The complete mitochondrial genome of Eodemus subtilis (Decapoda: Brachyura: Portunidae) and its phylogenetic analysis
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摘要: 微异类梭蟹（Eodemus subtilis）是一类栖息于潮间带至浅海区的十足目梭子蟹科物种，在中国主要分布于东南沿海。本研究利用高通量测序技术，结合生物信息学分析，对其线粒体基因组进行了全面解析。线粒体基因组大小为15 878 bp，包含13个蛋白质编码基因、22个tRNA基因、2个rRNA基因以及一个非编码控制区，其中24个基因均编码在重链（H链）上。线粒体全基因组具有A+T偏向性（69.81%），呈现负的AT偏斜（−0.021）和GC偏斜（−0.233）。在微异类梭蟹的相对同义密码子使用频率（RSCU）中，Ser2的UCU和Leu2的UUA密码子使用频率高，且高使用频率的密码子通常是以A/T结尾的。微异类梭蟹的基因排列具有一定的保守性，基因排列顺序与短尾下目祖先保持一致，没有基因重排发生。对它所在的梭子蟹科进行13个蛋白质编码的选择压力分析可以得出除COIII和ND1之外的其他11个基因的非同义替换率/同义替换率（Ka/Ks）。在系统发育树和时间分歧树中，微异类梭蟹与拥剑单梭蟹（Monomia gladiator）聚成一支，二者分化时间大约在44.34 Mya，这对研究短尾下目中梭子蟹科内的进化具有重要意义。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.
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Key words:
- Eodemus subtilis /
- Mitochondrial genome /
- Brachyura /
- Phylogeny
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图 7 基于时间校准的贝叶斯系统发育树构建的梭子蟹科的时间分歧树
红色字体为本研究物种及其所在的属
Fig. 7 The time-calibrated Bayesian phylogenetic tree construction of the divergence timeline in the Portunidae family
The red font indicates the species studied in this research and its genus
图 1 微异类梭蟹线粒体基因圈图，最内圈显示GC含量与GC偏斜度。大部分基因位于重链（H链），包括10个PCGs和14个tRNAs；非编码控制区位于12S rRNA与trnI之间。其余基因（含12S rRNA和16S rRNA）位于轻链（L链），部分基因间存在重叠。
Fig. 1 Circular map of the mitochondrial genome of Eodemus subtilis, with the innermost circle showing GC content and skew. Genes are predominantly encoded on the H-strand (10 PCGs, 14 tRNAs), with the control region between 12S rRNA and trnI; the remaining, including 12S rRNA and 16S rRNA, reside on the L-strand with minor overlaps.
图 2 微异类梭蟹线粒体基因组中的氨基酸组成（A）和相对同义密码子使用情况（B）
Fig. 2 Amino acid composition (A) and relative synonymous codon usage (B) in the mitochondrial genome of the E. subtilis
图 3 微异类梭蟹线粒体基因组的tRNA的二级结构
Fig. 3 The secondary structure of tRNA in the mitochondrial genome of E. subtilis
图 4 泛甲壳动物和短尾下目线粒体基因排序比较
Fig. 4 Comparison of mitochondrial gene orders between Pancrustacea and Brachyura
图 5 18个梭子蟹科物种中13个线粒体蛋白质编码基因的选择压力分析
Fig. 5 Analysis of selection pressure on 13 mitochondrial protein-coding genes in 18 Portunidae species
图 6 基于13个蛋白质编码基因（PCGs）构建的短尾下目部分物种贝叶斯系统发育树
红色字体为本研究物种
Fig. 6 Bayesian phylogenetic tree of selected species of Brachyura based on 13 protein-coding genes (PCGs)
The red font indicates the species studied.
