Comparative analysis of Phytophthora genomes data.

The data presented here are related to the article entitled "Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops" [1]. These data contain the description of genomic structure of the two plant pathogens, P. fragariae and P. rubi and characterize several gene families associated with pathogenicity of them: P450, ACX gene families, CAZymes and effector. This data presents the relevant results of two newly sequenced P. fragariae and P. rubi, so as to provide data for further studies by researchers.

Specifications Table

Value of the Data

Data provided in the article describe the genome characteristics, the mechanisms of pathogenicity of Phytophthora species, which are the most important plant pathogens.

Data are available for researchers and geneticists to search and compare the valuable information of different functions genes, gene family and protein information of different Phytophthora species

Data provided in this article provide important information on the description of the pathogenic mechanism of Phytophthora.

Data Description

This data article is composed of one table and seven figures. These data contain the characteristic description of genomic structure and pathogenicity of the two pathogens, P. fragariae and P. rubi, including the distribution of gene density at the genome level and several gene families associated with pathogenicity: P450 [2], ACX gene families [3], CAZymes [4] and effector [5]. These results complement the recent published literature on genomic and pathogenicity analyses of several Phytophthora pathogens [1].

The GO function of ACX motif is shown in Table. The mycelial growth in plate and the infection to plant seedlings of two Phytophthora strains is present in Figs. 1. 2 is the distribution of polymorphisms in P. fragariae and P. rubi according to local gene density. The structure of 19 predicted Acyl-coenzyme A oxidase gene families (ACX) motifs and the seven clades of these families is shown in Figs. 3 and 4 respectively. Fig. 5 contains the information about pathogenic types and structural variety of two kinds of effectors of RxLRs and CRN in Phytophthora species. the distribution of each type of CAZyme in six Phytophthora species and Plasmopara halstedii, including GHs, GTs, CEs, PLs, AAs and CBMs, is shown in Fig. 6. Fig. 7 is the phylogenetic tree constructed based on the P450 genes in P. fragariae, P. rubi and other relative species.

Fig. 1

The growth morphology in plate and the infection to plant seedlings of two Phytophthora strains. (a) Pictures of mycelial growth on V8 medium P. fragariae 309.62 (left) and P. rubi 109,892 (right). (b) The infected plants 30 days post inoculation (dpi). The four pictures in top are the infection to Dendrobium officinale seedlings of P. fragariae 309.62 under different inoculation conditions. From left to right, inoculated into growth medium without antibiotics, smeared on the leaves, needle inoculated into the leaves and inoculated into growth medium containing double antibiotics (ampicillin and streptomycin).The four pictures in bottom are the infection of P. rubi 109,892 under the same inoculation condition with P. fragariae 309.62 respectively.

Fig. 2

Distribution of polymorphisms in P. fragariae and P. rubi according to local gene density. The horizontal axis is the length of the 3' and 5′ intergenic regions of this gene, and each point represents the average dn/ds value of the interval length (bin). The average values of dn/ds ratio (nonsynoymous to synonymous substitution rate) associated with genes in each bin are shown as a color-coded heat map.

Fig. 3

19 predicted Acyl-coenzyme A oxidase gene families (ACX) motifs by Multiple Em for Motif Elicitation (MEME). The smaller the E-value, the more significant the motif is. Sites is the peak number supporting the motif, and width is the length of the motif.

Fig. 4

Seven clades of 19 predicted Acyl-coenzyme A oxidase gene families (ACX) motifs. There are seven clades (A, B, C, D, E, F, and G) of 71 ACX sequences which are classified based on the distribution of 19 predicted ACX motifs.

Fig. 5

The pathogenic types and structural variety of RxLRs (a) and CRN (b) in Phytophthora species. 20 RxLRs genes could be matched in PHI-base, and only 3 CRN genes were found. The motif distribution, host species and disease name are showed in the figure, the colored rectangles mean the different motifs.

Fig. 6

The distribution of each type of CAZyme. Glycoside Hydrolases (GHs), Glycosyl Transferases (GTs), Carbohydrate Esterases (CEs), Polysaccharide Lyases (PLs), Auxiliary Activities (AAs) and Carbohydrate-Binding Modules (CBMs). P. fragariae (PFRA), P. rubi (PRUB), P. sojae (PSOJ), P. ramorum (PRAM), P. infestans (PINF), P. parasitica (PPAR), P. nicotianae (PNIC), Plasmopara halstedii (PHAL).

Fig. 7

Phylogenetic tree constructed based on the P450 genes in P. fragariae, P. rubi and other relative species, the genes of each species marked with a special color.

