30株大肠杆菌的泛基因组学特征分析

doi:10.3724/SP.J.1005.2012.00765

遗传 ›› 2012, Vol. 34 ›› Issue (6): 765-772.doi: 10.3724/SP.J.1005.2012.00765

30株大肠杆菌的泛基因组学特征分析

付静^1,2, 秦启伟¹

1. 中国科学院南海海洋研究所海洋生物资源可持续利用重点实验室, 广州 510301 2. 中国科学院研究生院, 北京 100049

收稿日期:2011-10-11 修回日期:2012-01-13 出版日期:2012-06-20 发布日期:2012-06-25
通讯作者: 秦启伟 E-mail:qinqw@scsio.ac.cn
基金资助:
国家杰出青年基金项目(编号：30725027)资助

Pan-genomics analysis of 30 Escherichia coli genomes

FU Jing^{1, 2}, QIN Qi-Wei¹

1. Key Laboratory of Marine Bio-resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China 2. Graduate University of the Chinese Academy of Sciences, Beijing 100049, China

Received:2011-10-11 Revised:2012-01-13 Online:2012-06-20 Published:2012-06-25

摘要/Abstract

摘要： 泛基因组(Pan-genome)是某一物种全部基因的总称, 其中包括核心基因组(该物种所有个体中都存在的基因)和非必须基因组(只在部分个体中存在的基因, 以及某个体特有的基因)。文章从泛基因组学角度比较分析了30株已经完成测序的大肠杆菌的基因、基因组成及其进化特征, 结果表明核心基因只占据每株大肠杆菌全部基因数目的50%左右, 而平均每个菌株有146个特有基因, 结果表明随着更多大肠杆菌菌株的基因组被测序, 将会不断有新基因被发现。通过比较分析大肠杆菌不同菌株之间基因的保守性与基因的GC含量以及选择压力之间的关系, 发现越保守的基因其GC含量变化范围越窄, 同时在进化中受到的选择压力也越大。这些结果将有助于深入了解大肠杆菌基因组的进化特征及其基因组成的动态变化, 并为预防和控制由致病性大肠杆菌引发的流行疾病提供理论依据, 同时也为大规模病原菌基因组数据的分析方法提供借鉴。

关键词: 泛基因组, 大肠杆菌, GC含量, 选择压力

Abstract: A pan-genome describes the full complement of genes in species. It is a superset of all the genes in all the individuals of a species, which is composed of a ‘core genome’ containing genes present in all individuals, and a ‘dispensable genome’ containing genes present only in some individuals and individual-specific genes. From pan-genome sight, 30 finished genomes from Escherichia coli were employed to analyze their gene and genome compositions and evaluation in this study. The results indicated that the core genes accounted for about 50% of the total number of genes, while about 146 strain-specific genes existed in the each strain tested. The data suggests that the E. coli pan-genome is vast, and unique genes will continue to be identified when more E. coli genomes are sequenced. After analyzing relationships of the gene conservation, GC content and selection pressure in different strains tested, we found that more conserved genes had a narrow range of GC content, and they also bear more selection pressure. These results will be helpful for better understanding of the evolution profile of E. coli genome, and the dynamic changes of its gene compositions. The E. coli pan-genome provides useful information for prevention and control of the diseases caused by pathogenic E. coli, and also provides a paradigm for the large-scale analysis of pathogenic bacteria genomes.

Key words: Pan-genome, E. coli, GC-content, selection pressure

付静，秦启伟. 30株大肠杆菌的泛基因组学特征分析[J]. 遗传, 2012, 34(6): 765-772.

FU Jing, QIN Qi-Wei. Pan-genomics analysis of 30 Escherichia coli genomes[J]. HEREDITAS, 2012, 34(6): 765-772.

参考文献

[1] Muzzi A, Masignani V, Rappuoli R. The pan-genome: towards a knowledge-based discovery of novel targets for vaccines and antibacterials. Drug Discov Today, 2007, 12(11-12): 429-439.
[2] Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R. The microbial pan-genome. Curr Opin Genet Dev, 2005, 15(6): 589-594.
[3] Lefebure T, Stanhope MJ. Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol, 2007, 8(5): R71.
[4] Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarity Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Se-lengut J, Gwinn ML, Zhou LW, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O'Connor KJB, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM. Genome analysis of multiple pathogenic iso-lates of Streptococcus agalactiae: implications for the microbial pan-genome. Proc Natl Acad Sci, 2005, 102(39): 13950-13955.
[5] Bambini S, Rappuoli R. The use of genomics in microbial vaccine development. Drug Discov Today, 2009, 14(5-6): 252-260.
[6] Rasko DA, Rosovitz MJ, Myers GSA, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sebaihia M, Thomson NR, Chaudhuri R, Henderson IR, Sperandio V, Ravel J. The pangenome structure of Escherichia coli: com-parative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol, 2008, 190(20): 6881-6893.
[7] Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, Calteau A, Chiapello H, Clermont O, Cruveiller S, Dan-chin A, Diard M, Dossat C, Karoui ME, Frapy E, Garry L, Ghigo JM, Gilles AM, Johnson J, Le Bouguénec C, Lescat M, Mangenot S, Martinez-Jéhanne V, Matic I, Nassif X, Oztas S, Petit MA, Pichon C, Rouy Z, Ruf CS, Schneider D, Tourret J, Vacherie B, Vallenet D, Médigue C, Rocha EP, Denamur E. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet, 2009, 5(1): 1000344.
[8] Davids W, Zhang ZL. The impact of horizontal gene transfer in shaping operons and protein interaction networks--direct evidence of preferential attachment. BMC Evol Biol, 2008, 8: 23.
[9] Zhang R, Lin Y. DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res, 2009, 37(1): 455-458.
[10] Remm M, Storm CEV, Sonnhammer ELL. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol, 2001, 314(5): 1041-1052.
[11] Enright AJ, Dongen SV, Ouzounis CA. An efficient algo-rithm for large-scale detection of protein families. Nucleic Acids Res, 2002, 30(7): 1575-1584.
[12] Shi GQ, Zhang LQ, Jiang T. MSOAR 2.0: Incorporating tan-dem duplications into ortholog assignment based on genome rearrangement. BMC Bioinformatics, 2010, 11: 10.
[13] Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: A tool for genome-scale analysis of pro-tein functions and evolution. Nucleic Acids Res, 2000, 28(1): 33-36.
[14] Katoh K, Toh H. Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics, 2010, 26(15): 1899-1900.
[15] Hogg JS, Hu FZ, Janto B, Boissy R, Hayes J, Keefe R, Post JC, Ehrlich GD. Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains. Genome Biol, 2007, 8(6): R103.
[16] Hiller NL, Janto B, Hogg JS, Boissy R, Yu S, Powell E, Keefe R, Ehrlich NE, Shen K, Hayes J, Barbadora K, Klimke W, Dernovoy D

