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The analyses of the complete mitochondrial genomes of three crabs revealed novel gene rearrangements and phylogenetic relationships of Brachyura

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Abstract

Background

Brachyura crab is the largest branch of Decapoda crustacean. Phylogenetic relationships within Brachyura remain controversial to be investigated. The mitochondrial genome (mitogenome) is an important molecular marker for studying the phylogenetic relationships of Brachyura.

Methods and results

To understand the phylogeny of Brachyura, the three complete mitogenomes from Charybdis annulata, Leptodius exaratus, and Spider crab were sequenced and annotated. Their full length was 15,747, 15,716, and 16,608 bp long, respectively. The first two crabs both contained 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and a control region. However, Spider crab contained 13 PCGs, two rRNA genes, 25 tRNA genes and a control region. The mitogenomes of each of the three crabs exhibited high AT content (67.8%, 69.1%, and 70.8%), with negative AT skews (–0.014, − 0.028, and − 0.017) and GC skews (–0.269, − 0.286, and − 0.341). The gene order of C. annulata was identical to the ancestor of Brachyura. Compared with the ancestor of Brachyura, L. exaratus exhibited the gene rearrangements of Val (V)-rrnS-control region, and Spider crab had the four copies of Lys (K). Phylogenetic analyses indicated that C. annulata belonged to Portunidae family, Portunoidea superfamilies, L. exaratus belonged to Xanthidae family, Xanthoidea superfamilies, and Spider crab belonged to Mithracidae family, Majoidea superfamilies. Phylogenetic analyses showed that the two species (Somanniathelphusa boyangensis and Huananpotamon lichuanense) belonging to the Potamoidea were sister groups to the Thoracotremata, thus supporting the conclusion that Heterotremata is polyphyletic.

Conclusion

The results of this study enriched the crab mitogenome database and enabled us to better understand the phylogenetic relationships of Brachyura.

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Data Availability

Data will be made available on request.

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Acknowledgements

The authors would like to thank all participants in this study. Special thanks also go to Bo-Ping Tang and Qiu-Ning Liu. They used their expertise to contribute to the preparation of the manuscript and the analysis of the study.

Funding

This study was funded by the Natural Science Research General Program of Jiangsu Provincial Higher Education Institutions (21KJA240003), the Natural Science Foundation of Jiangsu Province (BE2020673), the National Key R&D Program of China (2019YFD0900404-05), the National Natural Science Foundation of China (32070526), the Qing Lan Project of Jiangsu Province, and the “Outstanding Young Talents” of YCTU, the Natural Science Foundation of Shandong Province (ZR2022QC250), the Special Support Program of Qingdao Agricultural University awarded to ZZ Xin.

Author information

Authors and Affiliations

  1. The Laboratory of Aquatic Parasitology, School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266237, Shandong, China

    Zhao-Zhe Xin

  2. Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224007, Jiangsu, China

    Sheng Tang, Xiang Lu, Hua-Bin Zhang, Dai-Zhen Zhang, Gang Wang, Bo-Ping Tang & Qiu-Ning Liu

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  1. Zhao-Zhe Xin
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Contributions

Zhao-Zhe Xin: Conceptualization, Methodology, Formal analysis, Investigation, Data Curation, Writing-Original Draft, Writing-Review and Editing, Sheng Tang and Xiang Lu: Formal analysis, Investigation, Data Curation, Hua-Bin Zhang, Dai-Zhen Zhang and Gang Wang: Investigation, Data Curation, Bo-Ping Tang and Qiu-Ning Liu: Conceptualization, Resources, Supervision, Project administration, Funding acquisition. All authors have read and agreed to the published version of the manuscript.

Corresponding authors

Correspondence to Bo-Ping Tang or Qiu-Ning Liu.

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Xin, ZZ., Tang, S., Lu, X. et al. The analyses of the complete mitochondrial genomes of three crabs revealed novel gene rearrangements and phylogenetic relationships of Brachyura. Mol Biol Rep 50, 10301–10313 (2023). https://doi.org/10.1007/s11033-023-08833-3

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