Genomic data resource of type strains of genus Pseudoxanthomonas.

Genus Pseudoxanthomonas represents a relatively newly characterized group of gamma-proteobacterium of environmental origin. Species of the genus have very similar morphology to strains belonging to Xanthomonas, Xylella and Stenotrophomonas. However, the genome resource of this genus was largely unexplored. The species belonging to the genus are from a wide range of environmental sites including hydrocarbon polluted fields. Here, we have provided the whole genome sequence of all available type strains of the genus of Pseudoxanthomonas. In order to deduce the differences with closely related genera, we have employed the whole genome-based investigation of the type species of genus Pseudoxanthomonas.

Specifications Table

Value of the Data

Species of genus Pseudoxanthomonas are from contaminated sites such as: heavy metal, oil, hydrocarbons etc. Genome resource of strains from such extreme environmental conditions will aid in identification of genomic signatures underlying their bioremediation potential.

These assembled genomes can be reused as a reference by the taxonomist and microbiologist in order to distinguish any putative species of the genera Pseudoxanthomonas.

Present genome resource of type strains will be valuable in addressing the taxonomic ambiguities of the family Lysobacteraceae and order Lysobacterales.

Data Description

Here, we have performed whole-genome sequencing of the 15 type strains of genus Pseudoxanthomonas comprising of 14 valid species and one non-valid type strain of P. jiangsuensis DSM 22398T based on LPSN latest classification v2.0. Whole genome data of P. dokdonesis DSM 21858T, P. indica P15T and P. spadix BD-a59 were obtained from the public repository of NCBI (Table 1). P. helianthi NRBC 110414T [2] and P. putridarboris LMG 25968T [3] could not retrieved and thus whole genome sequence information is not included in the study. 16S rRNA based phylogeny of all the twenty species of the genus Pseudoxanthomonas is depicted in Fig. 1. Whole genome sequence of the type strains of the genus Pseudoxanthomonas can be a valuable resource in taxonogenomics study of family Lysobacteraceae and its close relatives such as Xanthomonas and Stenotrophomonas [4,5]. Extreme environmental isolates such as P. taiwanensis [6] could be one of the key biotechnologically importance species to explore the heat stress mechanism. Genome resource of species of P. broegbernensis, P. indica, P. kalamensis, P. kaohsiungensis, P. sacheonensis, P. spadix and P. jiangsuensis [7], [8], [9], [10], [11], [12], [13] could be used for studying the stress tolerant genomics determinants.

Table 1

Genome assembly statistics of the species of genus Pseudoxanthomas.

Strain name	Genome size (bps)	Fold	# Contigs	N50 (bps)	% GC	Completeness/ Contamination	# CDS	tRNA + rRNA	#Putative Plasmids	Accession number	Refs.
P. broegbernensis DSM 12573T	3,547,767	267x	157	175,278	70.6	99.66/1.74	3024	54 + 3	6	MWIP00000000	Current study
P. kaohsiungensis DSM 17583T	3,774,556	269x	100	199,653	69.68	99.66/1.42	3420	52 + 3	6	PDWO00000000	Current study
P. daejeonensis DSM 17801T	3,563,566	131x	38	227,294	68.89	99.66/0.11	3143	58 + 3	3	PDWN00000000	Current study
P. yeongjuensis DSM 18204T	3,937,688	137x	28	610,842	65.11	99.95/0.76	3389	53 + 3	1	PDWT00000000	Current study
P. sacheonensis DSM 19373T	4,036,514	101x	44	165,077	64.3	100/0.91	3582	50 + 3	1	PDWS00000000	Current study
P. japonensis DSM 17109T	4,075,711	111x	74	108,688	67.3	99.95/0.34	3673	50 + 3	4	PDWW00000000	Current study
P. wuyuanensis DSM 100640T	4,686,433	112x	86	149,132	65.75	100/1.08	4003	51 + 6	6	PDWU00000000	Current study
P. sangjuensis DSM 28345T	3,289,016	91x	76	105,206	68.68	99.95/0.46	2908	51 + 3	3	PDWR00000000	Current study
P. jiangsuensis DSM 22398T	3,790,571	171x	154	121,587	70.35	99.31/1.03	3389	50 + 3	10	PDWL00000000	Current study
P. kalamensis DSM 18571T	3,034,522	239x	162	478,688	65.88	99.84/1.50	2697	48 + 3	-	PDWQ00000000	Current study
P. koreensis KCTC12208T	3,049,736	74x	93	60,801	70.17	99.48/0.04	2681	52 + 3	7	PDWM00000000	Current study
P. suwonensis DSM 17175T	3,428,455	65x	66	104,754	70.36	99.66/0.34	3071	55 + 3	2	PDWP00000000	Current study
P. mexicana DSM17121T	3,965,467	32x	115	63,754	67.4	99.49/1.71	3660	54 + 6	10	PDWV00000000	Current study
P. taiwanensis DSM22914T	3,043,352	69x	160	39,985	72.08	99.16/0.34	2729	56 + 3	14	PDWK00000000	Current study
P. gei KCTC32298T	3,431,103	173x	50	332,530	65.46	99.95/0.41	3,122	45 + 4	-	QOVG00000000	Current study
P. dokdonesis DSM21858T	3,553,658	170x	34	-	64.48	99.59/0.41	3153	50 + 2	NA	LDJL01000000	[4]
P. indica P15T	3,960,920	-	3	-	65.4	99.89/0.41	3593	49 + 6	NA	FUZV01000000	DOE-Joint Genome Institute
P. spadix BD-a59	3,452,554	-	1	-	67.65	97.1/1.3	3153	50 + 3	NA	CP003093	[22]

Fig. 1

Phylogenetic tree construction with maximum-likelihood method based on the 16S rRNA gene sequence of different species of genus Pseudoxanthomonas. Pseudomonas aeruginosa DSM 50071T was used as outgroup. Genomes sequenced in the present study are in black and genomes from public repository are in green color. Bootstrap values are shown at the node of each cluster in blue color as percentage of 1000 replicates.

