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霍乱弧菌O1血清群El Tor产毒株重组特征分析
作者:李臻鹏 逄波 卢昕 阚飙

摘要:

目的  分析霍乱弧菌O1血清群El Tor产毒株基因组的重组特征。方法  在美国国立生物技术信息中心数据库中,选取分离时间从1937—2015年的292株霍乱弧菌O1血清群El Tor菌株完成图序列或草图序列,以菌株N16961的基因组序列为参照,使用snippy软件获得菌株的全基因组比对信息,利用ClonalFrameML软件对数据进行重组分析,比较大小染色体间重组数目及重组区域总长度的差异,以及不同分离地区菌株的基因组重组片段数目和总长度的差异。使用KOBAS分析工具对重组热点基因进行基因本体富集分析。结果  292株霍乱弧菌菌株中,发生基因重组163株(55.8%);其中,归一化处理的小染色体重组片段数目MP25P75)为4.7×10-6(9.3×10-7,2.0×10-5),大于大染色体[2.4×10-6(3.4×10-7,5.7×10-6)](P<0.001);小染色体重组区域占小染色体长度的比例MP25P75)7.1%×10-5(3.7%×10-6,4.8%×10-4),大于大染色体[2.2%×10-5(2.4%×10-6,8.4%×10-5)](P<0.001)。分离自非洲、亚洲、欧洲、北美洲和南美洲的菌株重组片段数目MP25P75)分别为23(1.0,33.0)、1.0(0.0,34.0)、6.0(2.0,13.0)、0.0(0.0,1.0)和29.5(6.8,56.8)(P<0.001);分离自各大洲的菌株重组区域总长度MP25P75)分别为233.0(4.0,461.0)、11.0(0.0,695.5)、56.0(4.0,111.0)、0.0(0.0,9.0)和347.5(132.8,1 323.5)bp(P<0.001)。富集分析结果显示,62个重组热点编码基因的功能主要集中在趋化、趋性、对外界刺激的反应、受体活性和分子转导活性。结论  霍乱弧菌El Tor大小染色体的重组片段数目及区域长度存在差别,不同大洲菌株重组片段数目及重组区域总长度不同。

关键词:弧菌,霍乱;基因组;染色体;基因重组

Abstract:

Objective  To analyze the genomic recombination of the vibrio cholerae serogroup O1 El Tor pandemic strains.Methods  A total of 292 complete or draft genome sequences of Vibrio cholerae O1 serogroup El Tor strains isolated from 1937 to 2015 were selected from National Biotechnology Information Center database. The genome alignment of strains was computed by snippy software by using N16961 as reference sequence. Then ClonalFrameML software was used to do the recombinant analysis. The wilcox.test function in agricolae package was used to compare the number recombinant segments and the total length of recombinant regions between small and large chromosomes. The kruskal function was used to compare the number recombinant segments and the total length of recombinant regions among different isolation continents. The KOBAS tool was used to do the gene ontology enrichment analysis of recombinant hotspot genes.Results  Of all 292 strains of Vibrio cholerae, 163 strains (55.8%) were recombined. The median of normalized recombinant segment number of small chromosome was 4.7×10-6 (9.3×10-7, 2.0×10-5), which was significantly larger than that of large chromosome [2.4×10-6 (3.4×10-7, 5.7×10-6)] (P<0.001). The median (P25,P75) of recombinant segment number of strains isolated from Africa, Asia, Europe, North America and South America were 23(1.0,33.0), 1.0(0.0,34.0), 6.0(2.0,13.0), 0.0(0.0,1.0) and 29.5(6.8,56.8), respectively, and the difference was statistically significant (P<0.001). The median (P25,P75) of total length of recombinant regions of strains isolated from Africa, Asia, Europe, North America and South America were 233.0(4.0, 461.0), 11.0(0.0, 695.5), 56.0(4.0,111.0), 0.0(0.0,9.0) and 347.5(132.8,1 323.5) bp, respectively, and the difference was statistically significant (P<0.001). Gene ontology Enrichment analysis showed that the functions of 62 recombinant hotspot genes were mainly enrichment in chemotaxis, taxis, response to external stimulus, receptor activity and molecular transducer activity.Conclustion  In this study, we found that there were significant differences in the number of recombinant fragments and the length of recombinant regions between large and small chromosomes of Vibrio cholerae El Tor. We also found significant differences in the number of recombinant fragments and the total length of recombinant regions among different continents.

Key words: Vibrio cholerae;Genome;Chromosomes;Gene recombination

发表日期:2020/3

引用本文:

图/表:

  • 10.3760/cma.j.issn.0253-9624.2020.03.011.T001:表1 霍乱弧菌O1群El Tor生物型流行菌株重组热点基因列表

    10.3760/cma.j.issn.0253-9624.2020.03.011.T001:表1 霍乱弧菌O1群El Tor生物型流行菌株重组热点基因列表

  • 10.3760/cma.j.issn.0253-9624.2020.03.011.T002:表2 霍乱孤菌62个重组热点基因基于基因本体的生物学过程富集分析

    10.3760/cma.j.issn.0253-9624.2020.03.011.T002:表2 霍乱孤菌62个重组热点基因基于基因本体的生物学过程富集分析

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