Data from: Deep mitochondrial origin outside the sampled alphaproteobacteria

Mitochondria are ATP-generating organelles whose endosymbiotic origin has been a key event in the evolution of eukaryotic cells. Despite overwhelming phylogenetic evidence for an alphaproteobacterial ancestry, efforts to pinpoint the closest relatives among the sampled alphaproteobacteria have been conflicting, complicating detailed inferences about the identity and nature of the mitochondrial ancestor. While most studies support that mitochondria evolved from an ancestor related to Rickettsiales, an order that includes several host-associated pathogenic and endosymbiotic lineages, others suggest that mitochondria evolved from a free-living group. Here we re-evaluate the phylogenetic placement of mitochondria. We employ genome-resolved binning of oceanic metagenome datasets and increase the genomic sampling of Alphaproteobacteria with twelve novel divergent clades, and one novel clade representing a sister group to all Alphaproteobacteria. Subsequent phylogenomic analyses that specifically address long branch attraction and compositional bias artefacts suggest that mitochondria did not evolve from Rickettsiales or any other currently recognized alphaproteobacterial lineage. Rather, our analyses indicate that mitochondria evolved from a proteobacterial lineage that branched off prior to the divergence of all sampled alphaproteobacteria. In light of this new result, previous hypotheses on the nature of the mitochondrial ancestor should be re-evaluated.

线粒体（Mitochondria）是生成三磷酸腺苷（ATP）的细胞器，其内共生起源是真核细胞演化历程中的关键事件。尽管已有大量系统发育证据支持线粒体起源于α-变形菌纲（Alphaproteobacteria）的祖先，但针对已采样α-变形菌群中确定线粒体最亲近类群的相关研究始终存在争议，这使得关于线粒体祖先身份与本质的详细推断变得复杂。多数研究支持线粒体起源于与立克次体目（Rickettsiales）亲缘关系较近的祖先——该类群包含多种宿主相关的致病及内共生类群，而另有部分研究则认为线粒体起源于自由生活类群。本研究重新评估了线粒体的系统发育定位。我们通过对海洋宏基因组（metagenome）数据集进行基因组解析分箱（genome-resolved binning），新增12个全新的分歧类群以及1个作为所有α-变形菌姊妹群的新类群，从而扩大了α-变形菌的基因组采样范围。后续专门针对长枝吸引（long branch attraction）与组成偏倚伪迹（compositional bias artefacts）开展的系统基因组学分析表明，线粒体并非起源于立克次体目或其他任何目前已确认的α-变形菌类群。相反，我们的分析结果显示，线粒体起源于一个在所有已采样α-变形菌分化之前就已分支的变形菌类群。鉴于这一新发现，此前关于线粒体祖先本质的各类假说均需重新评估。