Experimental Design, Materials and Methods

Materials availability

P. fragariae and P. rubi are highly similar in morphology and physiology, but infect different hosts. Sequencing the genomes of these species will advance our understanding of the genomic mechanisms underlying host adaptation and knowledge of molecular mechanisms of plant pathogenicity [6]. The P. fragariae and P. rubi strains were imported from Westerdijk Fungal Biodiversity Institute (strain numbers 309.62 and 109,892, respectively). P. fragariae 309.62 was isolated from Fragaria fruit by C.J. Hickman in Scotland, and P. rubi 109,892 was isolated by C. Brasier from raspberry roots in Scotland. We induced the production of motile zoospores in sterile water for over 5 h at 13–14 °C. Single zoospores were picked by inoculating needles under a microscope, followed by germination in V8 plates at 18 °C. After 48 h, the mycelia began to form. On the plate, the mycelia of P. fragariae were concentric and round with dense mycelia, while the mycelia of P. rubi grew uniformly and was relatively loose, as shown in Fig. 1a. The two pathogens had different hosts, and were inoculated on Dendrobium candidum seedlings to observe the pathogenicity. Four different inoculation methods were performed using fresh mycelium blocks to discover the pathogenic characteristics respectively, inoculated into growth medium without antibiotics, smeared on the leaves, needle inoculated into the leaves and inoculated into growth medium containing double antibiotics (ampicillin and streptomycin). After 30 days, the difference in pathogenicity during the observation period is shown in Fig. 1b.

The evolutionary rate at the genome level

A fundamental insight from analyses of filamentous plant pathogen genomes is that genes located in repeat-rich regions tend to evolve more rapidly than those in the rest of the genome [7,8]. We calculated the distribution of gene evolution rate at the genomic level to verify the conclusions of previous studies. This pattern could be demonstrated through comparative genomics of closely related species. Blastp comparison was used to find out the mutually optimal gene pairs in the whole genome of P. fragariae and P. rubi. The dn/ds values calculated using CODEML in the PAML package are shown in each branch [9]. The gene pairs with dn/ds <1 are selected and mapped in Fig. 2.

ACX gene families

Together with the CoA synthetase, ACX is acting in the β-oxidation pathway involved in the suppression of plant resistance via signaling molecules, such as jasmonic acid. We analyzed the structure of ACX gene family in order to find out whether it has pathogenic characteristics in Phytophthora. The motif was predicted by the motif prediction software MEME, the motif distribution characteristics of each clade sequence were analyzed, and the motif function was analyzed by GOMO. The phylogenetic analysis shows the ACX gene family for Phytophthora and its relative species could be divided into seven clades according to the predicted 19 motifs. The ACX gene families in Fig. 2 are clustered into seven categories, but none of the species is unique to a category. As shown in Fig. 2, all seven categories (A, B, C, D, E, F, and G) contain Multiple species (Figs. 3 and 4). The enriched GO function of ACX motif of motif 6,7,8,15,17 and 19 is shown in Table 1.

Table 1

The GO function of ACX motif.

motif name	GO term	p-value	GO name	Functional description
motif 6	GO:0,010,467	8.05E-06	BP	gene expression
motif 7	GO:0,005,739	2.45E-06	CC	mitochondrion
motif 8	GO:0,006,414	4.03E-06	BP	translational elongation
motif 15	GO:0,044,446	7.70E-06	CC	intracellular organelle part
	GO:0,043,234	2.54E-05	CC	protein complex
motif 17	GO:0,009,225	4.03E-06	BP	nucleotide-sugar metabolic process
motif 19	GO:0,008,289	3.68E-06	MF	lipid binding
	GO:0,005,737	1.56E-05	CC	cytoplasm

The variety of RxLR and CRN

PHI-base is an expertly curated source for genes which have been proven to affect the pathogen-host interaction [10]. 4017 genes of P. fragariae are identified by PHI-base, among them 423 are annotated as ‘effector’ in other pathogen species. For P. rubi, 3710 genes are identified, among them 368 are effectors and 16 are having identity higher than 70%. RxLR and CRN genes, which dominate as effectors in some other Phytophthora species, play no or very minor role in P. fragariae and P. rubi. RxLR is named after an N-terminal motif (x is any amino acid) involved in uptake by host cells [11]. CRNs are named after a “crinkling” or necrotic phenotype that occurs when several of these proteins are overexpressed in plants [12]. Blastp comparison was used to find out the mutually optimal gene pairs in the whole genome of P. fragariae and P. rubi. Selection conditions of comparison results: E-value < 1e−5, Identity >95% and Coverage >0.7, the similarity of two sequences is greater than 95% and the length of similar fragments accounts for more than 80% of the predicted effect factor and the sequence length of PHI database). We used MEGA to construct the gene tree and used MEME to identify the motifs. Then, we summed the pathogenic and structural characterics of verified RxLR and CRN genes families in each Phytophthora species, including the motif distribution, the corresponding host and the disease to refer.

CAZymes

Although the previous study have done some analysis about cazymes, the comparisons among these Phytophthora species have not been made. We performed a scan of the seven Phytophthora genomes and allied Plasmopara halstedii against the CAZymes database (http://www.cazy.org/), and the statistically comparison was re-conducted in Fig. 6. We used run_dbCAN.py (https://github.com/linnabrown/run_dbcan) to identify the carbohydrate-active enzyme in each genome and used the Circos software to draw the distribution figure. It proves that the total copy numbers of cazymes homologs are P. sojae (470), P. nicotianae (462), P. parasitica (449), P. fragariae (396), P. ramorum (382), P. rubi (371) and P. infestans (364). We then analyze the similarity and dissimilarity between the cazyme family distributions between P. infestans and P. fragariae as well as P. rubi.

