葡萄球菌科和Gemella属包含几种具有临床或生物技术重要性的生物。我们在这里报告了对这些分类单元中物种的112个可用基因组的全面系统基因组和比较分析,以阐明它们的进化关系和分类。在基于678个核心蛋白的系统基因组树中,Gemella物种通过长分支与葡萄球菌分开,表明它们构成了一个不同的家族(Gemellaceaefam。11月。).在这棵树上,葡萄球菌形成了两个主要的进化枝,一个包含了阿利科属的,无节虫,医院细菌和盐细菌(“盐细菌科”),而另一个进化枝由大型球菌属组成,哺乳动物球菌和葡萄球菌(葡萄球菌科。).在这棵树上,来自Gemella属的物种,无节虫,大球菌和盐球菌分别形成两个不同的进化枝。在16SrRNA基因树中还观察到这些属的两个物种进化枝,并得到平均氨基酸同一性分析的支持。我们还在这里报告了对葡萄球菌科和Gemella基因组的蛋白质序列的详细分析,以确定保守的特征indel(CSIs),这些特征对不同属和家族水平的进化枝具有特异性。这些分析已经确定了120种新的CSI,这些CSI有力地划分了不同的拟议家族和属。确定的CSIs提供了独立的证据,无节虫,大型球菌和盐球菌由两个不同的进化枝组成,可以基于多个独占共享CSI进行可靠区分。我们建议将该物种从上述四个属的新分支转移到Gemelliphila属。11月。,Phococcusgen。11月。,大球菌。11月。和Lacicoccusgen。11月。,分别。确定的CSIs还提供了强有力的证据,将葡萄球菌科分为一个改良的葡萄球菌科和两个新的科,深渊科fam。11月。和盐生植物。11月。所有这些家族都可以基于几个专门共享的CSI来可靠地划分。
The family Staphylococcacae and genus
Gemella contain several organisms of clinical or biotechnological importance. We report here comprehensive phylogenomic and comparative analyses on 112 available genomes from species in these taxa to clarify their evolutionary relationships and classification. In a phylogenomic tree based on 678 core proteins,
Gemella species were separated from Staphylococcacae by a long branch indicating that they constitute a distinct family (Gemellaceae fam. nov.). In this tree, Staphylococcacae species formed two main clades, one encompassing the genera Aliicoccus, Jeotgalicoccus, Nosocomiicoccus and Salinicoccus (Family \"Salinicoccaceae\"), while the other clade consisted of the genera Macrococcus, Mammaliicoccus and Staphylococcus (Family Staphylococcaceae emend.). In this tree, species from the genera
Gemella, Jeotgalicoccus, Macrococcus and Salinicoccus each formed two distinct clades. Two species clades for these genera are also observed in 16S rRNA gene trees and supported by average amino acid identity analysis. We also report here detailed analyses on protein sequences from Staphylococcaceae and
Gemella genomes to identify conserved signature indels (CSIs) which are specific for different genus and family-level clades. These analyses have identified 120 novel CSIs robustly demarcating different proposed families and genera. The identified CSIs provide independent evidence that the genera
Gemella, Jeotgalicoccus, Macrococcus and Salinicoccus consist of two distinct clades, which can be reliably distinguished based on multiple exclusively shared CSIs. We are proposing transfers of the species from the novel clades of the above four genera into the genera Gemelliphila gen. nov., Phocicoccus gen. nov., Macrococcoides gen. nov. and Lacicoccus gen. nov., respectively. The identified CSIs also provide strong evidence for division of Staphylococcaceae into an emended family Staphylococcaceae and two new families, Abyssicoccaceae fam. nov. and Salinicoccaceae fam. nov. All of these families can be reliably demarcated based on several exclusively shared CSIs.