PDF(Pubmed)
Abstract：
BACKGROUND: The oceanic whitetip shark Carcharhinus longimanus (family Carcharhinidae) is one of the largest sharks inhabiting all tropical and subtropical oceanic regions. Due to their life history traits and mortality attributed to pelagic longline fishing practices, this species is experiencing substantial population decline. Currently, C. longimanus is considered by the IUCN Red List of Threatened Species as \"vulnerable\" throughout its range and \"critically endangered\" in the western north Atlantic. This study sequences and describes the complete mitochondrial genome of C. longimanus in detail.
RESULTS: The mitochondrial genome of C. longimanus was assembled through next-generation sequencing and then analyzed using specialized bioinformatics tools. The circular, double-stranded AT-rich mitogenome of C. longimanus is 16,704 bp long and contains 22 tRNA genes, 2 rRNA genes, 13 protein coding genes and a 1,065 bp long control region (CR). Out of the 22 tRNA genes, only one (tRNA-Ser1) lacked a typical \'cloverleaf\' secondary structure. The prevalence of TTA (Leu), ATT (Ile) and CTA (Leu) codons in the PCGs likely contributes to the AT-rich nature of this mitogenome. In the CR, ten microsatellites were detected but no tandem repeats were found. Stem-and-loop secondary structures were common along the entire length of the CR. Ka/Ks values estimated for all PCGs were < 1, indicating that all the PCGs experience purifying selection. A phylomitogenomic analysis based on translated PCGs confirms the sister relationship between C. longimanus and C. obscurus. The analysis did not support the monophyly of the genus Carcharhinus.
CONCLUSIONS: The assembled mitochondrial genome of this pelagic shark can provide insight into the phylogenetic relationships in the genus Carcharhinus and aid conservation and management efforts in the Central Pacific Ocean.
RESULTS: The mitochondrial genome of C. longimanus was assembled through next-generation sequencing and then analyzed using specialized bioinformatics tools. The circular, double-stranded AT-rich mitogenome of C. longimanus is 16,704 bp long and contains 22 tRNA genes, 2 rRNA genes, 13 protein coding genes and a 1,065 bp long control region (CR). Out of the 22 tRNA genes, only one (tRNA-Ser1) lacked a typical \'cloverleaf\' secondary structure. The prevalence of TTA (Leu), ATT (Ile) and CTA (Leu) codons in the PCGs likely contributes to the AT-rich nature of this mitogenome. In the CR, ten microsatellites were detected but no tandem repeats were found. Stem-and-loop secondary structures were common along the entire length of the CR. Ka/Ks values estimated for all PCGs were < 1, indicating that all the PCGs experience purifying selection. A phylomitogenomic analysis based on translated PCGs confirms the sister relationship between C. longimanus and C. obscurus. The analysis did not support the monophyly of the genus Carcharhinus.
CONCLUSIONS: The assembled mitochondrial genome of this pelagic shark can provide insight into the phylogenetic relationships in the genus Carcharhinus and aid conservation and management efforts in the Central Pacific Ocean.
摘要：
背景：海洋白鳍鲨Carcharhinuslongimanus（Carcharinidae科）是居住在所有热带和亚热带海洋地区的最大鲨鱼之一。由于他们的生活史特征和死亡率归因于远洋延绳钓捕捞活动，这个物种正在经历大量的种群减少。目前,C.longimanus被IUCN濒危物种红色名录认为在整个范围内都是“脆弱的”，在北大西洋西部是“极度濒危的”。本研究详细测序并描述了C.longimanus的完整线粒体基因组。
结果：通过下一代测序组装长毛梭菌的线粒体基因组，然后使用专门的生物信息学工具进行分析。圆形，C.longimanus的双链富含AT的有丝分裂基因组长16,704bp，包含22个tRNA基因，2个rRNA基因，13个蛋白质编码基因和1,065bp长的控制区(CR)。在22个tRNA基因中，只有一种(tRNA-Ser1)缺乏典型的“苜蓿叶”二级结构。TTA（Leu）的患病率，PCG中的ATT(Ile)和CTA(Leu)密码子可能有助于该有丝分裂基因组的富含AT的性质。在CR中，检测到10个微卫星，但没有发现串联重复序列。沿着CR的整个长度，茎环二级结构很常见。对所有PCG估计的Ka/Ks值<1,表明所有PCG经历纯化选择。基于翻译的PCGs的分生理基因组分析证实了C.longimanus和C.obscurus之间的姐妹关系。该分析不支持Carcharhinus属的单系。
结论：这种中上层鲨的组装线粒体基因组可以深入了解Carcharhinus属的系统发育关系，并有助于中太平洋的保护和管理工作。
结果：通过下一代测序组装长毛梭菌的线粒体基因组，然后使用专门的生物信息学工具进行分析。圆形，C.longimanus的双链富含AT的有丝分裂基因组长16,704bp，包含22个tRNA基因，2个rRNA基因，13个蛋白质编码基因和1,065bp长的控制区(CR)。在22个tRNA基因中，只有一种(tRNA-Ser1)缺乏典型的“苜蓿叶”二级结构。TTA（Leu）的患病率，PCG中的ATT(Ile)和CTA(Leu)密码子可能有助于该有丝分裂基因组的富含AT的性质。在CR中，检测到10个微卫星，但没有发现串联重复序列。沿着CR的整个长度，茎环二级结构很常见。对所有PCG估计的Ka/Ks值<1,表明所有PCG经历纯化选择。基于翻译的PCGs的分生理基因组分析证实了C.longimanus和C.obscurus之间的姐妹关系。该分析不支持Carcharhinus属的单系。
结论：这种中上层鲨的组装线粒体基因组可以深入了解Carcharhinus属的系统发育关系，并有助于中太平洋的保护和管理工作。
