomal biogenesis. If the latter is the case, this could lead to the formation of a ghost pseudogene with a specific function. Thus, the ghost pseudogene may undergo natural selection. Therefore, in the absence of sexual reproduction, the random appearance of pseudogenes may lead to the formation of new individuals that form sister clades.

On the other hand, compared to functional genes, pseudogenes have low C/G content and high sequence length variation. However, these characteristics in the two putative pseudogenes found in Ampelomyces were not different to those from the rest of the population. Interestingly, the minimum free energy value of the S2 formation of the 5.8S gene in one of the putative pseudogenes from Ampelomyces extracted from P. xanthii, was slightly less negative than those from 5.8S sequences belonging to Ampelomyces infecting the same or different PM hosts. This result indicated that this polymorphism may be a precursor in the early stages of pseudogene formation.

In addition, Keller et al. reported that variations in the hybridization model can naturally occur. Nevertheless, we do not believe this is the case in our study because amongst the observed variations in the proximal 5.8S and 28S stem S2, there were no predominant variants in the entire Ampelomyces population.

We found reliable evidence that the formation of pseudogenes may occur randomly in the ITS loci from two Ampelomyces populations. What we meant by the word drivers is that ghost pseudogenes may have occurred first in any loci and if they improved the maturation of the pre-rRNA, then these pseudogenes will undergo natural selection caused by either temporal isolation or geographical isolation instead of evolving by neutral drift. For clarity, we modified this section in the Discussion section. Please see Lines 827-850.

2. It is difficult to follow the significance and purpose of the different steps in the Result section. This may partly be due to the format where materials and methods comes after the discussion, but it may help to provide a little more info regarding this in the beginning of the different sections in the results.

2.1 Answer: In response to this, we have revised the original manuscript very carefully according to the PLOS ONE format where the Materials and Methods were described after the Introduction section (Line 134). In Methods, we described where the dataset was obtained and how we defined it.

Then, the methods used to compare sequences statistics of ITS region and its components among groups was described (Lines 205-295). We connected each subsequent section as follow:

Insertion-deletion polymorphic analysis of the ITS1 among Ampelomyces groups and between unrelated groups

We investigate the distribution of insertion-deletion polymorphisms in ITS1 sequences that could cause sequence length variations. Please see Lines 205-206.

ITS2 structure prediction

To evaluate the utility of ITS2 S2s, the ITS2 sequences... Please see Line 219.

Multiple ITS2 sequence-structure alignment and phylogenetic tree of Ampelomyces strains

To determine Ampelomyces lineages based on its ITS2 S2s, a simultaneous multiple sequence alignment of ITS2 S2s was firstly estimated. Please see Lines 236 and 237.

A second phylogenetic tree based on ITS sequences was built to compare the distribution of Ampelomyces clades and not related fungi with those obtained using ITS2 S2s. Please see Lines 259 and 260.

For a comprehensible analysis, a second phylogenetic tree was constructed as described above, but the input data consisted of 26 ITS2 S2s… Please see Lines 268-269.

Evolutionary distance estimation among Ampelomyces lineages and putative Ampelomyces

The resolution power of the phylogeny of Ampelomyces based on the ITS2 S2s to distinguish the ‘true’ Ampelomyces from putative Ampelomyces was evaluated by comparing the genetic divergences obtained among groups based on the simultaneous ITS2 sequences and structures alignment, and on the MSA of complete ITS sequences. Please see Lines 276-277.

Prediction of consensus ITS2 S2s from Ampelomyces

For comparative purposes of sequence-structure motifs among fungal groups, … Please see Line 288.

3. The discussion concerning pseudogenes (lines 459-472) is vague and is some aspects problematic. The provided reference for pseudogenes (Harpke and Peterson) merely discuss this in the context of the 5.8S gene, not the ITS. This is understandable, as the term pseudogene is usually related with expression, and Harpke and Peterson indeed takes this into account by comparing 5.8S sequences from genomic DNA verses cDNA. It is however clear that the secondary structure of ITS is important for the splicing but whether the observed polymorphisms are enough to discuss loss-of-function paralogs is not clear to me. This part of the discussion needs to be made more specific. The last part of this section (line 466 onwards) is difficult to understand. Why would these pseudogenes be naturally selected? It would be more reasonable to assume release of selective constraints, leading to continuous accumulation of mutations, with the ultimate fate determined by genetic drift. Also, the evolution of the rRNA repeat is very much depending on concerted evolution, but this is not even mentioned nor discussed. In fact, as concerted evolution at least partially can be connected with meiosis and sexual reproduction, it would make sense to discuss this in the current manuscript.

