鼠疫菌基因组差异编码序列的筛选研究
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摘要
目的对喜马拉雅旱獭鼠疫疫源地2株青藏高原型已测序鼠疫耶尔森菌株的全基因组编码序列进行比对,寻找青藏高原型鼠疫菌中存在的差异编码序列。方法应用BLAST软件、Perl编程及Excel软件等,对青藏高原型全基因测序鼠疫耶尔森菌株与测序鼠疫菌"默认编码序列数据库"进行编码序列比对和统计分析。结果初步比对喜马拉雅旱獭鼠疫疫源地2株青藏高原型鼠疫菌编码序列有418个差异编码序列,其与鼠疫菌"默认编码序列数据库"中存在差异的编码序列有135个,最终确定在鼠疫菌全基因组数据库中真实有差异的编码序列共86个。结论喜马拉雅旱獭鼠疫疫源地2株青藏高原型鼠疫菌编码序列存在差异,真实有差异的编码序列是鼠疫菌存在差异的编码序列集合,为研究青藏高原型鼠疫菌的遗传特征提供了资料信息。
Objectives To identify coding sequences in the genome of 2strains of Yersinia pestis from the Qinghai-Tibet Plateau,which is a natural focus of the Himalayan marmot,in order to ascertain the genetic diversity of Y.pestis.Methods The software BLAST,the Perl programming language,and the software Excel were used to compare coding sequences and statistically analyze the Z176003 strain of Y.pestis from Tibet,the D106004 strain from Yulong,Yunnan,and a "default coding sequence database." Results Preliminary comparison of the Z176003 strain of Y.pestis from Tibet and the D106004 strain from Yulong,Yunnan yielded 418 different coding sequences.The " default coding sequence database" had 135 different coding sequences.Eighty-six coding sequences were ultimately determined to differ between the 2strains and the database of the Y.pestis genome.Conclusion Coding sequences from the 2strains of Y.pestis from the Qinghai-Tibet Plateau differed.Coding sequences that truly differed were groups of different coding sequences of Y.pestis.This finding should provide reliable information for further study of the genetic characteristics of Y.pestis from the Qinghai-Tibet plateau.
Objectives To identify coding sequences in the genome of 2strains of Yersinia pestis from the Qinghai-Tibet Plateau,which is a natural focus of the Himalayan marmot,in order to ascertain the genetic diversity of Y.pestis.Methods The software BLAST,the Perl programming language,and the software Excel were used to compare coding sequences and statistically analyze the Z176003 strain of Y.pestis from Tibet,the D106004 strain from Yulong,Yunnan,and a "default coding sequence database." Results Preliminary comparison of the Z176003 strain of Y.pestis from Tibet and the D106004 strain from Yulong,Yunnan yielded 418 different coding sequences.The " default coding sequence database" had 135 different coding sequences.Eighty-six coding sequences were ultimately determined to differ between the 2strains and the database of the Y.pestis genome.Conclusion Coding sequences from the 2strains of Y.pestis from the Qinghai-Tibet Plateau differed.Coding sequences that truly differed were groups of different coding sequences of Y.pestis.This finding should provide reliable information for further study of the genetic characteristics of Y.pestis from the Qinghai-Tibet plateau.
引文
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[8]Garcia E,Worsham P,Bearden S,et al.Pestiodes F,an atypical Yersinia pestis strains from the former Soviet Union[J].Adv Exp Med Biol,2007(603):17-22.
[9]Liang Y,Hou XX,Wang XH,et al.Genome rearrangements of completely sequenced strains of Yersinia pestis[J].J Clin Microbiol,2010,48(5):1619-23.
[10]何建,靳娟,张青雯,等.一株鼠毒素基因缺失突变鼠疫耶尔森氏菌株的构建和鉴定[J].中国病原生物学杂志,2016,11(6):513-6.
[11]吴海莲,赵海红,张青雯,等.鼠疫耶尔森氏菌噬菌体耐受株的选育及稳定性评价[J].中国病原生物学杂志,2015,10(7):582-6.
[2]Shen X,Wang Q,Xia,et al.Complete genome sequences of Yersinia pestis from natural foci in China[J].J Bacteriol,2010,192(13):3551-2.
[3]Zhang Z,Hai R,Song Z,et al.Spatial variation of Yersinia pestis from Yunnan Province of China[J].Am J Trop Med Hyg,2009,81(4):714-7.
[4]Parkhill J,Wren BW,Thomson NR,et al.Genome sequence of Yersinia pestis,the causative agent of plague[J].Nature,2001(413):523-7.
[5]Deng W,Borland V,Plunkett G,et al.Genome sequences of Yersinia pestis KIM[J].J Bacterial,2002(184):4601-11.
[6]Song Y,Tong Z,Wang J,et al.Complete sequences of chromosome of Yersinia pestis strain 91001,an isolate virulent to humans[J].DNA Res,2004(11):179-97.
[7]Chain SG,Hu P,Malfatti SA,et al.Complete genome sequences of Yersinia pestis strains antiqua and Nepal516:evidence of gene reduction in an emerging pathogen[J].J Bacterial,2006(6):4453-63.
[8]Garcia E,Worsham P,Bearden S,et al.Pestiodes F,an atypical Yersinia pestis strains from the former Soviet Union[J].Adv Exp Med Biol,2007(603):17-22.
[9]Liang Y,Hou XX,Wang XH,et al.Genome rearrangements of completely sequenced strains of Yersinia pestis[J].J Clin Microbiol,2010,48(5):1619-23.
[10]何建,靳娟,张青雯,等.一株鼠毒素基因缺失突变鼠疫耶尔森氏菌株的构建和鉴定[J].中国病原生物学杂志,2016,11(6):513-6.
[11]吴海莲,赵海红,张青雯,等.鼠疫耶尔森氏菌噬菌体耐受株的选育及稳定性评价[J].中国病原生物学杂志,2015,10(7):582-6.