表 4 本研究中所分析的短尾下目物种列表及其基因库登录号
Tab. 4 List of Brachyura species analyzed in this study and their GenBank accession numbers
Order Family Species Size (bp) Accession no. Brachyura Dromiidae Lauridromia dehaani (Rathbun, 1923) 15755 NC_066660 Calappidae Calappa bilineata (Ng, Lai & Aungtonya, 2002) 15606 NC_047195 Matutidae Ashtoret lunaris (Forskål, 1775 )15807 NC_024435 Matuta planipes (Fabricius, 1798 )15760 NC_039351 Matuta victor (Fabricius, 1781 )15782 NC_053638 Menippidae Myomenippe fornasinii (Bianconi, 1851) 15658 NC_024437 Pseudocarcinus gigas (Lamarck, 1818) 15515 NC_006891 Oziidae Epixanthus frontalis (H.Milne Edwards, 1834) 15993 NC_039110 Leucosiidae Myra affinis (Bell, 1855) 15349 NC_061949 Pyrhila pisum (De Haan, 1841) 15516 NC_030047 Parthenopidae Enoplolambrus validus (De Haan, 1837) 15431 NC_072538 Daldorfia horrida (Linnaeus, 1758 )15737 NC_049029 Pilumnidae Pilumnopeus makianus (Rathbun, 1931) 15863 NC_068601 Echinoecus nipponicus (Miyake, 1939) 16173 NC_039618 Pilumnus vespertilio (Fabricius, 1793 )16222 NC_039108 Portunidae Thalamita crenata (Rüppell, 1830) 15787 NC_024438 Lupocycloporus gracilimanus (Stimpson, 1858) 15990 NC_040124 Thalamita sima (H.Milne Edwards, 1834) 15831 NC_039640 Charybdis bimaculata (Miers, 1886) 15714 NC_037695 Monomia gladiator (Fabricius, 1798 )15878 NC_037173 Charybdis natator (Herbst, 1794 )15664 NC_036132 Charybdis japonica (A.Milne-Edwards, 1861) 15738 NC_013246 Scylla paramamosain (Estampador, 1950) 15816 MG197997 Charybdis hellerii (A.Milne-Edwards, 1867) 15913 NC_060621 Charybdis annulata (Fabricius, 1798 )15747 NC_069011 Portunus sanguinolentus (Herbst, 1783 )16024 NC_028225 Portunus pelagicus (Linnaeus, 1758 )16157 NC_026209 Charybdis feriata (Linnaeus, 1758 )15660 NC_024632 Scylla tranquebarica (Fabricius, 1798 )15833 NC_012567 Scylla olivacea (Herbst, 1796 )15723 NC_012569 Scylla serrata (Forskål, 1775 )15775 NC_012565 Portunus trituberculatus (Miers, 1876) 16026 NC_005037 Eodemus subtilis (Nguyen & Ng, 2021) 15878 PV353959 Xanthidae Etisus laevimanus (Randall, 1840) 15714 NC_086869 Macromedaeus distinguendus (De Haan, 1835) 15710 NC_057473 Etisus dentatus (Herbst, 1785 )15884 NC_054248 Etisus anaglyptus (H.Milne Edwards, 1834) 16435 NC_042208 Atergatis floridus (Linnaeus, 1767 )16180 NC_037201 Atergatis integerrimus (Lamarck, 1818) 15924 NC_037172 Leptodius exaratus (H.Milne Edwards, 1834) 15716 MF198250 Gecarcinidae Tuerkayana celeste (Ng & Davie, 2012) 15556 NC_088507 Tuerkayana hirtipes (Dana, 1851) 15559 NC_088506 Tuerkayana rotundum (Quoy & Gaimard, 1824) 15562 NC_088505 Tuerkayana magnum (Ng & Shih, 2014) 15556 NC_088504 Cardisoma armatum (Herklots, 1851) 15586 NC_057477 Gecarcoidea lalandii (H.Milne Edwards, 1837) 15575 NC_057475 Cardisoma carnifex (Herbst, 1796 )15597 NC_039105 Grapsidae Metopograpsus frontalis (Miers, 1880) 15587 NC_042152 Grapsus albolineatus (Latreille, 1812) 15583 MZ262276 Pachygrapsus marmoratus (Fabricius, 1787 )15406 NC_039109 Camptandriidae Deiratonotus japonicus (Sakai, 1983) 15444 LC715473 Cleistostoma dilatatum (De Haan, 1833) 15444 NC_060620 Dotillidae Tmethypocoelis choreutes (Davie & Kosuge, 1995) 16283 LC715478 Ilyoplax pusilla (De Haan, 1835) 15465 LC715475 Ilyoplax integra (Tesch, 1918) 16163 LC715474 Scopimera intermedia (Balss, 1934) 16252 NC_057476 Ilyoplax deschampsi (Rathbun, 1913) 15460 NC_020040 Outgroups Munidopsis verrilli (Benedict, 1902) 17636 MH717896 Munidopsis lauensis (Baba & de Saint Laurent, 1992) 17483 MH717895 
