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KMID : 0381120230450030377
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Genes and Genomics
2023 Volume.45 No. 3 p.377 ~ p.391
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The complete mitochondrial genome of Hemigrapsus sinensis (Brachyura, Grapsoidea, Varunidae) and its phylogenetic position within Grapsoidea
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Xun Jin
Xingle Guo
Jian Chen
Jiasheng Li
Shufei Zhang
Sixu Zheng
Yunpeng Wang
Ying Peng
Kun Zhang
Yifan Liu
Bingjian Liu
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Abstract
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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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KEYWORD
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Grapsoidea, Hemigrapsus sinensis, Mitogenome, Phylogenetic
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