Institute of Oceanology, Chinese Academy of Science, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
Institute of Oceanology, Chinese Academy of Science, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China.
Comp Biochem Physiol Part D Genomics Proteomics. 2021 Sep;39:100839. doi: 10.1016/j.cbd.2021.100839. Epub 2021 Apr 22.
The deep-sea ecosystem is considered as the largest and most remote biome of the world. It is meaningful and important to elucidate the life origins by exploring the origin and adaptive genetic mechanisms of the large deep-sea organisms. Sea cucumbers (Holothuroidea) are abundant and economically important group of echinoderms, living from the shallow-waters to deep-sea. In this study, we present the mitochondrial genomes of the sea cucumber Chiridota heheva and Chiridota sp. collected from the deep-sea cold seep and hydrothermal vent, respectively. This is the first reported mitochondrial genomes from the order Apodida. The mitochondrial genomes of C. heheva (17,200 bp) and Chiridota sp. (17,199 bp) display novel gene arrangements with the first protein-coding gene rearrangements in the class Holothuroidea. Bases composition analysis showed that the A + T content of deep-sea holothurians were significantly higher than that of the shallow-water groups. We compared the arrangement of genes from the 24 available holothurian mitogenomes and found that the transposition, reverse transposition and tandem-duplication-random-losses (TDRL) may be involved in the evolution of mitochondrial gene arrangements in Holothuroidea. Phylogenetic analysis revealed that the Apodida clustered with Elasipodida, forming two basal deep-sea holothurian clades. The divergence between the deep-sea and shallow-water holothurians was located at 386.93 Mya, during the Late Devonian. Mitochondrial protein-coding genes of deep-sea holothurians underwent relaxed purifying selection. There are 57 positive selected amino acids sites for some mitochondrial genes of the three deep-sea clades, implying they may involve in the adaption of deep-sea sea cucumbers.
深海生态系统被认为是世界上最大和最偏远的生物群落。通过探索大型深海生物的起源和适应遗传机制来阐明生命起源具有重要意义。海参（海参纲）是棘皮动物门中丰富且具有经济重要性的一个类群，生活在浅水区到深海区。在这项研究中，我们分别展示了从深海冷渗区和热液喷口区采集的海参 Chiridota heheva 和 Chiridota sp 的线粒体基因组。这是首次报道的来自 Apodida 目的线粒体基因组。C. heheva（17,200 bp）和 Chiridota sp.（17,199 bp）的线粒体基因组显示出新颖的基因排列，这是棘皮动物门中第一个蛋白编码基因重排的例子。碱基组成分析表明，深海海参的 A+T 含量明显高于浅水区群体。我们比较了 24 个已有的海参线粒体基因组的基因排列，并发现转位、反转录转位和串联重复-随机丢失（TDRL）可能参与了 Holothuroidea 中线粒体基因排列的进化。系统发育分析表明，Apodida 与 Elasipodida 聚类，形成两个基底深海海参类群。深海和浅海海参之间的分化发生在 386.93 Mya，即晚泥盆世。深海海参的线粒体蛋白编码基因经历了松弛的纯化选择。三个深海类群的一些线粒体基因有 57 个正选择氨基酸位点，表明它们可能参与了深海海参的适应。
