1887

Access Microbiology open research platform logo

Volume 4, Issue 10

Genome dynamics mediated by repetitive and mobile elements in pv. Open Access

Abstract

is a highly evolved group of phytopathogenic bacteria infecting nearly 400 host plants having vast genomic resources available with heterogenicity in representation from different species and pathovars. Unfortunately, the wealth of data is extremely biased and restricted to a few pathogens that infect economically important plants, while those reported to infect the most diverse plants remain neglected. In the present study, we report the first complete genome sequence of pv. that was reported to infect . or golden dewdrop, a hedge plant of ornamental importance native to the American region. Phylogenomic analysis with its closest relatives placed it amongst pv. A* pathotype strains and further comparative studies revealed various large unique genomic regions of chromosomal origin. The association of integrative and conjugative elements and prophages with unique genomic regions suggests the role of mobilome in genome dynamics. A large number of IS elements and transcription activator-like effectors encoding genes on each of the four plasmids indicate the further scope of diversification in .

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): comparative genomics , integrative and conjugative elements , IS elements , pathovar , transcription activator-like effectors (TALEs) and Xanthomonas citri pv. durantae
Funding
This study was supported by the:
  • Department of Biotechnology (DBT), the government of India. (Award GAP0187-grant number BT/HRD/NBA/38/14/2018-19)
    • Principle Award Recipient: B. PatilPrabhu
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Loading

Article metrics loading...

/content/journal/acmi/10.1099/acmi.0.000415
2022-10-03
2024-05-17
Loading full text...

Full text loading...

/deliver/fulltext/acmi/4/10/acmi000415.html?itemId=/content/journal/acmi/10.1099/acmi.0.000415&mimeType=html&fmt=ahah

