The complete mitochondrial genome of <i>Eodemus subtilis</i> (Decapoda: Brachyura: Portunidae) and its phylogenetic analysis

Bao Yingxuan; Ye Yingying; Ma Jiale; Jiang Xinqin

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Bao Yingxuan，Ye Yingying，Ma Jiale, et al. The complete mitochondrial genome of Eodemus subtilis (Decapoda: Brachyura: Portunidae) and its phylogenetic analysis[J]. Haiyang Xuebao，2025, 48(x)：1–15

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Bao Yingxuan，Ye Yingying，Ma Jiale, et al. The complete mitochondrial genome of Eodemus subtilis (Decapoda: Brachyura: Portunidae) and its phylogenetic analysis[J]. Haiyang Xuebao，2025, 48(x)：1–15

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The complete mitochondrial genome of Eodemus subtilis (Decapoda: Brachyura: Portunidae) and its phylogenetic analysis

1.
Fisheries college, Zhejiang Ocean University, Zhoushan 316022, China
2.
National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China

Received Date: 2025-07-14
Rev Recd Date: 2025-10-21

Available Online: 2025-11-08

Abstract

Abstract

Eodemus subtilis is an intertidal to shallow-water crab species belonging to the family Portunidae (Order: Decapoda), primarily distributed along the southeastern coastal waters of China. In this study, we conducted a comprehensive characterization of its mitochondrial genome using high-throughput sequencing and bioinformatic analyses. The complete mitochondrial genome of E. subtilis is 15,878 bp in length and comprises 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and one non-coding control region. Notably, 24 of these genes are encoded on the heavy strand (H-strand). The mitochondrial genome exhibits a strong A+T bias (69.81%), with negative AT-skew (-0.021) and GC-skew (-0.233). Analysis of relative synonymous codon usage (RSCU) revealed that the codons UCU (Ser2) and UUA (Leu2) are highly frequent, with preferred codons predominantly ending in A/T. The gene arrangement in E. subtilis is highly conserved, maintaining the ancestral gene order typical of Brachyura crabs, with no observed rearrangements. Selection pressure analysis (Ka/Ks) of the 13 PCGs across Portunidae crabs indicated that 11 genes (excluding COIII and ND1) underwent purifying selection. Phylogenetic and divergence time estimation analyses demonstrated that E. subtilis forms a clade with Monomia gladiator, with an estimated divergence time of approximately 44.34 million years ago (Mya). These findings provide significant new insights into the evolutionary history and molecular adaptations of E. subtilis within Portunidae, as well as into the evolutionary relationships of Portunidae within Brachyura.
- Eodemus subtilis,
- Mitochondrial genome,
- Brachyura,
- Phylogeny

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