Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum.
Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum.
复制标题
DOI：
10.1098/rsob.140133
复制
发表时间：
2015-01
期刊：
影响因子：
5.8
通讯作者：
Bailly X
中科院分区：
文献类型：
--
作者：
Kumar N;Lad G;Giuntini E;Kaye ME;Udomwong P;Shamsani NJ;Young JP;Bailly X
生物物种可能由于遗传隔离或生态适应而保持独特，但这两个方面并不总是一致的。要建立一个本地细菌种群内的物种边界的性质，我们的特点是一个同域的人口的细菌根瘤菌豆科72株的基因组测序。尽管所有菌株都具有R.根据平均核苷酸同一性（ANI）标准，将它们分为5个基因种。质粒和染色体上的许多基因支持这种分裂：核心基因的重组主要发生在基因种内。然而，生态特性的变化，包括共生宿主范围和碳源利用，跨越这些基因种，使这些表型是基因种的诊断。这种表型变异是由移动的基因赋予的。基因种在其核心基因方面符合生物物种的迈尔标准，但不对应于连贯的生态群体，因此周期性选择可能无法有效清除其中的变异。该种群结构与传统的“多相分类法”不相容，传统的“多相分类法”要求细菌物种具有系统发育一致性和独特的表型。更一般地说，基因组学已经揭示，许多细菌物种通过水平基因转移共享适应模块，我们设想了一个更一致的分类框架，明确承认这一点。重要的表型应该被认为是由核心基因遗传学定义的物种内的“生物变种”。
Biological species may remain distinct because of genetic isolation or ecological adaptation, but these two aspects do not always coincide. To establish the nature of the species boundary within a local bacterial population, we characterized a sympatric population of the bacterium Rhizobium leguminosarum by genomic sequencing of 72 isolates. Although all strains have 16S rRNA typical of R. leguminosarum, they fall into five genospecies by the criterion of average nucleotide identity (ANI). Many genes, on plasmids as well as the chromosome, support this division: recombination of core genes has been largely within genospecies. Nevertheless, variation in ecological properties, including symbiotic host range and carbon-source utilization, cuts across these genospecies, so that none of these phenotypes is diagnostic of genospecies. This phenotypic variation is conferred by mobile genes. The genospecies meet the Mayr criteria for biological species in respect of their core genes, but do not correspond to coherent ecological groups, so periodic selection may not be effective in purging variation within them. The population structure is incompatible with traditional ‘polyphasic taxonomy′ that requires bacterial species to have both phylogenetic coherence and distinctive phenotypes. More generally, genomics has revealed that many bacterial species share adaptive modules by horizontal gene transfer, and we envisage a more consistent taxonomic framework that explicitly recognizes this. Significant phenotypes should be recognized as ‘biovars' within species that are defined by core gene phylogeny.
登录
查看更多内容
影响因子：
3.3
作者：
Didelot, Xavier;Falush, Daniel
通讯作者：
Falush, Daniel
DOI：
10.1073/pnas.37.3.146
发表时间：
1951-01-01
影响因子：
11.1
作者：
ATWOOD, KC;SCHNEIDER, LK;RYAN, FJ
通讯作者：
RYAN, FJ
影响因子：
5.1
作者：
Cummings, Stephen P.;Gyaneshwar, Prasad;James, Euan K.
通讯作者：
James, Euan K.
影响因子：
9.8
作者：
Cadillo-Quiroz H;Didelot X;Held NL;Herrera A;Darling A;Reno ML;Krause DJ;Whitaker RJ
通讯作者：
Whitaker RJ
DOI：
10.1073/pnas.1101591108
发表时间：
2011-08-23
影响因子：
11.1
作者：
Burke, Catherine;Steinberg, Peter;Thomas, Torsten
通讯作者：
Thomas, Torsten