Answer: The sequence and structure of the ITS region are essential for the formation of mature rRNA. The ITS2 contains specific cleavage sites and S2 motifs used by the enzymatic machinery responsible for processing pre-rRNA; and mutations that are adjacent to these critical regions have decreased or abolished 28S rRNA maturation (Côté et al. 2001). Our revision is in Lines 847-849. We have made these points clearer in the revised manuscript.

We modified the entire paragraph for clarity in the Discussion section. We can assume the polymorphisms observed in the proximal 5.8S and 28S stem and the ITS2 can be either homogenized across the rRNA cistrons by unequal crossing over or gene conversion, and their fate determined by genetic drift. Nevertheless, the modifications observed in the proximal 5.8S and 28S stem may affect ITS2 processing in two ways. For example, the first variation of the hybridization model, an ITS2 derived from an Ampelomyces strain extracted from P. xanthii contains a short proximal 5.8S and 28S stem. This short stem may affect the enzymatic machinery that processes the ITS2 because the length of the stem is important for processing. Conversely, the second variation of the hybridization model, an ITS2 derived from an Ampelomyces isolated from U. necator, may have a more relaxed structure that is still functional. The function of the secondary molecules resulting from the processing of the ITS2 remains to be elucidated. In addition, it remains to be determined whether these secondary molecules provide a specific trait to the fungus. Indeed, it has recently been shown that ribosomes containing rRNA variants have altered gene expression and physiology (Parks et al., 2019). If the ITS sequence becomes a ghost pseudogene that favours the synthesis of proteins via ribosomal regulation, then it may be naturally selected by inhabiting a new environment under different biotic or abiotic pressures. Please see Lines 843-868.

4. The comparison of the secondary structure prediction and the phylogenetic analysis is lacking from the discussion. The authors repeatedly state that the secondary structure prediction of ITS is a valuable tool for identifying Ampelomyces sequences from the environment. This may indeed be the case, but it seems to me that the phylogenetic analysis provides exactly the same result and resolution. What exactly is the gain from using secondary structure prediction? I am lacking a critical discussion of this in the manuscript.

Answer: The discussion of the predicted ITS2 S2s were included in the discussion section. Please see Lines 805-817.

The section of phylogenetic analysis based on ITS2 S2s was also discussed. Please see Lines 869-874.

Ampelomyces can be misidentified with other related picnidial mycoparasites that infect PMs. For initial identification purposes, cultures obtained by conidial isolation are grown and assayed for the formation of Ampelomyces pycnidia in PM conidiophores. Direct environmental DNA sequencing may facilitate identification, but the inter- and intra-specific distances of the ITS vary among some fungal groups. For instance, some ‘true’ Ampelomyces strains can have ITS sequence divergence up to 15% (Kiss and Nakasone, 1998 and Liang et al., 2007).

This limitation may be resolved by the use of phylogenetic analysis based on ITS2 sequences and S2s. The different ITS2 models obtained in the whole mycoparasitic Ampelomyces population have clear differences to other fungi that have been misidentified as Ampelomyces. The genetic divergences between Ampelomyces and those fungi misidentified are higher when using the ITS2 S2 phylogenetic analysis than those from the analysis based on ITS sequences. Our revision is in Lines 869-874.

5. The analysis of length variation. First, it would be useful to provide a statement regarding the distribution of the ITS1 length variation between Ampelomyces and the other groups, is it due to specific indels or more evenly spread out over the sequence?

Answer: We found that the number of indels between groups of Ampelomyces isolated from the same PM genera varied as assessed with DnaSP software. Visualization of a multiple sequence alignment of ITS1 sequences revealed that Ampelomyces ITS1 sequences extracted from PM of the genera Erysiphe, Golovinomyces and Podosphaera have indels evenly distributed along the sequence. In contrast, the ITS1 from Ampelomyces extracted from Podosphaera fusca in Korea, contained indels which were more distributed at the beginning of the ITS1 sequence (first 100 nucleotides), while the Ampelomyces derived from the same PM but sampled in China harboured indels at the end of the sequence. Conversely, Ampelomyces extracted from the genera Arthrocladiella, Oidium and the subgenus Pseudoidium had indels at the beginning and at the end of the sequence, while Ampelomyces derived from Phyllactinia contained indels localized at the end of the sequence. We also compared the number of indels for all Ampelomyces ITS1 sequences with those from putative Ampelomyces Groups 1 and 2 as well as the outgroup taxa. This analysis revealed that ITS1 sequences for all outgroup samples contained indels at various positions across the ITS1 sequence. Please see Lines 415-427.

