The extent of genome flux and its role in the differentiation of bacterial lineages.
The extent of genome flux and its role in the differentiation of bacterial lineages.
复制标题
DOI：
10.1093/gbe/evu123
复制
发表时间：
2014-06-12
影响因子：
3.3
通讯作者：
Sharp PM
中科院分区：
文献类型：
--
作者：
Nowell RW;Green S;Laue BE;Sharp PM
水平基因转移（HGT）和基因丢失是细菌进化的关键过程。然而，基因获得和丢失在生态分化细菌种群的出现和维持中的作用仍然是一个悬而未决的问题。在这里，我们使用全基因组序列数据来量化植物相关细菌丁香假单胞菌 27 个谱系的基因获得和损失。我们应用广泛的错误控制程序来解释基因组草图数据中的错误，并极大地提高这些基因组中基因发生模式的准确性。我们展示了该物种广泛的基因组波动的历史，并表明单个谱系可能在同一时期获得了数千个基因，其中核心基因组中出现 1% 的氨基酸差异。阐明基因组波动的动态揭示了获得的基因的快速周转，使得大多数最近获得的基因很快丢失。尽管观察到波动率很高，但从基因发生模式推断的系统发育与基于核心基因组内氨基酸替换的系统发育相似。此外，核心基因组系统发育表明，丁香假单胞菌应被视为许多不同的物种，其分化程度至少相当于公认的细菌物种之间的分化程度。获得的基因从多种来源转移，反映了通过 HGT 可获得的潜在基因库的深度和多样性。总体而言，我们的结果为基因组波动的进化动力学提供了进一步的见解，并表明 HGT 是促进丁香假单胞菌谱系多样化的主要因素。
Horizontal gene transfer (HGT) and gene loss are key processes in bacterial evolution. However, the role of gene gain and loss in the emergence and maintenance of ecologically differentiated bacterial populations remains an open question. Here, we use whole-genome sequence data to quantify gene gain and loss for 27 lineages of the plant-associated bacterium Pseudomonas syringae. We apply an extensive error-control procedure that accounts for errors in draft genome data and greatly improves the accuracy of patterns of gene occurrence among these genomes. We demonstrate a history of extensive genome fluctuation for this species and show that individual lineages could have acquired thousands of genes in the same period in which a 1% amino acid divergence accrues in the core genome. Elucidating the dynamics of genome fluctuation reveals the rapid turnover of gained genes, such that the majority of recently gained genes are quickly lost. Despite high observed rates of fluctuation, a phylogeny inferred from patterns of gene occurrence is similar to a phylogeny based on amino acid replacements within the core genome. Furthermore, the core genome phylogeny suggests that P. syringae should be considered a number of distinct species, with levels of divergence at least equivalent to those between recognized bacterial species. Gained genes are transferred from a variety of sources, reflecting the depth and diversity of the potential gene pool available via HGT. Overall, our results provide further insights into the evolutionary dynamics of genome fluctuation and implicate HGT as a major factor contributing to the diversification of P. syringae lineages.
登录
查看更多内容
影响因子：
6.7
作者：
Baltrus DA;Nishimura MT;Romanchuk A;Chang JH;Mukhtar MS;Cherkis K;Roach J;Grant SR;Jones CD;Dangl JL
通讯作者：
Dangl JL
影响因子：
5.8
作者：
Cohen, Ofir;Ashkenazy, Haim;Pupko, Tal
通讯作者：
Pupko, Tal
影响因子：
3.7
作者：
Green S;Studholme DJ;Laue BE;Dorati F;Lovell H;Arnold D;Cottrell JE;Bridgett S;Blaxter M;Huitema E;Thwaites R;Sharp PM;Jackson RW;Kamoun S
通讯作者：
Kamoun S
影响因子：
10.7
作者：
Cohen O;Pupko T
通讯作者：
Pupko T
影响因子：
3.5
作者：
Almeida, Nalvo F.;Yan, Shuangchun;Vinatzer, Boris A.
通讯作者：
Vinatzer, Boris A.