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. 2022 Apr 15;42:108145. doi: 10.1016/j.dib.2022.108145

Genomic data resource of type strains of genus Pseudoxanthomonas

Kanika Bansal 1,1, Sanjeet Kumar 1,1, Prashant P Patil 1, Shikha Sharma 1, Prabhu B Patil 1,⁎
PMCID: PMC9065704  PMID: 35515983

Abstract

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.

Keywords: Pseudoxanthomonas, Type strains, Phylogenomics, OrthoANI, Whole genome sequencing, Illumina MiSeq

Specifications Table

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 Raw
Analyzed
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 source
location		 Institution: CSIR-Institute of Microbial Technology, Chandigarh
City/Town/Region: Chandigarh
Country: INDIA
Data
accessibility		 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/PDWS00000000
NCBI: PDWW00000000: https://www.ncbi.nlm.nih.gov/nuccore/PDWW00000000
NCBI: 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/PDWP00000000
NCBI: PDWV00000000: https://www.ncbi.nlm.nih.gov/nuccore/PDWV00000000
NCBI: PDWK00000000: https://www.ncbi.nlm.nih.gov/nuccore/PDWK00000000
NCBI: 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].
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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.

1. 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]
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Fig. 1.

Fig 1

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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.

2. Experimental Design, Materials and Methods

2.1. 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.

2.2. 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.

2.3. 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.

Acknowledgments

All the work in the present study was supported by “Mega-genomic insights into co-evolution of rice and its Microbiome” (MICRA/MLP0020) and “GEAR- Genomic Evolutionary and Big-Data Analytic Strategies to Address Antimicrobial Resistance” (MLP0016).

Data Availability

  • Genomic data resource of type strains of genus Pseudoxanthomonas (Original data) (NCBI genome).