P450 analysis

As a key mechanism in evading host plant defense, the cytochrome P450 genes are important for plant pathogen Phytophthora species. We downloaded 1088 P450 gene sequences belonging to all available Phytophthora species from NCBI, and blasted the P. fragariae and P. rubi genomes against these query collections. Only those with matched identity≥40%, evalue≤1e−10 and score ≥ 200 were retained as candidates. We further annotated these candidates using Pfam, and genes containing the PF00067 domain were deemed as authentic P450 genes. After the multiple sequence alignment by muscle, Treebest was used to construct the P450 gene tree. As can be seen from the phylogenetic tree we constructed based on the P450 genes in these Phytophthora species (Fig. 7), in most of the cases, the genes in P. fragariae and P. rubi appear in pair on the tree. However, there are some exceptions.

Ethics Statement

This data does not include human studies and animal experiments, has not been published previously, that it is not under consideration for publication elsewhere, that its publication is approved by all authors and tacitly or explicitly by the responsible authorities where the work was carried out, and that, if accepted, it will not be published elsewhere in the same form, in English or in any other language, including electronically without the written consent of the copyright-holder.

CrediT Author Statement

Rui-Fang Gao: Conceptualization, Methodology, Formal analysis, Investigation, Resources, Writing - Original Draft Jie-Yu Wang: Formal analysis, Data Curation, Ke-Wei Liu: Investigation, Data Curation Zhi-Wen Wang: Software, Investigation, Data Curation Diyang Zhang: Investigation, Data Curation, Visualization Xiang Zhao: Software, Investigation, Data Curation Wen-Ying Zhong: Software, Investigation Wen-Chieh Tsai: Methodology, Supervision Zhong-Jian Liu: Conceptualization, Visualization, Supervision, Project administration Gui-Ming Zhang: Conceptualization, Resources, Visualization, Project administration

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships which have, or could be perceived to have, influenced the work reported in this article.

Subject	Agricultural and Biological Sciences (General)
Specific subject area	Plant pathogens, genomic features associated with pathogenicity of Phytophthora species
Type of data	Table, Chart, Graph, Figure
How data were acquired	The whole genome sequences of two Phytophthora species were sequenced by Illumina HiSeq 2500 platform. The other available whole genome sequences, protein-coding genes, repeat sequences, gene families were from public datasets.
Data format	Raw, Analyzed
Parameters for data collection	The genome assembled by ourselves was of good quality with the coverage more than 200, the length of contigs N50 almost 50 kb and the length of scaffold N50 almost 100 kb. The genomic data from public datasets had complete information, well assembled and annotated, and were all published in authoritative journals with more citations.
Description of data collection	We sequenced and assembled the genome of using a strategy that combined paired-end and mate-paired libraries. The paired-end libraries of 180 bp, 300 bp and 500 bp, and mate-paired libraries of 3 kb and 5 kb were constructed for each genome. De novo assembly was performed using Allpaths-LG. The assembled genome scaffolds were aligned to the most closely related publicly available genomes using MUMmer which included P. infestans T30–4, P. parasitica INRA-310, P. sojae V3.0, P. nicotianae and P. ramorum. Scaffolds were broken at points where non-contiguous regions of the reference genome were juxtaposed and then re-ordered so that the scaffolds were syntenic with the reference genome.
Data source location	The sequenced strains were imported from Westerdijk Fungal Biodiversity Institute, Netherlands. The original genome sequenced data was stored in Shenzhen, Fuzhou and Wuhan. The other genome sequence and data were downloaded from public sources, all freely available.
Data accessibility	This article provides the analyzed data. Raw data are deposited in a public repository.The genome assemblies of two Phytophthora species were uploaded to NCBI database.Repository name: NCBI databaseRaw data identification number (SRA):Phytophthora fragairae: SRR16352867, SRR16352866, SRR16352865, SRR16352864Phytophthora rubi: SRR16351716, SRR16351717The genome assembly of two Phytophthora species was uploaded to NCBI databaseDirect URL to genome assembly: https://www.ncbi.nlm.nih.gov/assembly/GCA_000686205.4 (Phytophthora fragairae),https://www.ncbi.nlm.nih.gov/assembly/GCA_000687305.2 (Phytophthora rubi)
Related research article	R.F. Gao, J.Y.Wang, K.W. Liu, K. Yoshida, Y.Y. Hsiao, Y.X. Shi, K.C. Tsai, Y.Y. Chen, N. Mitsuda, C. K. Liang. et al. Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops. Heliyon. 2021, 7, e6317. https://doi.org/10.1016/j.heliyon.2021.e06317