The complete mitochondrial genome of Hemigrapsus sinensis (Brachyura, Grapsoidea, Varunidae) and its phylogenetic position within Grapsoidea
文献类型： 外文期刊
作者： Jin, Xun 1 ; Guo, Xingle 1 ; Chen, Jian 1 ; Li, Jiasheng 1 ; Zhang, Shufei 2 ; Zheng, Sixu 1 ; Wang, Yunpeng 1 ; Peng, Ying 1 ; Zhang, Kun 1 ; Liu, Yifan 1 ; Liu, Bingjian 1 ;
作者机构： 1.Zhejiang Ocean Univ, Natl Engn Lab Marine Germplasm Resources Explorat, Zhoushan 316022, Peoples R China
2.Chinese Acad Fisheries Sci, South China Sea Fisheries Res Inst, Guangdong Prov Key Lab Fishery Ecol & Environm, Guangzhou 510300, Guangdong, Peoples R China
3.Zhejiang Ocean Univ, Marine Sci & Technol Coll, Natl Engn Res Ctr Facilitated Marine Aquaculture, 1 Haida South Rd, Zhoushan 316022, Zhejiang, Peoples R China
关键词： Grapsoidea; Hemigrapsus sinensis; Mitogenome; Phylogenetic
期刊名称：GENES & GENOMICS （ 影响因子：2.164； 五年影响因子：1.625 ）
ISSN： 1976-9571
年卷期：
页码：
收录情况： SCI
摘要： Background In this study, the complete mitogenome of Hemigrapsus sinensis was the first identified and analyzed. Objective The complete mitochondrial genome of Hemigrapsus sinensis (Brachyura, Grapsoidea, Varunidae) and its phylogenetic position within Grapsoidea. Methods The sample of Hemigrapsus sinensis was collected and DNA was extracted. After sequencing, NOVOPlasty was used for sequence assembly. Annotate sequences with MITOS WebServer, tRNAscan-SE2.0, and NCBI database. MEGA was used for sequence analysis and Phylosuite was used for phylogenetic tree construction. DnaSP was used to calculate Ka/Ks. Results This mitochondrial genome shows that it was 15,900 bp and encoded 13 PCGs, 22 tRNA genes, two rRNA genes, and one control region. The genome composition tends to A + T (74.34%) and presents a negative GC-skew (- 0.22) and AT-skew (- 0.03). The PCGs initiation codon was the typical ATN and termination codon was the typical TAN, incomplete T or missing. The ML and BI trees showed that H. sinensis was most closely related to Hemigrapsus and clustered together with the Varunidae. And our phylogenetic trees provide proof that Ocypodoidea and Grapsoidea may be of common origin. Meanwhile, in the phylogenetic tree, parallel mixing of Chiromantes and Orisarma raised doubts over the traditional classification system. Besides, Incomplete Lineage sorting (ILS) was observed in Varunidae. In the subsequent analysis of evolution rate, we found that all of the PCGs (NAD4 was not calculated) had undergone negative selections, indicating the conservation of mitochondrial genes of H. sinensis during the evolution. Conclusion Therefore, researching the complete mitogenome of H. sinensis would be contributing to molecular taxonomy, phylogenetic relationship, and breeding optimization within the Grapsoidea superfamily.
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