References

  • 1.Bansal K., et al. Deep phylo-taxono genomics reveals Xylella as a variant lineage of plant associated Xanthomonas and supports their taxonomic reunification along with Stenotrophomonas and Pseudoxanthomonas. Genomics. 2021;113(6):3989–4003. doi: 10.1016/j.ygeno.2021.09.021. [DOI] [PubMed] [Google Scholar]
  • 2.Kittiwongwattana C., Thawai C. Pseudoxanthomonas helianthi sp. nov., isolated from roots of Jerusalem artichoke (Helianthus tuberosus) Int. J. Syst. Evol. Microbiol. 2016;66(12):5034–5038. doi: 10.1099/ijsem.0.001465. [DOI] [PubMed] [Google Scholar]
  • 3.Lee J.K., et al. Pseudoxanthomonas putridarboris sp. nov. isolated from rotten tree. Int. J. Syst. Evol. Microbiol. 2017;67(6):1807–1812. doi: 10.1099/ijsem.0.001867. [DOI] [PubMed] [Google Scholar]
  • 4.Patil P.P., et al. Genome sequence of type strains of genus Stenotrophomonas. Front. Microbiol. 2016;7:309. doi: 10.3389/fmicb.2016.00309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Kumar S., et al. Phylogenomics insights into order and families of Lysobacterales. Access Microbiol. 2019;1(2):1–9. doi: 10.1099/acmi.0.000015. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Chen M.Y., et al. Pseudoxanthomonas taiwanensis sp. nov., a novel thermophilic, N2O-producing species isolated from hot springs. Int. J. Syst. Evol. Microbiol. 2002;52(6):2155–2161. doi: 10.1099/00207713-52-6-2155. [DOI] [PubMed] [Google Scholar]
  • 7.Finkmann W., et al. Characterization of N2O-producing Xanthomonas-like isolates from biofilters as Stenotrophomonas nitritireducens sp. nov., Luteimonas mephitis gen. nov., sp. nov. and Pseudoxanthomonas broegbernensis gen. nov., sp. nov. Int. J. Syst. Evol. Microbiol. 2000;50(1):273–282. doi: 10.1099/00207713-50-1-273. [DOI] [PubMed] [Google Scholar]
  • 8.Kumari K., et al. Pseudoxanthomonas indica sp. nov., isolated from a hexachlorocyclohexane dumpsite. Int. J. Syst. Evol. Microbiol. 2011;61(9):2107–2111. doi: 10.1099/ijs.0.017624-0. [DOI] [PubMed] [Google Scholar]
  • 9.Harada R.M., Campbell S., Li Q.X. Pseudoxanthomonas kalamensis sp. nov., a novel gammaproteobacterium isolated from Johnston Atoll, North Pacific Ocean. Int. J. Syst. Evol. Microbiol. 2006;56(5):1103–1107. doi: 10.1099/ijs.0.63556-0. [DOI] [PubMed] [Google Scholar]
  • 10.Chang J.S., et al. Pseudoxanthomonas kaohsiungensis, sp. nov., a novel bacterium isolated from oil-polluted site produces extracellular surface activity. Syst. Appl. Microbiol. 2005;28(2):137–144. doi: 10.1016/j.syapm.2004.11.003. [DOI] [PubMed] [Google Scholar]
  • 11.Lee D.S., et al. Pseudoxanthomonas sacheonensis sp. nov., isolated from BTEX-contaminated soil in Korea, transfer of Stenotrophomonas dokdonensis Yoon et al. (2006) to the genus Pseudoxanthomonas as Pseudoxanthomonas dokdonensis comb. nov. and emended description of the genus Pseudoxanthomonas. Int. J. Syst. Evol. Microbiol. 2008;58(9):2235–2240. doi: 10.1099/ijs.0.65678-0. [DOI] [PubMed] [Google Scholar]
  • 12.Young C.C., et al. Pseudoxanthomonas spadix sp. nov., isolated from oil-contaminated soil. Int. J. Syst. Evol. Microbiol. 2007;57(8):1823–1827. doi: 10.1099/ijs.0.65053-0. [DOI] [PubMed] [Google Scholar]
  • 13.Wang G.L., et al. Pseudoxanthomonas jiangsuensis sp. nov., a DDT-degrading bacterium isolated from a long-term DDT-polluted soil. Curr. Microbiol. 2011;62(6):1760–1766. doi: 10.1007/s00284-011-9925-1. [DOI] [PubMed] [Google Scholar]
  • 14.Bankevich A., et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 2012;19(5):455–477. doi: 10.1089/cmb.2012.0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15.Gurevich A., et al. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29(8):1072–1075. doi: 10.1093/bioinformatics/btt086. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 16.Bushnell, B., BBMap: a fast, accurate, splice-aware aligner. (2014). (No. LBNL-7065E). Lawrence Berkeley National Lab.(LBNL), Berkeley, CA (United States) doi: https://www.osti.gov/servlets/purl/1241166.
  • 17.Antipov D., et al. PlasmidSPAdes: assembling plasmids from whole genome sequencing data. Bioinformatics. 2016;32(22):3380–3387. doi: 10.1093/bioinformatics/btw493. [DOI] [PubMed] [Google Scholar]
  • 18.Tatusova T., et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016;44(14):6614–6624. doi: 10.1093/nar/gkw569. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 19.Lagesen K., et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35(9):3100–3108. doi: 10.1093/nar/gkm160. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Larkin M.A., et al. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23(21):2947–2948. doi: 10.1093/bioinformatics/btm404. [DOI] [PubMed] [Google Scholar]
  • 21.Kumar S., Stecher G., Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 2016;33(7):1870–1874. doi: 10.1093/molbev/msw054. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 22.Lee S.H., et al. Complete genome sequence of the BTEX-degrading bacterium Pseudoxanthomonas spadix BD-a59. J. Bacteriol. 2012;194(2):544. doi: 10.1128/JB.06436-11. [DOI] [PMC free article] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

  • Genomic data resource of type strains of genus Pseudoxanthomonas (Original data) (NCBI genome).

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