霍乱弧菌O1血清群产毒株重复基因分析
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摘要
目的对霍乱弧菌O1血清群产毒株基因组中重复基因数量分布、多样性及两种生物型中重复基因的差异进行分析。方法选择300株引起第6次和第7次大流行的O1群古典型和埃尔托型生物型菌株,使用BLAST和MCL等软件分析重复基因数量分布及两种生物型差异的重复基因;使用序列两两平均距离作为多样性的度量方法分析重复基因的遗传多样性以及在两种生物型之间存在遗传多样性差异的重复基因。结果每株菌平均包含242.63个同源基因簇,其中每株埃尔托型和古典型菌株分别平均包含244.85和209.74个。筛选到13个在埃尔托生物型与古典生物型之间拷贝数存在显著差异同源基因簇,功能主要包括阴离子、氨基酸等物质的转运、定位、跨膜转运等。对存在重复基因的同源基因簇的遗传多样性分析,发现在两种生物型之间多样性存在差异的同源基因簇50个,这些基因簇的功能主要包括阴离子、氨基酸、有机底物等转运、定植、底物特异的跨膜转运活性等。结论霍乱弧菌重复基因的进化有一定的功能倾向性,其特征解析对于理解其基因组适应性进化、菌株多样性及两种生物型基因组差异进化提供了新依据。
Objective Gene duplication through paralogous gene evolution is an important way of prokaryotic genome evolution, while the characteristics of duplication genes in Vibrio cholerae genome are poorly understood. In this study, we analyzed the number, diversity of duplication genes and difference in duplication genes between two biotypes of toxigenic strains of V. cholerae O1. Methods We selected 300 strains of V. cholerae O1 of two biotypes causing the sixth and seventh pandemics. The numeric distribution and differential duplication genes between two biotypes were analyzed by using blastp and MCL; the diversity of duplication genes and genes of diversity difference were analyzed by measuring the average distance between any two sequences. Results The results showed that the average number of homologous gene clusters per strain was242.63, the average number of that was 244.85 for El Tor biotype strains, and 209.74 for classical biotype strains. El Tor biotype had more duplication homologous gene clusters than classical biotype. Thirteen homologous gene clusters with significant different copies numbers between El Tor biotype and classical biotype were screened out; their functions mainly include the anions, amino acids or other substances transport, localization and transmembrane transport. By analyzing the genetic diversity of homologous gene clusters with duplication genes, we found 50 homologous gene clusters with different diversity between the two biotypes, the biological processes they participate in mainly include anions, amino acids or other substances transport, localization and substrate-specific transmembrane transport activity, etc. Conclusion The evolution of the duplication genes of V. cholerae has a certain functional tendency; the characterization of it could provide a new point for the understanding of the adaptive evolution of the genome, the diversity of strains and the differential evolution of the genomes of two biotypes.
Objective Gene duplication through paralogous gene evolution is an important way of prokaryotic genome evolution, while the characteristics of duplication genes in Vibrio cholerae genome are poorly understood. In this study, we analyzed the number, diversity of duplication genes and difference in duplication genes between two biotypes of toxigenic strains of V. cholerae O1. Methods We selected 300 strains of V. cholerae O1 of two biotypes causing the sixth and seventh pandemics. The numeric distribution and differential duplication genes between two biotypes were analyzed by using blastp and MCL; the diversity of duplication genes and genes of diversity difference were analyzed by measuring the average distance between any two sequences. Results The results showed that the average number of homologous gene clusters per strain was242.63, the average number of that was 244.85 for El Tor biotype strains, and 209.74 for classical biotype strains. El Tor biotype had more duplication homologous gene clusters than classical biotype. Thirteen homologous gene clusters with significant different copies numbers between El Tor biotype and classical biotype were screened out; their functions mainly include the anions, amino acids or other substances transport, localization and transmembrane transport. By analyzing the genetic diversity of homologous gene clusters with duplication genes, we found 50 homologous gene clusters with different diversity between the two biotypes, the biological processes they participate in mainly include anions, amino acids or other substances transport, localization and substrate-specific transmembrane transport activity, etc. Conclusion The evolution of the duplication genes of V. cholerae has a certain functional tendency; the characterization of it could provide a new point for the understanding of the adaptive evolution of the genome, the diversity of strains and the differential evolution of the genomes of two biotypes.
引文
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[2]Gevers D,Vandepoele K,Simillion C,et al.Gene duplication and biased functional retention of paralogs in bacterial genomes[J].Trends Microbiol,2004,12(4):148-154.DOI:10.1016/j.tim.2004.02.007.
[3]Bratlie MS,Johansen J,Sherman BT,et al.Gene duplications in prokaryotes can be associated with environmental adaptation[J].BMC Genomics,2010,11:588.
[4]Hyatt D,Chen GL,Locascio PF,et al.Prodigal:prokaryotic gene recognition and translation initiation site identification[J].BMCBioinformatics,2010,11:119.DOI:10.1186/1471-2105-11-119.
[5]Enright AJ,Van Dongen S,Ouzounis CA.An efficient algorithm for large-scale detection of protein families[J].Nucleic Acids Res,2002,30(7):1575-1584.DOI:10.1093/nar/30.7.1575.
[6]Fu LM,Niu BF,Zhu ZW,et al.CD-HIT:accelerated for clustering the next-generation sequencing data[J].Bioinformatics,2012,28(23):3150-3152.DOI:10.1093/bioinformatics/bts565.
[7]Sievers F,Wilm A,Dineen D,et al.Fast,scalable generation of high-quality protein multiple sequence alignments using Clustal Omega[J].Mol Syst Biol,2011,7:539.DOI:10.1038/msb.2011.75.
[8]Dziejman M,Balon E,Boyd D,et al.Comparative genomic analysis of Vibrio cholerae:genes that correlate with cholera endemic and pandemic disease[J].Proc Natl Acad Sci USA,2002,99(3):1556-1561.DOI:10.1073/pnas.042667999.
[9]Mutreja A,Kim DW,Thomson NR,et al.Evidence for several waves of global transmission in the seventh cholera pandemic[J].Nature,2011,477(7365):462-465.DOI:10.1038/nature10392.
[10]Safa A,Nair GB,Kong RYC.Evolution of new variants of Vibrio cholerae O1[J].Trends Microbiol,2010,18(1):46-54.DOI:10.1016/j.tim.2009.10.003.
[11]Keasler SP,Hall RH.Detecting and biotyping Vibrio cholerae 01with multiplex polymerase chain reaction[J].Lancet,1993,341(8861):48-86.DOI:10.1016/0140-6736(93)90792-F.
[12]Lin W,Fullner KJ,Clayton R,et al.Identification of a Vibrio cholerae RTX toxin gene cluster that is tightly linked to the cholera toxin prophage[J].Proc Natl Acad Sci USA,1999,96(3):1071-1076.DOI:10.1073/pnas.96.3.1071.
[13]Rader AE,Murphy JR.Nucleotide sequences and comparison of the hemolysin determinants of Vibrio cholerae El Tor RV79(Hly+)and RV79(Hly-)and classical 569B(Hly-)[J].Infect Immun,1988,56(6):1414-1419.