References

  1. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article]
     [Google Scholar]
  2. Jacques M-A, Arlat M, Boulanger A, Boureau T, Carrère S et al. Using ecology, physiology, and genomics to understand host specificity in Xanthomonas. Annu Rev Phytopathol 2016; 54:163–187 [View Article] [PubMed]
     [Google Scholar]
  3. Ryan RP, Vorhölter F-J, Potnis N, Jones JB, Van Sluys M-A et al. Pathogenomics of Xanthomonas: understanding bacterium-plant interactions. Nat Rev Microbiol 2011; 9:344–355 [View Article] [PubMed]
     [Google Scholar]
  4. Timilsina S, Potnis N, Newberry EA, Liyanapathiranage P, Iruegas-Bocardo F et al. Xanthomonas diversity, virulence and plant-pathogen interactions. Nat Rev Microbiol 2020; 18:415–427 [View Article] [PubMed]
     [Google Scholar]
  5. NRCS U. The PLANTS Database Greensboro, USA: National Plant Data Team; 2018
     [Google Scholar]
  6. Srinivasan M, Patel M. Two new phytopathogenic bacteria on verbenaceous hosts. Curr Sci 1957; 26:90–91
     [Google Scholar]
  7. Srinivasan MC, Patel MK, Thirumalachar MJ. Two new phytopathogenic bacteria on verbenaceous hosts. Proceedings of the Indian Academy of Sciences - Section B 1962; 56:88–92 [View Article]
     [Google Scholar]
  8. Gumtow RL, Khan AA, Bocsanczy AM, Yuen JMF, Palmateer AJ et al. First report of a leaf spot disease of golden dewdrop (Duranta erecta) caused by Pseudomonas cichorii and a Xanthomonas species in Florida. Plant Dis 2013; 97:836 [View Article] [PubMed]
     [Google Scholar]
  9. Bansal K, Midha S, Kumar S, Patil PB. Ecological and evolutionary insights into Xanthomonas citri Pathovar diversity. Appl Environ Microbiol 2017; 83:e02993–02916 [View Article] [PubMed]
     [Google Scholar]
  10. Parkinson N, Cowie C, Heeney J, Stead D. Phylogenetic structure of Xanthomonas determined by comparison of gyrB sequences. Int J Syst Evol Microbiol 2009; 59:264–274 [View Article] [PubMed]
     [Google Scholar]
  11. Bansal K, Kumar S, Patil PB. Phylo-taxonogenomics supports revision of taxonomic status of 20 Xanthomonas Pathovars to Xanthomonas citri. Phytopathology 2022; 112:1201–1207 [View Article]
     [Google Scholar]
  12. Patané JSL, Martins J Jr, Rangel LT, Belasque J, Digiampietri LA et al. Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses. BMC Genomics 2019; 20:700 [View Article] [PubMed]
     [Google Scholar]
  13. Boch J, Bonas U. Xanthomonas AvrBs3 family-type III effectors: discovery and function. Annu Rev Phytopathol 2010; 48:419–436 [View Article] [PubMed]
     [Google Scholar]
  14. Vandecraen J, Chandler M, Aertsen A, Van Houdt R. The impact of insertion sequences on bacterial genome plasticity and adaptability. Crit Rev Microbiol 2017; 43:709–730 [View Article] [PubMed]
     [Google Scholar]
  15. Lee H, Gurtowski J, Yoo S, Nattestad M, Marcus S et al. Third-generation sequencing and the future of genomics. Bioinformatics 2016; 048603 [View Article]
     [Google Scholar]
  16. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
     [Google Scholar]
  17. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963 [View Article] [PubMed]
     [Google Scholar]
  18. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
     [Google Scholar]
  19. Bushnell B, Egan R, Copeland A, Foster B, Clum A et al. BBMap: a fast, accurate, splice-aware aligner; 2019 https://sourceforge.net/projects/bbmap
  20. Grant JR, Arantes AS, Stothard P. Comparing thousands of circular genomes using the CGView Comparison Tool. BMC Genomics 2012; 13:1–8 [View Article] [PubMed]
     [Google Scholar]
  21. Stothard P, Wishart DS. Circular genome visualization and exploration using CGView. Bioinformatics 2005; 21:537–539 [View Article] [PubMed]
     [Google Scholar]
  22. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  23. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article] [PubMed]
     [Google Scholar]
  24. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59:307–321 [View Article] [PubMed]
     [Google Scholar]
  25. Didelot X, Wilson DJ. ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLoS Comput Biol 2015; 11:e1004041 [View Article]
     [Google Scholar]
  26. Letunic I, Bork P. Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021; 49:W293–W296 [View Article]
     [Google Scholar]
  27. Alikhan N-F, Petty NK, Ben Zakour NL, Beatson SA. BLAST ring image generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 2011; 12:1–10 [View Article] [PubMed]
     [Google Scholar]
  28. Liu M, Li X, Xie Y, Bi D, Sun J et al. ICEberg 2.0: an updated database of bacterial integrative and conjugative elements. Nucleic Acids Res 2019; 47:D660–D665 [View Article] [PubMed]
     [Google Scholar]
  29. Arndt D, Grant JR, Marcu A, Sajed T, Pon A et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016; 44:W16–21 [View Article] [PubMed]
     [Google Scholar]
  30. Varani AM, Siguier P, Gourbeyre E, Charneau V, Chandler M. ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes. Genome Biol 2011; 12:R30 [View Article] [PubMed]
     [Google Scholar]
  31. Grau J, Reschke M, Erkes A, Streubel J, Morgan RD et al. AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences. Sci Rep 2016; 6:21077 [View Article]
     [Google Scholar]
  32. Pérez-Quintero AL, Lamy L, Gordon JL, Escalon A, Cunnac S et al. QueTAL: a suite of tools to classify and compare TAL effectors functionally and phylogenetically. Front Plant Sci 2015; 6:545 [View Article] [PubMed]
     [Google Scholar]
  33. Gordon JL, Lefeuvre P, Escalon A, Barbe V, Cruveiller S et al. Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges. BMC Genomics 2015; 16:1–20 [View Article] [PubMed]
     [Google Scholar]
  34. Moscou MJ, Bogdanove AJ. A simple cipher governs DNA recognition by TAL effectors. Science 2009; 326:1501 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/acmi/10.1099/acmi.0.000415
Loading
Genome dynamics mediated by repetitive and mobile elements in Xanthomonas citri pv. durantae
Access Microbiology 4, 000415 (2022); https://doi.org/10.1099/acmi.0.000415
/content/journal/acmi/10.1099/acmi.0.000415
/content/journal/acmi/10.1099/acmi.0.000415
Loading

Data & Media loading...

Supplements

Supplementary material 1

EXCEL

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error