5.1 Secondly, what was the basis for defining groups 1 and 2? This was not clear to me.

Answer: Group 1 is defined as those Ampelomyces extracted from PMs or plants. Group 2 comprises those Ampelomyces extracted from non-plant material or PM-free environments. We clarified this point in the text (Please see Lines 156-159).

5.2 Third, why is the normalization of the length even necessary? The authors argue that it was necessary due to the use of different primers, but if all used sequences were complete full-length (ITS1-5.8S-ITS2) as stated, the primers should not matter.

Answer: We agree with your comment. Some environmental ITS sequences deposited in the GenBank database do not contain the known motifs ATCATTA or TTGACC, which delimitate the full-length ITS. It makes difficult to delimitate the complete ITS sequence and delete the partial nucleotide sequences of the 18S and 28S. For instance, the sequence obtained from an air sample (Group 2), GenBank Identifier: LN808951, did not contain the motif TTGACC. In order to address your comment, we restructured the paragraph (Please see Lines 196-198).

5.3. I assume that partial 18S and 28S sequences should be deleted before the analysis. This is not clear to me.

Answer: Yes, partial 18S and 28S rRNA sequences were deleted before the analysis. This has been clarified in the revised text. Please see line 195.

Minor issues:

1. Lines 41-43. The 5.8S gene is not assumed to evolve neutrally. Probably an error in the sentence.

Answer: The sentence has been corrected. The introduction has been modified for clarity. Please see Line 87.

2. Line 53. I would exchange “although only” with “and” in order to be a bit more positive concerning the application aspects. Commercialization is a complicated process, so it is great that two strains have gone the whole way to products.

Answer: The change has been made (Line 100).

3. Line 55. Delete “conidia, fruiting bodies”.

Answer: The change has been made (Line 102).

4. Line 97. Table 3 comes before Table 2.

Answer: We modified the order and content of the supplemental material as follows: Supplemental Material 1 consisted of the datasets used in each method while Supplemental material 2 contains DNA ITS and ITS2 secondary structures sequence analyses. Supplemental material 3 contains all the ITS2 sequence structures predicted by using the ITS2-DB. Please see Lines 898-902.

5. Line 109. Replace “extracted” with “retrieved”.

Answer: The change has been made. Please see Line 327.

6. Line 110. Replace “the mycoparasites” with “Ampelomyces mycoparasites”.

Answer: The change has been made (Lines 163 and 164).

7. The figures were of poor quality, but it may be related with the review versions.

Answer: The changes have been made. We used PACE to check the quality of the figures.

8. Line 274. “Major” should be “major”.

Answer: The change has been made. Line 525.

9. Line 282. “helices IIII” should be “helices III”, I guess.

Answer: Yes, it is helices III. The change has been made. Line 534.

10. Line 369. What is the significance of mentioning the free energy value for this structure but not for the others?

Answer: Despite we had a small number of samples, we noticed that the integrity of the hybridization model of the proximal stem of the ITS2 is compromised by energy values over -13.7. For instance, the variation observed in the ITS2 sequence of Ampelomyces from P. xanthii. Conversely, energy values between -15 and -19 conferred to the structure with some flexibility that may be necessary for post transcriptional processes of the pre-rRNA. We included a description of this finding in the Results section, Lines 451-453.

On the other hand, we also included in the text (Please see Lines 637-639) the comparison of energy values for folding of the ITS2 S2 from putative Ampelomyces spp. and Ampelomyces spp. sensu stricto:

The ITS2 S2s from putative Ampelomyces spp. were homology modelled or directly folded and exhibited lower negative energy values (between -25.8 and -35.9) than those from Ampelomyces spp. sensu stricto (between -47.3 and -36.8) that were obtained by direct folding. This was another difference found between both fungal groups.

11. Line 410. Replace “from” with “with”.

Answer: The change has been made. Please see Line 706.

12. Figure 9 + legend. Bootstrap support values are typically reported as the percentage, e.g. 53 instead of 0.53.

Answer: The bootstrap support values were expressed as percentages. The change has been made in the figure together with its legend. Please see Line693.

13. Line 446. “neighbor-joining” should be “maximum likelihood”, right?

Answer: Yes, it is maximum likelihood. The change has been made. Line 668.

14. Lines 450-452. Is the Bartys et al reference really appropriate here? The reference seems to deal with hairpin structures in mRNA, while the importance in non-coding RNA may be different.

Answer: The reference was replaced (please see Line 670) with a suitable reference. Please see Line 810:

Svoboda, P. and Di Cara, A. (2006). Hairpin RNA: a secondary structure of primary importance. Cell. Mol. Life Sci. doi: 10.1007/s00018-005-5558-5.

