Comparative Genomic Analyses of the Moraxella catarrhalis Serosensitive and Seroresistant Lineages Demonstrate Their Independent Evolution
Comparative Genomic Analyses of the Moraxella catarrhalis Serosensitive and Seroresistant Lineages Demonstrate Their Independent Evolution
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DOI：
10.1093/gbe/evw039
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发表时间：
2016-04-01
影响因子：
3.3
通讯作者：
Ehrlich, Garth D.
中科院分区：
文献类型：
--
作者：
Earl, Joshua P.;de Vries, Stefan P. W.;Ehrlich, Garth D.
卡特莫拉氏菌被认为由两个不同的谱系组成(称为血清耐药[SR]和血清敏感[SS])，根据几种分子分型方法有不同的进化历史，而165核糖体分型表明SS谱系中存在额外的分裂。此前，我们描述了12个SR谱系分离株的全基因组序列，与其他机会性鼻咽病原体相比，显示出相对较小的超基因组，这表明进化历史相对较短。在这里，我们对来自SS谱系的两种核糖体类型的18株菌株进行了全基因组测序，另一种SR菌株，以及之前基于多位点序列分型分析发现的四种高度分化的菌株。所有35个菌株都进行了一系列比较基因组分析，清楚地表明SR有三个谱系。和分歧者。SR和SS谱系密切相关，但基于三种不同的比较方法而彼此不同：在核心基因之间观察到的等位基因差异；拥有谱系特有的核心和分布基因集；以及通过与基因注释无关的串联核心序列的比对。所有这些方法都表明，SS谱系的品系间分支比SR谱系长得多，这表明该谱系可能比SR谱系进化得更长或更快。有证据表明，在这两个谱系中都存在广泛的水平基因转移(HGT)，而且它们之间的程度较小。特别是，我们确定了这两个β-内酰胺酶基因谱系之间非常高的HGT比率。这四个不同的菌株都是独立属，与SR和SS组的亲缘关系比其他两个组之间的亲缘关系要远得多。根据平均核苷酸同源性、基因含量、GC含量和基因组大小，这个组可以被认为是一个单独的分类组。SR和SS谱系虽然不同，但基于多个标准显然形成了一个单一物种，包括大的共同核心基因组、平均核苷酸同一性值、GC含量和基因组大小。尽管根据系统发育分析，这两个谱系都不是来自对方内部，但这些谱系如何以及何时分裂，然后在人类鼻咽中重新结合的问题被探索出来。
The bacterial species Moraxella catarrhalis has been hypothesized as being composed of two distinct lineages (referred to as the seroresistant [SR] and serosensitive [SS] with separate evolutionary histories based on several molecular typing methods, whereas 165 ribotyping has suggested an additional split within the SS lineage. Previously, we characterized whole-genome sequences of 12 SR lineage isolates, which revealed a relatively small supragenome when compared with other opportunistic nasopharyngeal pathogens, suggestive of a relatively short evolutionary history. Here, we performed whole-genome sequencing on 18 strains from both ribotypes of the SS lineage, an additional SR strain, as well as four previously identified highly divergent strains based on multilocus sequence typing analyses. All 35 strains were subjected to a battery of comparative genomic analyses which clearly show that there are three lineages the SR. O. and the divergent. The SR and SS lineages are closely related, but distinct from each other based on three different methods of comparison: Allelic differences observed among core genes; possession of lineage-specific sets of core and distributed genes; and by an alignment of concatenated core sequences irrespective of gene annotation. All these methods show that the SS lineage has much longer interstrain branches than the SR lineage indicating that this lineage has likely been evolving either longer or faster than the SR lineage. There is evidence of extensive horizontal gene transfer (HGT) within both of these lineages, and to a lesser degree between them. In particular, we identified very high rates of HGT between these two lineages for beta-lactamase genes. The four divergent strains are sui generis, being much more distantly related to both the SR and SS groups than these other two groups are to each other. Based on average nucleotide identities, gene content, GC content, and genome size, this group could be considered as a separate taxonomic group. The SR and SS lineages, although distinct, clearly form a single species based on multiple criteria including a large common core genome, average nucleotide identity values, GC content, and genome size. Although neither of these lineages arose from within the other based on phylogenetic analyses, the question of how and when these lineages split and then subsequently reunited in the human nasopharynx is explored.