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表 1 微异类梭蟹线粒体基因组结构
Tab. 1 Organization of the E. subtilis mitochondrial genome
Gene Position(bp) Length (bp) Start/stop codon Intergenic Nucleotide (bp) Anticodon Strand From To COI 1 1534 1534 ATG/ACT 0 H trnL 1535 1600 66 25 TAA H COII 1626 2310 685 ATG/ACT 0 H trnK 2311 2378 68 0 TTT H trnD 2379 2445 67 0 GTC H ATP8 2446 2607 162 ATG/TAG −7 H ATP6 2601 3278 678 ATT/TAA −1 H COIII 3278 4069 792 ATG/TAA 0 H trnG 4070 4131 62 0 TCC H ND3 4132 4485 354 ATT/TAA 3 H trnA 4489 4554 66 1 TGC H trnR 4556 4621 66 0 TCG H trnN 4622 4686 65 2 GTT H trnS 4689 4755 67 0 TCT H trnE 4756 4823 68 27 TTC H trnH 4851 4914 64 0 GTG L trnF 4915 4978 64 −1 GAA L ND5 4978 6705 1728 TTA/CAT 20 L ND4 6726 8060 1335 TTA/CAT −7 L ND4L 8054 8356 303 TTA/CAT 2 L trnT 8359 8424 66 0 TGT H trnP 8425 8491 67 2 TGG L ND6 8494 9000 507 ATG/TAA −1 H CYTB 9000 10157 1158 ATG/AAT −23 H trnS 10135 10203 69 28 TGA H ND1 10232 11188 957 CTA/AAT 5 L trnL 11194 11262 69 −46 TAG L 16S rRNA 11217 12618 1402 ATT/TGA −14 L trnV 12605 12678 74 2 TAC L 12S rRNA 12681 13537 857 TCC/TCC 930 L trnI 14468 14534 67 −3 GAT H trnQ 14532 14601 70 3 TTG L trnM 14605 14673 69 0 CAT H ND2 14674 15684 1011 ATG/TAG −2 H trnW 15683 15749 67 −1 TCA H trnC 15749 15812 64 0 GCA L trnY 15813 15878 66 0 GTA L
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表 2 微异类梭蟹线粒体基因组的核苷酸组成与偏斜度
Tab. 2 Nucleotide composition and skewness of the E. subtilis mitochondrial genome
gene A (%) T (%) G (%) C (%) A+T (%) AT-skew GC-skew Mito 34.18 35.63 18.62 11.58 69.81 -0.021 -0.233 COI 28.10 36.18 19.56 16.17 64.28 -0.126 -0.095 COII 30.51 33.72 21.02 14.74 64.23 -0.050 -0.176 ATP8 31.48 43.83 19.14 5.56 75.31 -0.164 -0.550 ATP6 27.43 40.86 19.32 12.39 68.29 -0.197 -0.219 COIII 27.90 35.10 21.97 15.03 63.01 -0.114 -0.188 ND3 27.40 38.70 20.62 13.28 66.10 -0.171 -0.217 ND5 32.06 39.06 10.71 18.17 71.12 -0.098 0.259 ND4 29.89 41.72 9.81 18.58 71.61 -0.165 0.309 ND4L 29.70 40.59 9.90 19.80 70.30 -0.155 0.333 ND6 28.21 47.53 16.77 7.50 75.74 -0.255 -0.382 CYTB 28.11 36.74 21.23 13.92 64.85 -0.133 -0.208 ND1 25.81 43.05 10.87 20.27 68.86 -0.250 0.302 ND2 25.22 41.84 23.94 9.00 67.06 -0.248 -0.453 tRNAs 36.51 35.69 12.51 15.30 72.20 0.011 0.100 rRNAs 37.32 36.61 9.74 16.33 73.93 0.010 0.253 PCGs 28.64 39.33 16.73 15.30 67.96 -0.157 -0.045
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表 3 微异类梭蟹线粒体基因组密码子数量和相对同义密码子使用率
Tab. 3 Codon numbers and relative synonymous codon usage in the mitochondrial genome of the E. subtilis
