PDF(Pubmed)
Abstract：
BACKGROUND: The holothurians, commonly known as sea cucumbers, are marine organisms that possess significant dietary, nutritional, and medicinal value. However, the National Center for Biotechnology Information (NCBI) currently possesses only approximately 70 complete mitochondrial genome datasets of Holothurioidea, which poses limitations on conducting comprehensive research on their genetic resources and evolutionary patterns. In this study, a novel species of sea cucumber belonging to the genus Benthodytes, was discovered in the western Pacific Ocean. The genomic DNA of the novel sea cucumber was extracted, sequenced, assembled and subjected to thorough analysis.
RESULTS: The mtDNA of Benthodytes sp. Gxx-2023 (GenBank No. OR992091) exhibits a circular structure spanning 17,386 bp, comprising of 13 protein-coding genes (PCGs), 24 non-coding RNAs (2 rRNA genes and 22 tRNA genes), along with two putative control regions measuring 882 bp and 1153 bp, respectively. It exhibits a high AT% content and negative AT-skew, which distinguishing it from the majority of sea cucumbers in terms of environmental adaptability evolution. The mitochondrial gene homology between Gxx-2023 and other sea cucumbers is significantly low, with less than 91% similarity to Benthodytes marianensis, which exhibits the highest level of homology. Additionally, its homology with other sea cucumbers is below 80%. The mitogenome of this species exhibits a unique pattern in terms of start and stop codons, featuring only two types of start codons (ATG and ATT) and three types of stop codons including the incomplete T. Notably, the abundance of AT in the Second position of the codons surpasses that of the First and Third position. The gene arrangement of PCGs exhibits a relatively conserved pattern, while there exists substantial variability in tRNA. Evolutionary analysis revealed that it formed a distinct cluster with B. marianensis and exhibited relatively distant phylogenetic relationships with other sea cucumbers.
CONCLUSIONS: These findings contribute to the taxonomic diversity of sea cucumbers in the Elasipodida order, thereby holding significant implications for the conservation of biological genetic resources, evolutionary advancements, and the exploration of novel sea cucumber resources.
RESULTS: The mtDNA of Benthodytes sp. Gxx-2023 (GenBank No. OR992091) exhibits a circular structure spanning 17,386 bp, comprising of 13 protein-coding genes (PCGs), 24 non-coding RNAs (2 rRNA genes and 22 tRNA genes), along with two putative control regions measuring 882 bp and 1153 bp, respectively. It exhibits a high AT% content and negative AT-skew, which distinguishing it from the majority of sea cucumbers in terms of environmental adaptability evolution. The mitochondrial gene homology between Gxx-2023 and other sea cucumbers is significantly low, with less than 91% similarity to Benthodytes marianensis, which exhibits the highest level of homology. Additionally, its homology with other sea cucumbers is below 80%. The mitogenome of this species exhibits a unique pattern in terms of start and stop codons, featuring only two types of start codons (ATG and ATT) and three types of stop codons including the incomplete T. Notably, the abundance of AT in the Second position of the codons surpasses that of the First and Third position. The gene arrangement of PCGs exhibits a relatively conserved pattern, while there exists substantial variability in tRNA. Evolutionary analysis revealed that it formed a distinct cluster with B. marianensis and exhibited relatively distant phylogenetic relationships with other sea cucumbers.
CONCLUSIONS: These findings contribute to the taxonomic diversity of sea cucumbers in the Elasipodida order, thereby holding significant implications for the conservation of biological genetic resources, evolutionary advancements, and the exploration of novel sea cucumber resources.
摘要：
背景：Holothurians，通常被称为海参，是具有大量饮食的海洋生物，营养,和药用价值。然而,国家生物技术信息中心（NCBI）目前仅拥有约70个完整的Holothurioidea线粒体基因组数据集，这限制了对其遗传资源和进化模式进行全面研究。在这项研究中,海参的一种新物种，属于底偶属，是在西太平洋发现的.提取了新型海参的基因组DNA,测序，组装并进行全面分析。
结果：底偶的mtDNA。Gxx-2023(GenBank编号OR992091)显示出跨越17,386bp的圆形结构，由13个蛋白质编码基因（PCGs）组成，24个非编码RNA（2个rRNA基因和22个tRNA基因），连同两个推定的控制区，测量882bp和1153bp，分别。它具有很高的AT％含量和负的AT偏斜，在环境适应性演变方面与大多数海参区分开。Gxx-2023与其他海参的线粒体基因同源性明显较低,与海绵体的相似性不到91%，表现出最高水平的同源性。此外,与其他海参的同源性在80%以下。该物种的有丝分裂基因组在启动和停止密码子方面表现出独特的模式，仅具有两种类型的起始密码子（ATG和ATT）和三种类型的终止密码子，包括不完整的T。值得注意的是，密码子第二位置的AT丰度超过第一和第三位置。PCGs的基因排列表现出相对保守的模式，而tRNA存在实质性变异性。进化分析表明，它与B.marianensis形成了一个独特的簇，并与其他海参表现出相对较远的系统发育关系。
结论：这些发现有助于海参的分类学多样性。从而对生物遗传资源的保护具有重要意义，进化进步，以及新型海参资源的探索。
结果：底偶的mtDNA。Gxx-2023(GenBank编号OR992091)显示出跨越17,386bp的圆形结构，由13个蛋白质编码基因（PCGs）组成，24个非编码RNA（2个rRNA基因和22个tRNA基因），连同两个推定的控制区，测量882bp和1153bp，分别。它具有很高的AT％含量和负的AT偏斜，在环境适应性演变方面与大多数海参区分开。Gxx-2023与其他海参的线粒体基因同源性明显较低,与海绵体的相似性不到91%，表现出最高水平的同源性。此外,与其他海参的同源性在80%以下。该物种的有丝分裂基因组在启动和停止密码子方面表现出独特的模式，仅具有两种类型的起始密码子（ATG和ATT）和三种类型的终止密码子，包括不完整的T。值得注意的是，密码子第二位置的AT丰度超过第一和第三位置。PCGs的基因排列表现出相对保守的模式，而tRNA存在实质性变异性。进化分析表明，它与B.marianensis形成了一个独特的簇，并与其他海参表现出相对较远的系统发育关系。
结论：这些发现有助于海参的分类学多样性。从而对生物遗传资源的保护具有重要意义，进化进步，以及新型海参资源的探索。