Experimental Design, Materials and Methods

Bacterial strains and culture conditions

Type strains of the genus Pseudoxanthomonas were procured from two culture collection of Korean Collection for Type Cultures (KCTC) and The Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (Table 1). Ampoules containing respective bacterial cultures were processed in the recommended media and condition in accordance with the bacterial strains collection.

Genome sequencing, assembly and annotation

Bacterial genomic DNA was extracted using ZR Fungal/Bacterial DNA MiniPrep Kit (Zymo Research, Irvine, CA, USA) and quantified using Qubit 2.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). 1 ng of DNA sample was used in the preparation of Illumina sequencing libraries using Nextera XT sample preparation kit with dual indexing following provider's instructions. Sequencing libraries were pooled and sequenced in-house on Illumina MiSeq platform with 2*250 bp paired-end sequencing kit.

The raw sequencing reads were assembled into the high-quality draft genome using SPAdes v3.10 [14] which is a de Bruijn graph-based assembler for the bacterial genome. Quality of the assembled genome was accessed using QUAST v4.4 [15] and overall coverage of the assembled genome was calculated using BBMap [16]. Presence of putative plasmid in the assembled genome was accessed using plasmidSPAdes [17] with a minimum cut-off of 1Kb length. The assembled genomes were annotated using the NCBI prokaryotic genome annotation pipeline [18]. Assembly information with the putative number of plasmids is summarized in Table 1.

Phylogenetic assessment

Phylogenetic analysis based on the traditional 16S rRNA gene sequence was performed, for which 16S rRNA gene sequence was fetched from the respective assembled genome using from a standalone academic version of RNAmmer v1.2 [19] except for the type strains for species P. spadix, P. helanthi and P. putridarboris. 16S rRNA for these 3 species were taken from LPSN of the respective species definition. Multiple sequence alignment of 16S rRNA gene sequences was performed using ClustalW [20]. Phylogenetic tree based on Maximum Likelihood method with 1000 bootstrap replication was generated using MEGA v7.0.18 [21].

Ethics Statement

There is no ethical concern involved in the study.

Author Contributions

SK, SS and PPP have carried out strain procurement from culture collection and strain revival. KB and SK have performed whole genome sequencing and submission of assembled genomes to NCBI. PBP has conceived the study and participated in the design. All the authors have read and approved the manuscript.

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	Biological sciences
Specific subject area	Microbiology: Bacteriology
Type of data	Whole genome sequence assembled genome with gene annotation and phylogeny of genus Pseudoxanthomonas and its related genera.
How the data were acquired	Whole genome sequencing (WGS) library was prepared for Illumina MiSeq sequencing platform. Assembly of the raw reads were performed using SPAdes v3.10.
Data format	RawAnalyzed
Parameters for data collection	Sequencing library for all the available type strains were prepared for Illumina MiSeq following manufacturer's instructions. Sequencing was performed with 2*250 bp paired end sequencing kit.
Description of data collection	WGS data obtained from the sequencer was quality trimmed by control software of Illumina MiSeq. Raw reads were de novo assembled into high quality draft genome was performed using SPAdes v3.10 and quality checked using CheckM v1.1.0
Data sourcelocation	Institution: CSIR-Institute of Microbial Technology, ChandigarhCity/Town/Region: ChandigarhCountry: INDIA
Dataaccessibility	NCBI: MWIP00000000: https://www.ncbi.nlm.nih.gov/nuccore/MWIP00000000 NCBI: PDWO00000000: https://www.ncbi.nlm.nih.gov/nuccore/PDWO00000000 NCBI: PDWN00000000: https://www.ncbi.nlm.nih.gov/nuccore/PDWN00000000 NCBI: PDWT00000000: https://www.ncbi.nlm.nih.gov/nuccore/PDWT00000000 NCBI: PDWS00000000: https://www.ncbi.nlm.nih.gov/nuccore/PDWS00000000NCBI: PDWW00000000: https://www.ncbi.nlm.nih.gov/nuccore/PDWW00000000NCBI: PDWU00000000: https://www.ncbi.nlm.nih.gov/nuccore/PDWU00000000 NCBI: PDWR00000000: https://www.ncbi.nlm.nih.gov/nuccore/PDWR00000000 NCBI: PDWL00000000: https://www.ncbi.nlm.nih.gov/nuccore/PDWL00000000 NCBI: PDWQ00000000: https://www.ncbi.nlm.nih.gov/nuccore/PDWQ00000000 NCBI: PDWM00000000: https://www.ncbi.nlm.nih.gov/nuccore/PDWM00000000 NCBI: PDWP00000000: https://www.ncbi.nlm.nih.gov/nuccore/PDWP00000000NCBI: PDWV00000000: https://www.ncbi.nlm.nih.gov/nuccore/PDWV00000000NCBI: PDWK00000000: https://www.ncbi.nlm.nih.gov/nuccore/PDWK00000000NCBI: QOVG00000000: https://www.ncbi.nlm.nih.gov/nuccore/QOVG00000000
Related research article	Bansal, K., Kumar, S., Kaur, A., Singh, A. & Patil, P. B. (2021) Deep phylo-taxono genomics reveals Xylella as a variant lineage of plant associated Xanthomonas and supports their taxonomic reunification along with Stenotrophomonas and Pseudoxanthomonas. https://doi.org/10.1016/j.ygeno.2021.09.021[1].