References

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Côté, C. and Peculis, B. (2001) Role of the ITS2-proximal stem and evidence for indirect recognition of processing sites in pre-rRNA processing in yeast. Nucleic Acids Res. 29:2106–2116.

Elder, JJ. and Turner, B. (1995) Concerted evolution of repetitive DNA sequences in eukaryotes. Q. Rev. Biol. 70:297–320.

Gazis, R., Rehner, S. and Chaverri, P. (2011) Species delimitation in fungal endophyte diversity studies and its implications in ecological and biogeographic inferences. Mol. Ecol. 20: 3001–3013.

Gomes, EA., Kasuya, MCM., de Barros, EG., Borges, AC. and Araujo, EF. (2002) Polymorphism in the internal transcribed spacer (ITS) of the ribosomal DNA of 26 isolates of ectomycorrhizal fungi. Genet. Mol. Biol. 25:477–483.

Gottschling, M. and Plötner, J. (2004) Secondary structure models of the nuclear internal transcribed spacer regions and 5.8S rRNA in Calciodinelloideae (Peridiniaceae) and other dinoflagellates. Nucleic Acids Res. 32:307–315.

Joseph, N., Krauskopf, E., Vera, MI. and Michot, B. (1999) Ribosomal internal transcribed spacer 2 (ITS2) exhibits a common core of secondary structure in vertebrates and yeast. Nucleic Acids Res. 27:4533–4540.

Keller, A., Schleicher, T., Schultz, J., Müller, T., Dandekar, T. and Wolf, M. (2009) 5.8S-28S rRNA interaction and HMM-based ITS2 annotation. Gene. 430:50−57.

Kiss, L., Pintye, A., Kovács, G, Jankovics, T., Fontaine, M., Harvey, N. et al. (2011) Temporal isolation explains host-related genetic differentiation in a group of widespread mycoparasitic fungi. Mol. Ecol. 20:1492−1507.

Kiss, L. and Nakasone, K. (1998) Ribosomal DNA internal transcribed spacer sequences do not support the species status of Ampelomyces quisqualis, a hyperparasite of powdery mildew fungi. Curr. Genet. 33:362–367.

Kovács, GM., Balázs, TK., Calonge, FD. and Martín, MP. (2011) The diversity of Terfezia desert truffles: New species and a highly variable species complex with intrasporocarpic nrDNA ITS heterogeneity. Mycologia 103:841–853.

Krüger, M., Krüger, C., Walker, C., Stockinger, H. and Schüssler, A. (2012) Phylogenetic reference data for systematics and phylotaxonomy of arbuscular mycorrhizal fungi from phylum to species level. New Phytol. 193:970–984.

Liang, C., Yang, J., Kovács, G., Szentiványi, O., Li, B., Xu, X., et al. (2007) Genetic diversity of Ampelomyces mycoparasites isolated from different powdery mildew species in China inferred from analyses of rDNA ITS sequences. Fungal Divers. 24:225−240.

Lindner, DL and Banik, MT. (2011) Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus. Mycologia 103:731–740.

Naidoo, K., Steenkamp, ET., Coetzee, MP., Wingfield, MJ. and Wingfield, BD. (2013) Concerted evolution in the ribosomal RNA cistron. PLoS One. 8:e59355.

Park, M., Choi, Y., Hong, S. and Shin, H. (2010) Genetic variability and mycohost association of Ampelomyces quisqualis inferred from phylogenetic analyses of ITS rDNA and actin gene sequences. Fungal Biol. 114:235−247.

Parks, MM., Kurylo, CM., Batchelder, JE., Vincent, CT. and Blanchard, SC. (2019) Implications of sequence variation on the evolution of rRNA. Chromosome Res. 27:89–93.

Schoch, CL., Seifert, KA., Huhndorf, S., Robert, V., Spouge, JL., Levesque, CA., Chen, W.; Fungal Barcoding Consortium; Fungal Barcoding Consortium Author List. (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc. Natl.. Acad Sci U S A. 17: 6241-6246.

Simon, UK. and Weiss, M. (2008) Intragenomic variation of fungal ribosomal genes is higher than previously thought. Mol. Biol. Evol. 25:2251–2254.

Smith, ME., Douhan, GW. and Rizzo, DM. (2007) Intra-specific and intra-sporocarp ITS variation of ectomycorrhizal fungi as assessed by rDNA sequencing of sporocarps and pooled ectomycorrhizal roots from a Quercus woodland. Mycorrhiza 18:15–22.