Codon Count RSCU Codon Count RSCU Codon Count RSCU Codon Count RSCU UUU(F) 238 1.33 UCU(S) 137 2.11 UAU(Y) 229 1.37 UGU(C) 47 1.16 UUC(F) 121 0.67 UCC(S) 77 1.19 UAC(Y) 106 0.63 UGC(C) 34 0.84 UUA(L) 248 1.98 UCA(S) 90 1.39 UAA(*) 239 1.46 UGA(W) 61 1.39 UUG(L) 63 0.5 UCG(S) 24 0.37 UAG(*) 89 0.54 UGG(W) 27 0.61 CUU(L) 159 1.27 CCU(P) 94 1.63 CAU(H) 86 1.26 CGU(R) 17 0.92 CUC(L) 80 0.64 CCC(P) 58 1 CAC(H) 50 0.74 CGC(R) 11 0.59 CUA(L) 157 1.26 CCA(P) 59 1.02 CAA(Q) 98 1.4 CGA(R) 32 1.73 CUG(L) 43 0.34 CCG(P) 20 0.35 CAG(Q) 42 0.6 CGG(R) 14 0.76 AUU(I) 259 1.48 ACU(T) 129 1.8 AAU(N) 214 1.42 AGU(S) 48 0.74 AUC(I) 90 0.52 ACC(T) 68 0.95 AAC(N) 87 0.58 AGC(S) 52 0.8 AUA(M) 249 1.64 ACA(T) 76 1.06 AAA(K) 241 1.45 AGA(S) 68 1.05 AUG(M) 55 0.36 ACG(T) 13 0.18 AAG(K) 91 0.55 AGG(S) 23 0.35 GUU(V) 60 1.38 GCU(A) 64 1.88 GAU(D) 67 1.24 GGU(G) 41 1.3 GUC(V) 34 0.78 GCC(A) 32 0.94 GAC(D) 41 0.76 GGC(G) 14 0.44 GUA(V) 60 1.38 GCA(A) 34 1 GAA(E) 84 1.24 GGA(G) 53 1.68 GUG(V) 20 0.46 GCG(A) 6 0.18 GAG(E) 51 0.76 GGG(G) 18 0.57
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[1] 张小蜂, 徐一扬. 中国潮间带螃蟹生态图鉴[M]. 重庆: 重庆大学出版社, 2023: 650.Zhang Xiaofeng, Xu Yiyang. Chinese Intertidal Brachyuran Crabs Illustrated[M]. Chongqing: Chongqing University Press, 2023: 650. [2] Wong K J H, Leung K M Y, Chan B K K. On the identities of three common shallow-water swimming crabs Portunus hastatoides fabricius, 1798, P. dayawanensis Chen, 1986, and P. pseudohastatoides Yang and Tang, 2006 (Crustacea: Decapoda: Portunidae): essentials for benthic ecological monitoring and biodiversity studies[J]. Zoological Studies, 2010, 49(5): 669−680. [3] Koch M, Spiridonov V A, Ďuriš Z. Revision of the generic system for the swimming crab subfamily Portuninae (Decapoda: Brachyura: Portunidae) based on molecular and morphological analyses[J]. Zoological Journal of the Linnean Society, 2023, 197(1): 127−175. doi: 10.1093/zoolinnean/zlac017 [4] Nguyen T S, Ng P K L. A revision of the swimming crabs of the Indo-West Pacific Xiphonectes hastatoides (Fabricius, 1798) species complex (Crustacea: Brachyura: Portunidae)[J]. Arthropoda Selecta, 2021, 30(3): 386−404. doi: 10.15298/arthsel.30.3.11 [5] Hickerson M J, Cunningham C W. Dramatic mitochondrial gene rearrangements in the hermit crab Pagurus longicarpus (Crustacea, Anomura)[J]. Molecular Biology and Evolution, 2000, 17(4): 639−644. doi: 10.1093/oxfordjournals.molbev.a026342 [6] 师国慧, 崔朝霞. 蛙蟹线粒体全基因组序列分析及其分类地位[C]//“全球变化下的海洋与湖沼生态安全”学术交流会论文摘要集. 南京: 中国海洋湖沼学会, 2014: 1.Shi Guohui, Cui Zhaoxia. Analysis of the complete mitochondrial genome sequence of frog crabs and their taxonomic status[C]//“Marine and Limnological Ecological Security under Global Change”Collection of Academic Conference Paper Abstracts. Nanjing: Chinese Society of Oceanography and Limnology, 2014: 1. [7] 王兴强, 曹梅, 阎斌伦, 等. 三疣梭子蟹综合养殖技术[J]. 水产科学, 2009, 28(2): 105−108.Wang Xingqiang, Cao Mei, Yan Binlun, et al. Integrated culture of swimming crab Portunus trituberculatus[J]. Fisheries Science, 2009, 28(2): 105−108. [8] Chen Fangyi, Wang Kejian. Characterization of the innate immunity in the mud crab Scylla paramamosain[J]. Fish & Shellfish Immunology, 2019, 93: 436−448. [9] Lü Jiayin, Xia Liping, Liu Xiaojuan, et al. The mitochondrial genome of Grapsus albolineatus (Decapoda: Brachyura: Grapsidae) and phylogenetic associations in Brachyura[J]. Scientific Reports, 2022, 12(1): 2104. doi: 10.1038/s41598-022-06080-3 [10] Tan M H, Gan Hanming, Lee Y P, et al. Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition[J]. Scientific Reports, 2019, 9(1): 10756. doi: 10.1038/s41598-019-47145-0 [11] Ballard J W O, Whitlock M C. The incomplete natural history of mitochondria[J]. Molecular Ecology, 2004, 13(4): 729−744. doi: 10.1046/j.1365-294X.2003.02063.x [12] Saccone C, Gissi C, Lanave C, et al. Evolution of the mitochondrial genetic system: an overview[J]. Gene, 2000, 261(1): 153−159. doi: 10.1016/S0378-1119(00)00484-4 [13] 迪丽娜·茹斯坦木, 袁晓倩, 张琪, 等. 基于线粒体基因组数据的裂腹鱼类系统发育研究[J]. 中国水产科学, 2022, 29(6): 781−791.Rustam D, Yuan Xiaoqian, Zhang Qi, et al. Study on the phylogeny of Schizothoracids based on complete mitochondrial genome[J]. Journal of Fishery Sciences of China, 2022, 29(6): 781−791. [14] Sant’Anna B S, Santos D M, Marchi M R R, et al. Surface-sediment and hermit-crab contamination by butyltins in southeastern Atlantic estuaries after ban of TBT-based antifouling paints[J]. Environmental Science and Pollution Research, 2014, 21(10): 6516−6524. doi: 10.1007/s11356-014-2521-8 [15] Ma Hongyu, Ma Chunyan, Li Chenhong, et al. First mitochondrial genome for the red crab (Charybdis feriata) with implication of phylogenomics and population genetics[J]. Scientific Reports, 2015, 5(1): 11524. doi: 10.1038/srep11524 [16] Ma Hongyu, Ma Chunyan, Li Xincang, et al. The complete mitochondrial genome sequence and gene organization of the mud crab (Scylla paramamosain) with phylogenetic consideration[J]. Gene, 2013, 519(1): 120−127. doi: 10.1016/j.gene.2013.01.028 [17] Yamauchi M M, Miya M U, Nishida M. Complete mitochondrial DNA sequence of the swimming crab, Portunus trituberculatus (Crustacea: Decapoda: Brachyura)[J]. Gene, 2003, 311: 129−135. doi: 10.1016/S0378-1119(03)00582-1 [18] Wang Guizhong, Kong Xianghui, Wang Kejian, et al. Variation of specific proteins, mitochondria and fatty acid composition in gill of Scylla serrata (Crustacea, Decapoda) under low temperature adaptation[J]. Journal of Experimental Marine Biology and Ecology, 2007, 352(1): 129−138. doi: 10.1016/j.jembe.2007.07.017 [19] 张茜茜, 朱志煌, 王健鑫, 等. 梭子蟹科线粒体基因组特征与系统发育遗传分析[J]. 渔业研究, 2025, 47(4): 408−420.Zhang Xixi, Zhu Zhihuang, Wang Jianxin, et al. Mitochondrial genome characteristics and phylogenetic analysis in Portunidae[J]. Journal of Fisheries Research, 2025, 47(4): 408−420. [20] Xie Zhuofang, Lai Tinghe, Waiho K, et al. Complete mitochondrial genome of the spiny rock crab Thalamita crenata (rüppell, 1830) (Crustacea: Decapoda: Portunidae) from China coast and its phylogeny[J]. Mitochondrial DNA Part B, 2018, 3(2): 1019−1020. doi: 10.1080/23802359.2018.1508384 [21] Chen Shifu, Zhou Yanqing, Chen Yaru, et al. fastp: an ultra-fast all-in-one FASTQ preprocessor[J]. Bioinformatics, 2018, 34(17): i884−i890. doi: 10.1093/bioinformatics/bty560 [22] Jin Jianjun, Yu Wenbin, Yang Junbo, et al. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes[J]. Genome Biology, 2020, 21(1): 241. doi: 10.1186/s13059-020-02154-5 [23] Meng Guanliang, Li Yiyuan, Yang Chentao, et al. MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization[J]. Nucleic Acids Research, 2019, 47(11): e63. doi: 10.1093/nar/gkz173 [24] Bernt M, Donath A, Jühling F, et al. MITOS: improved de novo metazoan mitochondrial genome annotation[J]. Molecular Phylogenetics and Evolution, 2013, 69(2): 313−319. doi: 10.1016/j.ympev.2012.08.023 [25] Lu J, Salzberg S L. SkewIT: the Skew Index Test for large-scale GC Skew analysis of bacterial genomes[J]. PLoS Computational Biology, 2020, 16(12): e1008439. doi: 10.1371/journal.pcbi.1008439 [26] Grant J R, Stothard P. The CGView Server: a comparative genomics tool for circular genomes[J]. Nucleic Acids Research, 2008, 36(S2): W181−W184. [27] Batut B, van den Beek M, Doyle M A, et al. RNA-Seq data analysis in galaxy[J]. Methods in Molecular Biology, 2021, 2284: 367−392. [28] Kerpedjiev P, Hammer S, Hofacker I L. Forna (force-directed RNA): simple and effective online RNA secondary structure diagrams[J]. Bioinformatics, 2015, 31(20): 3377−3379. doi: 10.1093/bioinformatics/btv372 [29] Kumar S, Stecher G, Suleski M, et al. MEGA12: molecular evolutionary genetic analysis version 12 for adaptive and green computing[J]. Molecular Biology and Evolution, 2024, 41(12): msae263. doi: 10.1093/molbev/msae263 [30] Rozas J, Ferrer-Mata A, Sánchez-DelBarrio J C, et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets[J]. Molecular Biology and Evolution, 2017, 34(12): 3299−3302. doi: 10.1093/molbev/msx248 [31] Xiang Chuanyu, Gao Fangluan, Jakovlić I, et al. Using PhyloSuite for molecular phylogeny and tree‐based analyses[J]. iMeta, 2023, 2(1): e87. doi: 10.1002/imt2.87 [32] 刘慧, 张辉贤, 刘馨蔓, 等. 南海小叶海蛞蝓(Phyllidiella nanhaiensis sp. nov. )线粒体基因组特征与系统进化[J]. 热带海洋学报, 2025, 44(1): 1−8.Liu Hui, Zhang Huixian, Liu Xinman, et al. Complete mitogenome data of sea slug Phyllidiella nanhaiensis sp. nov. and its phylogenetic implications[J]. Journal of Tropical Oceanography, 2025, 44(1): 1−8. [33] Letunic I, Bork P. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool[J]. Nucleic Acids Research, 2024, 52(W1): W78−W82. doi: 10.1093/nar/gkae268 [34] Kumar S, Stecher G, Suleski M, et al. TimeTree: a resource for timelines, timetrees, and divergence times[J]. Molecular Biology and Evolution, 2017, 34(7): 1812−1819. doi: 10.1093/molbev/msx116 [35] Drummond A J, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees[J]. BMC Evolutionary Biology, 2007, 7(1): 214. doi: 10.1186/1471-2148-7-214 [36] Rambaut A, Drummond A J, Xie Dong, et al. Posterior summarization in Bayesian phylogenetics using Tracer 1.7[J]. Systematic Biology, 2018, 67(5): 901−904. doi: 10.1093/sysbio/syy032 [37] Xin Zhaozhe, Liu Yu, Zhang Daizhen, et al. Complete mitochondrial genome of Clistocoeloma sinensis (Brachyura: Grapsoidea): gene rearrangements and higher-level phylogeny of the Brachyura[J]. Scientific Reports, 2017, 7(1): 4128. doi: 10.1038/s41598-017-04489-9 [38] Wang Zhengfei, Wang Ziqian, Shi Xuejia, et al. Complete mitochondrial genome of Parasesarma affine (Brachyura: Sesarmidae): gene rearrangements in Sesarmidae and phylogenetic analysis of the Brachyura[J]. International Journal of Biological Macromolecules, 2018, 118: 31−40. doi: 10.1016/j.ijbiomac.2018.06.056 [39] Ki J S, Dahms H U, Hwang J S, et al. The complete mitogenome of the hydrothermal vent crab Xenograpsus testudinatus (Decapoda, Brachyura) and comparison with brachyuran crabs[J]. