Yuan Siqi, Xia Yun, Zheng Yuchi, Zeng Xiaomao
Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China; University of Chinese Academy of Sciences, Beijing, China.
Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , Sichuan , China.
PeerJ. 2016 Dec 15;4:e2786. doi: 10.7717/peerj.2786. eCollection 2016.
Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order, and , to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome of and are typical neobatrachian pattern except for rearrangements at the position of "WANCY" tRNA genes cluster. Further, the mitogenome of is characterized with a tandem duplication of . Moreover, we utilize 13 protein-coding genes of , and other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity of and . In this work, we provide nearly complete mitochondrial genomes of and .
新一代测序（NGS）技术的最新进展有助于获取线粒体基因组。然而，尚不清楚NGS是否能有效地用于重建具有高度基因重排的有丝分裂基因组。这些高度重排会导致扩增失败和/或组装及比对错误。在此，我们选择两种基因顺序重排的蛙类， 和 ，通过使用NGS来测试基因重排是否会影响有丝分裂基因组的组装和比对。通过Illumina MiSeq基因组测序对具有基因重排的有丝分裂基因组进行测序，并由Trinity v2.1.0和SOAPdenovo2有效地进行组装。 和 的有丝分裂基因组中的基因顺序和内容除了在“WANCY”tRNA基因簇位置存在重排外，是典型的新蛙类模式。此外， 的有丝分裂基因组的特征是 的串联重复。此外，我们利用 、 和其他新蛙类的13个蛋白质编码基因来重建系统发育树，以评估 和 的线粒体序列真实性。在这项工作中，我们提供了 和 的近乎完整的线粒体基因组。
