Whole-genome sequence and genome annotation of Xanthomonas citri pv. mangiferaeindicae, causal agent of bacterial black spot on Mangifera indica

Short Communication

Abstract

A newly isolated strain XC01 was identified as Xanthomonas citri pv. mangiferaeindicae, isolated from an infected mango fruit in Guangxi, China. The complete genome sequence of XC01 was carried out using the PacBio RSII platform. The genome contains a circular chromosome with 3,865,165 bp, 3442 protein-coding genes, 53 tRNAs, and 2 rRNA operons. Phylogenetic analysis revealed that this pathogen is very close to the soybeans bacterial pustule pathogen X. citri pv. glycines CFBP 2526, with a completely different host range. The genome sequence of XC01 may shed a highlight genes with a demonstrated or proposed role in on the pathogenesis.

Keywords

Xanthomonas citri pv. mangiferaeindicae Mango Complete genome sequence 

Notes

Acknowledgements

This research was supported by the Chinese Special Fund of Basic Scientific Research Projects for State Level and Public Welfare-Scientific Research Institutes (No. 1630062014007), the special fund for Agroscientific Research in the Public Interest (No. 201203092), and Hainan Province Science Foundation (No. 20163109).

Supplementary material

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References

  1. Apweiler R, Bairoch A, Wu C, Yeh LL (2004) UniProt: the universal protein knowledgebase. Nucleic Acids Res 32:115–119CrossRefGoogle Scholar
  2. Ashburner M, Ball CA, Blake JA, Botstein D et al (2000) Gene ontology: tool for the unification of biology. Nat Genetics 25(1):25–29CrossRefPubMedGoogle Scholar
  3. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genom 9:75CrossRefGoogle Scholar
  4. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C et al (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569CrossRefPubMedGoogle Scholar
  5. Clarke CR, Cai R, Studholme DJ, Guttman DS, Vinatzer BA (2010) Pseudomonas syringae strains naturally lacking the classical P. syringae hrp/hrc locus are common leaf colonizers equipped with an atypical type III secretion system. Mol Plant Microbe Interact 23:198–210CrossRefPubMedGoogle Scholar
  6. Cummings MP (2014) PAUP*(Phylogenetic analysis using parsimony (*and other methods)). 4.0 ed. Sinauer Associates, SunderlandGoogle Scholar
  7. Darrasse A, Bolot S, Serres-Giardi L, Charbit E, Boureau T, Fisher-Le Saux M, Briand M, Arlat M, Gagnevin L, Koebnik R, Noël LD, Carrère S, Jacques MA (2013) High-quality draft genome sequences of Xanthomonas axonopodis pv. glycines strains CFBP 2526 and CFBP 7119. Genome Announcements 1(6):e01036–13CrossRefPubMedPubMedCentralGoogle Scholar
  8. Gagnevin L, Pruvost O (2001) Epidemiology and control of mango bacterial black spot. Plant Dis 85(9):928–935CrossRefGoogle Scholar
  9. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ, (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 11:119CrossRefGoogle Scholar
  10. Kanehisa M, Goto S, Kawashima S, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32:277–280CrossRefGoogle Scholar
  11. Lagesen K, Hallin PF, Rødland E, Stærfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108CrossRefPubMedPubMedCentralGoogle Scholar
  12. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F et al. (2007) ClustalW2 and ClustalX version 2. Bioinformatics 23:2947–2948CrossRefPubMedGoogle Scholar
  13. Li L, Stoeckert CJ, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genom Res 13:2178–2189CrossRefGoogle Scholar
  14. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964CrossRefPubMedPubMedCentralGoogle Scholar
  15. Ochiai H, Inoue Y, Takeya M, Sasaki A, Kaku H (2005) Genome sequence of Xanthomonas oryzae pv. oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity. JARQ 39(4):275–287CrossRefGoogle Scholar
  16. Palmer LE, McCombie. WR (2002) On the importance of being finished. Genom Biol 3:201CrossRefGoogle Scholar
  17. Patel MK, Moniz L, Kulkarni YS (1948) A new bacterial disease of Mangifera indica L. Curr Sci 17(6):189–190PubMedGoogle Scholar
  18. Ploetz R, Ploetz R (2003) Diseases of tropical fruit crops. CABI Publishing, pp 327–363Google Scholar
  19. Ploetz RC, Prakash O (1997) Foliar, floral and soil borne diseases. In: Litz RE (ed) The mango: botany, production and uses. CAB International, Oxon, pp 281–327Google Scholar
  20. Ray SK, Rajeshwari R, Sonti RV (2000) Mutants of Xanthomonas oryzae deficient in general secretory pathway are virulent deficient and unable to secrete xylase. Mol. Plant Microbe Interact 13:394–401CrossRefGoogle Scholar
  21. Singh Z, Singh RK, Sane VA, Nath P (2013) Mango-postharvest biology and biotechnology. Crit Rev Plant Sci 32(4):217–236CrossRefGoogle Scholar
  22. Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28(1):33–36CrossRefPubMedPubMedCentralGoogle Scholar
  23. Triplett LR, Hamilton JP, Buell CR, Tisserat NA, Verdier V, Zink F, Leach JE (2011) Genomic analysis of Xanthomonas oryzae isolates from rice grown in the United States reveals substantial divergence from known X. oryzae pathovars. Appl Environ Microbiol 77:3930–3937CrossRefPubMedPubMedCentralGoogle Scholar
  24. Vauterin L, Hoste B, Kersters K, Swings J (1995) Reclassification of xanthomonas. Int J Syst Bacteriol 45:472–489CrossRefGoogle Scholar
  25. Winnenburg R, Baldwin TK, Urban M, Rawlings C, Kohler J, Hammond-Kosack KE (2006). PHI-base: a new database for pathogen host interactions. Nucleic Acids Res. 34:459–464CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Southern Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Tropical Fruit Biology, Ministry of AgricultureZhanjiangChina

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