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 2009, 4(4): 290−299. doi: 10.1016/j.cbd.2009.07.002 [40] Meng Xianliang, Jia Fulong, Zhang Xiaohui, et al. Complete sequence and characterization of mitochondrial genome in the swimming crab Portunus sanguinolentus (Herbst, 1783) (Decapoda, Brachyura, Portunidae)[J]. Mitochondrial DNA Part A, 2016, 27(4): 3052−3053. doi: 10.3109/19401736.2015.1063130 [41] Wang Ziqian, Shi Xuejia, Guo Huayun, et al. Characterization of the complete mitochondrial genome of Uca lacteus and comparison with other Brachyuran crabs[J]. Genomics, 2020, 112(1): 10−19. doi: 10.1016/j.ygeno.2019.06.004 [42] Tang Boping, Liu Yu, Xin Zhaozhe, et al. Characterisation of the complete mitochondrial genome of Helice wuana (Grapsoidea: Varunidae) and comparison with other Brachyuran crabs[J]. Genomics, 2018, 110(4): 221−230. doi: 10.1016/j.ygeno.2017.10.001 [43] Zhang Yuyang, Ma Yunqi, Yu Huanxi, et al. Deciphering codon usage patterns in the mitochondrial genome of the Oryza species[J]. Agronomy, 2024, 14(11): 2722. doi: 10.3390/agronomy14112722 [44] Zhang Ying, Gong Li, Lu Xinting, et al. Gene rearrangements in the mitochondrial genome of Chiromantes eulimene (Brachyura: Sesarmidae) and phylogenetic implications for Brachyura[J]. International Journal of Biological Macromolecules, 2020, 162: 704−714. doi: 10.1016/j.ijbiomac.2020.06.196 [45] 孟磊, 韦丽明, 龚理, 等. 长脚蟹科首个线粒体基因组测定及系统发育分析[J]. 南方农业学报, 2023, 54(1): 250−260.Meng Lei, Wei Liming, Gong Li, et al. The first complete mitochondrial genome of Goneplacidae (Decapoda: Brachyura) and its phylogenetic positionamong Brachyura[J]. Journal of Southern Agriculture, 2023, 54(1): 250−260. [46] Gong Li, Liu Bingjian, Liu L, et al. The complete mitochondrial genome of Terapon jarbua (Centrarchiformes: Terapontidae) and comparative analysis of the control region among eight centrarchiformes species[J]. Russian Journal of Marine Biology, 2019, 45(2): 137−144. doi: 10.1134/S1063074019020068 [47] Romanova E V, Aleoshin V V, Kamaltynov R M, et al. Evolution of mitochondrial genomes in Baikalian amphipods[J]. BMC Genomics, 2016, 17(S14): 1016. doi: 10.1186/s12864-016-3357-z [48] Ma Hongyu, Ma Chunyan, Li Xincang, et al. The complete mitochondrial genome sequence and gene organization of the mud crab (Scylla paramamosain) with phylogenetic consideration[J]. Gene, 2013, 519(1): 120-127. (查阅网上资料, 本条文献与第16条文献重复, 请确认) [49] Bian Dandan, Tang Sheng, Wang Songnan, et al. Comparative analysis of Metopograpsus quadridentatus (Crustacea: Decapoda: Grapsidae) mitochondrial genome reveals gene rearrangement and phylogeny[J]. Animals, 2025, 15(8): 1162. doi: 10.3390/ani15081162 [50] Segawa R D, Aotsuka T. The mitochondrial genome of the Japanese freshwater crab, