Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer.
Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer.
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DOI：
10.1186/1741-7007-7-78
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发表时间：
2009-11-18
期刊：
影响因子：
5.4
通讯作者：
Keim P
中科院分区：
文献类型：
--
作者：
Pearson T;Giffard P;Beckstrom-Sternberg S;Auerbach R;Hornstra H;Tuanyok A;Price EP;Glass MB;Leadem B;Beckstrom-Sternberg JS;Allan GJ;Foster JT;Wagner DM;Okinaka RT;Sim SH;Pearson O;Wu Z;Chang J;Kaul R;Hoffmaster AR;Brettin TS;Robison RA;Mayo M;Gee JE;Tan P;Currie BJ;Keim P
一些细菌种群的系统地理学重建受到低多样性和高水平横向基因转移的阻碍。比较11种细菌的7个管家基因的重组水平和多样性，其中大多数通常被认为具有高水平的横向基因转移，表明类鼻疽伯克霍尔德氏菌的同源重组与突变的相对贡献比肺炎链球菌高两倍以上，因此是细菌中报道的最高值。尽管同源重组有可能增加多样性，但B。类鼻疽在这些基因座上表现出相对缺乏多样性。在这些情况下，使用下一代测序技术发现的直链淀粉共享单核苷酸多态性位点的全基因组基因分型可以提供能够估计核心系统发育关系的非常大的数据集。我们比较和搜索了43个B的全基因组序列。类鼻疽及其最近的亲属在orthopathic共享区域的单核苷酸多态性，用于系统发育重建。贝叶斯系统发育分析> 14，000单核苷酸多态性产生了这43个菌株的完全解析的树，具有高水平的统计支持。这些结果使我们能够更好地理解在> 1，700个B中对种群分化的单独分析。如通过来自七个管家基因的序列数据所定义的类鼻疽假单胞菌分离物。我们分析了这个较大的数据集的人口结构和等位基因共享，可以归因于横向基因转移。我们的研究结果表明，尽管几乎是一个全交配的人口，我们可以检测到两个不同的人口B。假鼻疽符合在许多植物和动物物种中发现的地理模式。也就是说，分离沿着华莱士线，东南亚和澳大利亚之间的地理边界。我们描述了B的澳大利亚起源。pseudomallei，其特点是在最近的冰川期单一的引入事件到东南亚，和变量水平的横向基因转移的人群。这些模式提供了对B中遗传多样性机制的见解。pseudomallei及其最近的亲戚，并提供了一个框架，整合传统上独立的领域的人口遗传学和遗传学的其他细菌物种与高水平的横向基因转移。
Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. We describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer.
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影响因子：
30.8
作者：
Holt, Kathryn E.;Parkhill, Julian;Mazzoni, Camila J.;Roumagnac, Philippe;Weill, Francois-Xavier;Goodhead, Ian;Rance, Richard;Baker, Stephen;Maskell, Duncan J.;Wain, John;Dolecek, Christiane;Achtman, Mark;Dougan, Gordon
通讯作者：
Dougan, Gordon
影响因子：
5.3
作者：
DeCelles, PG;Gehrels, GE;Garzanti, E
通讯作者：
Garzanti, E
DOI：
10.1073/pnas.0803070105
发表时间：
2008-06-03
影响因子：
11.1
作者：
Fuhrman, Jed A.;Steele, Joshua A.;Brown, James H.
通讯作者：
Brown, James H.
影响因子：
3.2
作者：
Feil, EJ;Li, BC;Spratt, BG
通讯作者：
Spratt, BG
影响因子：
9.4
作者：
Cheng, AC;Godoy, D;Currie, BJ
通讯作者：
Currie, BJ