Svoboda, P. and Di Cara, A. (2006) Hairpin RNA: a secondary structure of primary importance. Cell Mol. Life Sci. :901−908.

Zheng, D. and Gerstein, MB. (2007) The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they? . Trends Genet. 23:219–224.

24 May 2021

PONE-D-20-39142R1

The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces

PLOS ONE

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3 Jun 2021

All amendments have been made. Thank you.

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14 Jun 2021

The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces

PONE-D-20-39142R2

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21 Jun 2021

PONE-D-20-39142R2

The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces

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Table 1

Characterization of the ITS region and their constituents ITS1, 5.8S and ITS2 from Ampelomyces spp.

	ITS	ITS1	5.8S	ITS2
Sequence length (bp)	492–502	182–193	157	149–155
Average length (S.E.M.)	498 (0.004)	188 (0.005)	157 (0.00)	152 (0.002)
A/T content (%) range	54.05–58.92	54.59–60.75	53.5–57.32	50.00–58.82
G/C content (%) range	41.08–45.95	39.25–46.5	42.68–46.5	41.18–50.00

n = 376 Ampelomyces ITS sequences. Abbreviations: Base pair (bp); Standard error of the mean (S.E.M.).

Table 2

Variations in ITS region sequence length can distinguish between Ampelomyces spp. and misidentified fungi.

	ITS1 (bp)	5.8S (bp)	ITS2 (bp)	ITS (bp)
Ampelomyces spp. sensu stricto	182–193	157	149–155	492–502
Putative Ampelomyces, Group 1	139–143	156–157	156–157	452–457
Putative Ampelomyces, Group 2	140–142	157	148–157	446–456
Outgroup taxa	139	157	156	452

The sequence lengths of the ITS region from Ampelomyces spp. (n = 376) were significantly higher than those from putative Ampelomyces Groups 1 and 2 (n = 5 each) as well as the outgroup (n = 5) with a Kruskal-Wallis chi-squared statistic value of 53.27 and p-values of 1.598204e-11. No differences in the sequence lengths of the ITS regions were observed between the misidentified fungi and the outgroup taxa with p-values of 1.0 and 3 degrees of freedom.

Table 3

The maximum normalized sequence lengths of the 5.8S gene and ITS2 spacer were conserved among all fungal groups.

	ITS1 (%)	5.8S (%)	ITS2 (%)
Ampelomyces spp. sensu stricto, n = 376	27.01 (0.00)	22.52 (4.9.e-6)	21.85 (0.00)
Putative Ampelomyces, Group 1, n = 5	20.14 (0.04)	22.46 (0.14)	22.46 (0.01)
Putative Ampelomyces, Group 2, n = 5	20.25 (0.02)	22.52 (0.00)	22.20 (0.09)
Outgroup taxa, n = 5	19.94 (0.00)	22.52 (0.00)	22.38 (0.00)

Only the normalized ITS1 sequence length from Ampelomyces spp. sensu stricto was significantly different to those from the other groups, with a Kruskal-Wallis chi-squared statistic value of 46.26 and a p-value of 4.972997e-10 with 3 degrees of freedom. The S.E.M. is indicated in parenthesis.

Table 4

Estimates of evolutionary divergence over sequence pairs between fungal groups when analysing the ITS2 sequences and structures.

ITS2	1	2	3	4	5
1. Clade 1a		0.045	0.050	0.056	0.090
2. Clade 1b	0.238		0.049	0.042	0.079
3. Clade 2	0.275	0.235		0.033	0.080
4. Clade 3	0.298	0.204	0.137		0.073
5. Outgroup taxa	0.533	0.477	0.444	0.403

The simultaneous ITS2 S2 alignment was used to calculate the genetic distances among groups via the log-det (Tamura-Kumar) method using MEGA-X V10.1.8 software. The values represent the number of base substitutions per site obtained by averaging over all sequence pairs between groups. The standard error estimates are shown in blue.

Table 5

Estimates of evolutionary divergence over sequence pairs between fungal groups when analysing the ITS region.

ITS	1	2	3	4	5
1. Clade 1a		0.0197	0.0189	0.0206	0.0265
2. Clade 1b	0.1659		0.0125	0.0203	0.0247
3. Clade 2a	0.1561	0.0798		0.0183	0.0213
4. Clade 2b	0.1861	0.1717	0.1532		0.0263
5. Outgroup taxa	0.2733	0.2287	0.1948	0.2548

The values represent the number of base substitutions per site obtained by averaging over all sequence pairs between groups. The distances were determined via the log-det (Tamura-Kumar) method using MEGA-X V10.1.8 software. The standard error estimates are shown in blue.