Comparative genomic analysis of two Burkholderia glumae strains from different geographic origins reveals a high degree of plasticity in genome structure associated with genomic islands

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• 作者：Felix Francis (1) <br> Joohyun Kim (2) <br> Thiru Ramaraj (3) <br> Andrew Farmer (3) <br> Milton C. Rush (1) <br> Jong Hyun Ham (1) <br>
• 关键词：Burkholderia glumae ; Genome plasticity ; Bacterial panicle blight ; Genomic island
• 刊名：Molecular Genetics and Genomics
• 出版年：2013
• 出版时间：4 - April 2013
• 年：2013
• 卷：288
• 期：3
• 页码：195-203
• 全文大小：501KB
• 参考文献：1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403鈥?10 <br> 2. Birol I, Jackman SD, Nielsen CB, Qian JQ, Varhol R, Stazyk G, Morin RD, Zhao Y, Hirst M, Schein JE, Horsman DE, Connors JM, Gascoyne RD, Marra MA, Jones SJM (2009) / De novo transcriptome assembly with ABySS. Bioinformatics 25:2872鈥?877 bioinformatics/btp367">CrossRef <br> 3. Bocsanczy AM, Nissinen RM, Oh CS, Beer SV (2008) HrpN of / Erwinia amylovora functions in the translocation of DspA/E into plant cells. Mol Plant Pathol 9:425鈥?34 CrossRef <br> 4. Dalca AV, Brudno M (2010) Genome variation discovery with high-throughput sequencing data. Brief Bioinform 11:3鈥?4 bib/bbp058">CrossRef <br> 5. Devescovi G, Bigirimana J, Degrassi G, Cabrio L, LiPuma JJ, Kim J, Hwang I, Venturi V (2007) Involvement of a quorum-sensing-regulated lipase secreted by a clinical isolate of / Burkholderia glumae in severe disease symptoms in rice. Appl Environ Microbiol 73:4950鈥?958 CrossRef <br> 6. Gao F, Zhang CT (2006) GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences. Nucleic Acids Res 34(Web Server issue): W686鈥?91 <br> 7. Ham JH, Melanson RA, Rush MC (2011) / Burkholderia glumae: next major pathogen of rice? Mol Plant Pathol 12:329鈥?39 CrossRef <br> 8. Holden MT, Seth-Smith HM, Crossman LC, Sebaihia M, Bentley SD, Cerdeno-Tarraga AM, Thomson NR, Bason N, Quail MA, Sharp S, Cherevach I, Churcher C, Goodhead I, Hauser H, Holroyd N, Mungall K, Scott P, Walker D, White B, Rose H, Iversen P, Mil-Homens D, Rocha EP, Fialho AM, Baldwin A, Dowson C, Barrell BG, Govan JR, Vandamme P, Hart CA, Mahenthiralingam E, Parkhill J (2009) The genome of / Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients. J Bacteriol 191:261鈥?77 CrossRef <br> 9. Hu B, Xie G, Lo CC, Starkenburg SR, Chain PS (2011) Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics. Brief Funct Genomics 10:322鈥?33 bfgp/elr042">CrossRef <br> 10. Juhas M, van der Meer JR, Gaillard M, Harding RM, Hood DW, Crook DW (2009) Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol Rev 33:376鈥?93 CrossRef <br> 11. Karki HS, Shrestha BK, Han JW, Groth DE, Barphagha IK, Rush MC, Melanson RA, Kim BS, Ham JH (2012) Diversities in virulence, antifungal activity, pigmentation and DNA fingerprint among strains of / Burkholderia glumae. PLoS ONE 7(9):e45376 CrossRef <br> 12. Kim J, Kim JG, Kang Y, Jang JY, Jog GJ, Lim JY, Kim S, Suga H, Nagamatsu T, Hwang I (2004) Quorum sensing and the LysR-type transcriptional activator ToxR regulate toxoflavin biosynthesis and transport in / Burkholderia glumae. Mol Microbiol 54:921鈥?34 CrossRef <br> 13. Kim J, Kang Y, Choi O, Jeong Y, Jeong JE, Lim JY, Kim M, Moon JS, Suga H, Hwang I (2007) Regulation of polar flagellum genes is mediated by quorum sensing and FlhDC in / Burkholderia glumae. Mol Microbiol 64:165鈥?79 CrossRef <br> 14. Langille MG, Brinkman FS (2009) IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 25:664鈥?65 bioinformatics/btp030">CrossRef <br> 15. Langille MG, Hsiao WW, Brinkman FS (2008) Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinform 9:329 CrossRef <br> 16. Lessie TG, Hendrickson W, Manning BD, Devereux R (1996) Genomic complexity and plasticity of / Burkholderia cepacia. FEMS Microbiol Lett 144:117鈥?28 b08517.x">CrossRef <br> 17. Li H, Homer N (2010) A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform 11:473鈥?83 bib/bbq015">CrossRef <br> 18. Lim J, Lee TH, Nahm BH, Choi YD, Kim M, Hwang I (2009) Complete genome sequence of / Burkholderia glumae BGR1. J Bacteriol 191:3758鈥?759 CrossRef <br> 19. Lu H, Patil P, Van Sluys MA, White FF, Ryan RP, Dow JM, Rabinowicz P, Salzberg SL, Leach JE, Sonti R, Brendel V, Bogdanove AJ (2008) Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in xanthomonas. PLoS ONE 3:e3828 CrossRef <br> 20. Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24:133鈥?41 CrossRef <br> 21. Petnicki-Ocwieja T, van Dijk K, Alfano JR (2005) The / hrpK operon of / Pseudomonas syringae pv. / tomato DC3000 encodes two proteins secreted by the type III (Hrp) protein secretion system: HopB1 and HrpK, a putative type III translocator. J Bacteriol 187:649鈥?63 CrossRef <br> 22. Slater GS, Birney E (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinform 6:31 CrossRef <br> 23. Smits TH, Rezzonico F, Kamber T, Blom J, Goesmann A, Frey JE, Duffy B (2010) Complete genome sequence of the fire blight pathogen / Erwinia amylovora CFBP 1430 and comparison to other / Erwinia spp. Mol Plant-Microbe Interact 23:384鈥?93 CrossRef <br> 24. Stothard P, Wishart DS (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21:537鈥?39 bioinformatics/bti054">CrossRef <br> 25. Takeuchi T, Sawada H, Suzuki F, Matsuda I (1997) Specific detection of / Burkholderia plantarii and / B. glumae by PCR using primers selected from the 16S鈥?3S rDNA spacer regions. Ann Phytopathol Soc Jpn 63:455鈥?62 CrossRef <br> 26. Tsushima S (1996) Epidemiology of bacterial grain rot of rice caused by / Pseudomonas glumae. JARQ 30:85鈥?9 <br> 27. Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, Surovcik K, Meinicke P, Merkl R (2006) Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinform 7:142 CrossRef <br> 28. Winsor GL, Khaira B, Van Rossum T, Lo R, Whiteside MD, Brinkman FS (2008) The Burkholderia genome database: facilitating flexible queries and comparative analyses. Bioinformatics 24:2803鈥?804 bioinformatics/btn524">CrossRef <br>
• 作者单位：Felix Francis (1) <br> Joohyun Kim (2) <br> Thiru Ramaraj (3) <br> Andrew Farmer (3) <br> Milton C. Rush (1) <br> Jong Hyun Ham (1) <br><br>1. Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803-1720, USA <br> 2. Center for Computation and Technology, Louisiana State University, Baton Rouge, LA, 70803, USA <br> 3. National Center for Genome Resources, Santa Fe, NM, 87505, USA <br>
• ISSN：1617-4623

文摘

Burkholderia glumae is the major causal agent of bacterial panicle blight of rice, a growing disease problem in global rice production. To better understand its genome-scale characteristics, the genome of the highly virulent B. glumae strain 336gr-1 isolated from Louisiana, USA was sequenced using the Illumina Genome Analyser II system. De novo assembled 336gr-1 contigs were aligned and compared with the previously sequenced genome of B. glumae strain BGR1, which was isolated from an infected rice plant in South Korea. Comparative analysis of the whole genomes of B. glumae 336gr-1 and B. glumae BGR1 revealed numerous unique genomic regions present only in one of the two strains. These unique regions contained accessory genes including mobile elements and phage-related genes, and some of the unique regions in B. glumae BGR1 corresponded to predicted genomic islands. In contrast, little variation was observed in known and potential virulence genes between the two genomes. The considerable amount of plasticity largely based on accessory genes and genome islands observed from the comparison of the genomes of these two strains of B. glumae may explain the versatility of this bacterial species in various environmental conditions and geographic locations.