Galapagos Science Center, Universidad San Francisco de Quito, Isla San Cristóbal, Islas Galápagos, Ecuador.
Department of Evolutionary Genetics, Max Planck Institute, Plön, Germany.
PeerJ. 2023 Sep 28;11:e16047. doi: 10.7717/peerj.16047. eCollection 2023.
The Galapagos sea lion, , is an endemic and endangered otariid, which is considered as a sentinel species of ecosystem dynamics in the Galapagos archipelago. Mitochondrial DNA is an important tool in phylogenetic and population genetic inference. In this work we use Illumina sequencing to complement the mitogenomic resources for genus-the other two species employed Sanger sequencing-by a complete mitochondrial genome and a molecular clock of this species, which is not present in any case.
We used DNA obtained from a fresh scat sample of a Galapagos sea lion and shotgun-sequenced it on the Illumina NextSeq platform. The obtained raw reads were processed using the GetOrganelle software to filter the mitochondrial DNA reads (∼16% survive the filtration), assemble them, and set up a molecular clock.
From the obtained 3,511,116 raw reads, we were able to assemble a full mitogenome of a length of 16,676 bp, consisting of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNA), and two ribosomal RNAs (rRNA). A time-calibrated phylogeny confirmed the phylogenetic position of in a clade with , and , and sister to ; as well as establishing the divergence time for 0.65 million years ago. Our study illustrates the possibility of seamlessly sequencing full mitochondrial genomes from fresh scat samples of marine mammals.
加拉帕戈斯海狮（Zalophus wollebaeki）是一种特有且濒危的海豹，被认为是加拉帕戈斯群岛生态系统动态变化的指示物种。线粒体 DNA 是系统发育和种群遗传推断的重要工具。在这项工作中，我们使用 Illumina 测序技术，通过对一个加拉帕戈斯海狮的新鲜粪便样本进行测序，补充了线粒体基因组资源。这是对其他两个物种采用 Sanger 测序的补充，因为之前这两个物种的线粒体基因组都没有完成。
我们使用从加拉帕戈斯海狮新鲜粪便样本中提取的 DNA，在 Illumina NextSeq 平台上进行了 shotgun 测序。使用 GetOrganelle 软件对获得的原始reads 进行处理，以过滤线粒体 DNA reads（约 16% 的 reads 通过过滤），对其进行组装，并建立分子钟。
从获得的 3511116 条原始reads 中，我们成功组装了一个全长为 16676 bp 的完整线粒体基因组，其中包含 13 个蛋白质编码基因（PCGs）、22 个转移 RNA（tRNA）和两个核糖体 RNA（rRNA）。一个时间校准的系统发育树证实了在一个包含、和、以及姐妹群的分支中，的系统发育位置；并建立了 0.65 百万年前的分化时间。我们的研究说明了从海洋哺乳动物的新鲜粪便样本中无缝测序完整线粒体基因组的可能性。