编辑推荐

Metrics

www.chinagene.cn
备案号：京ICP备09063187号-4
总访问:,今日访问:,当前在线:

30株大肠杆菌的泛基因组学特征分析

Pan-genomics analysis of 30 Escherichia coli genomes

PDF (PC)

可视化

被引次数

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

[1]	边培培, 张禹, 姜雨. 泛基因组：高质量参考基因组的新标准[J]. 遗传, 2021, 43(11): 1023-1037.
[2]	邓雯文, 李才武, 赵思越, 李仁贵, 何永果, 吴代福, 杨盛智, 黄炎, 张和民, 邹立扣. 大熊猫源致病大肠杆菌CCHTP全基因组测序及耐药和毒力基因分析[J]. 遗传, 2019, 41(12): 1138-1147.
[3]	邓海君,黄勇,黄爱龙,龙泉鑫. 儿童与成人慢性乙型肝炎患者乙型肝炎病毒Core基因区准种特征及正选择压力差异分析[J]. 遗传, 2015, 37(5): 465-472.
[4]	姚远, 乔佳鑫, 李静, 李慧, 莫日根. 大肠杆菌TorS/TorR二组分体应答蛋白TorR对DNA复制起始的影响[J]. 遗传, 2015, 37(3): 302-308.
[5]	宋晓军,谢凯斌,张艳萍,金萍. 水稻抗逆相关基因的分子进化分析[J]. 遗传, 2014, 36(10): 1027-1035.
[6]	叶兰，訾臣，刘璐，朱璟，谢恺舟，朱国强，黄小国，包文斌，吴圣龙，王金玉. 仔猪BPI基因表达水平与大肠杆菌F18菌株感染的关系[J]. 遗传, 2011, 33(11): 1225-1230.
[7]	包文斌，叶兰，潘章源，朱璟，杜子栋，蔡家嘉，黄小国，朱国强，吴圣龙. 大肠杆菌F18菌株敏感和抵抗基因型仔猪十二指肠基因表达谱差异分析[J]. 遗传, 2011, 33(1): 60-66.
[8]	王中山，向泉桔，王海燕，张义正. 大肠杆菌细胞周质底物结合蛋白gsiB基因的克隆及其表达条件的优化[J]. 遗传, 2010, 32(5): 505-511.
[9]	陈祥贵，胡军，杨潇. 人类蛋白编码基因局部GC水平相关性分析[J]. 遗传, 2008, 30(9): 1169-1174.
[10]	吴圣龙，包文斌，鞠慧萍，朱国强，李碧春，陈国宏. 猪a1-岩藻糖转移酶基因(FUT1) M857位点遗传变异分析[J]. 遗传, 2007, 29(9): 1071-1071―1076.
[11]	庄娟，尤永进，陈波，饶忠潘洁. O型口蹄疫病毒VP1 T细胞、B细胞表位双拷贝基因与大肠杆菌LTB、STI肠毒素基因融合表达产物的免疫应答[J]. 遗传, 2006, 28(5): 557-562.
[12]	肖海龙，任爱霞，张耀洲. 破骨细胞形成抑制因子TNFR结构区在大肠杆菌中表达、抗体制备及活性测定[J]. 遗传, 2005, 27(5): 779-782.
[13]	孙艳菊，周忠卫，姚建秀，孙体昌，许琰艳，文雅，鲍时来. 钩端螺旋体liprmA基因的表达及其产物的纯化与功能分析[J]. 遗传, 2005, 27(5): 792-796.
[14]	孙奕钢，高雷，张忠华，薛庆中. 寻找水稻DNA编码与非编码区边界方法的比较研究[J]. 遗传, 2005, 27(4): 629-635.
[15]	张汉波，沙涛，程立忠，丁骅孙，施雯，于春蓓，张会荣. 大肠杆菌FC40系统静止期突变中的F因子转移[J]. 遗传, 2003, 25(4): 428-432.