Plazzi Federico, Puccio Guglielmo, Passamonti Marco
Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126 Bologna, Italy
Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126 Bologna, Italy.
Genome Biol Evol. 2016 Sep 2;8(8):2544-64. doi: 10.1093/gbe/evw187.
Despite the figure of complete bivalve mitochondrial genomes keeps growing, an assessment of the general features of these genomes in a phylogenetic framework is still lacking, despite the fact that bivalve mitochondrial genomes are unusual under different aspects. In this work, we constructed a dataset of one hundred mitochondrial genomes of bivalves to perform the first systematic comparative mitogenomic analysis, developing a phylogenetic background to scaffold the evolutionary history of the class' mitochondrial genomes. Highly conserved domains were identified in all protein coding genes; however, four genes (namely, atp6, nad2, nad4L, and nad6) were found to be very divergent for many respects, notwithstanding the overall purifying selection working on those genomes. Moreover, the atp8 gene was newly annotated in 20 mitochondrial genomes, where it was previously declared as lacking or only signaled. Supernumerary mitochondrial proteins were compared, but it was possible to find homologies only among strictly related species. The rearrangement rate on the molecule is too high to be used as a phylogenetic marker, but here we demonstrate for the first time in mollusks that there is correlation between rearrangement rates and evolutionary rates. We also developed a new index (HERMES) to estimate the amount of mitochondrial evolution. Many genomic features are phylogenetically congruent and this allowed us to highlight three main phases in bivalve history: the origin, the branching of palaeoheterodonts, and the second radiation leading to the present-day biodiversity.
尽管双壳类线粒体全基因组的数量不断增加，但在系统发育框架下对这些基因组的一般特征仍缺乏评估，尽管双壳类线粒体基因组在不同方面都很独特。在这项工作中，我们构建了一个包含100个双壳类线粒体基因组的数据集，以进行首次系统的比较线粒体基因组分析，构建一个系统发育背景来构建该类线粒体基因组的进化历史。在所有蛋白质编码基因中都鉴定出了高度保守的结构域；然而，发现四个基因（即atp6、nad2、nad4L和nad6）在许多方面差异很大，尽管这些基因组总体上受到纯化选择。此外，在20个线粒体基因组中对atp8基因进行了新的注释，此前该基因被认为不存在或仅被标记。对超数线粒体蛋白进行了比较，但仅在亲缘关系密切的物种之间发现了同源性。分子上的重排率过高，无法用作系统发育标记，但我们在此首次证明，在软体动物中，重排率与进化率之间存在相关性。我们还开发了一个新的指标（HERMES）来估计线粒体进化的程度。许多基因组特征在系统发育上是一致的，这使我们能够突出双壳类历史上的三个主要阶段：起源、古异齿类的分支以及导致当今生物多样性的第二次辐射。
