Institut des Sciences de l'Evolution (ISEM, UMR 5554 UM2-CNRS-IRD), Université Montpellier II, Place Eugène Bataillon - CC 064 - 34095 Montpellier Cedex 5, France; Center for Macroecology Evolution and Climate at the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken, 15, DK-2100 Copenhagen Ø, Denmark.
Gene. 2013 Dec 1;531(2):388-97. doi: 10.1016/j.gene.2013.07.059. Epub 2013 Aug 23.
An RNA-Seq strategy was used to obtain the complete set of protein-coding mitochondrial genes from two rodent taxa. Thanks to the next generation sequencing (NGS) 454 approach, we determined the complete mitochondrial DNA genome from Graphiurus kelleni (Mammalia: Rodentia: Gliridae) and partial mitogenome from Pedetes capensis (Pedetidae), and compared them with published rodent and outgroup mitogenomes. We finished the mitogenome sequencing by a series of amplicons using conserved PCR primers to fill the gaps corresponding to tRNA, rRNA and control regions. Phylogenetic analyses of the mitogenomes suggest a well-supported rodent phylogeny in agreement with nuclear gene trees. Pedetes groups with Anomalurus into the clade Anomaluromorpha, while Graphiurus branches within the squirrel-related clade. Moreover, Pedetes+Anomalurus branch with Castor into the mouse-related clade. Our study demonstrates the utility of NGS for obtaining new mitochondrial genomes as well as the importance of choosing adequate models of sequence evolution to infer the phylogeny of rodents.
采用 RNA-Seq 策略从两个啮齿动物分类群中获得完整的蛋白质编码线粒体基因集。得益于下一代测序 (NGS) 454 方法，我们从 Graphiurus kelleni（哺乳动物：啮齿动物：睡鼠科）中确定了完整的线粒体 DNA 基因组，并从 Pedetes capensis（Pedetidae）中获得了部分线粒体基因组，并将其与已发表的啮齿动物和外群线粒体基因组进行了比较。我们使用保守的 PCR 引物完成了一系列扩增子的线粒体基因组测序，以填补对应于 tRNA、rRNA 和控制区的空白。线粒体基因组的系统发育分析表明，啮齿动物的系统发育与核基因树一致，得到了很好的支持。Pedetes 与 Anomalurus 一起归入 Anomaluromorpha 分支，而 Graphiurus 分支则与松鼠相关的分支内。此外，Pedetes+Anomalurus 分支与海狸鼠一起归入与老鼠相关的分支。我们的研究表明，NGS 可用于获取新的线粒体基因组，选择适当的序列进化模型对于推断啮齿动物的系统发育也很重要。
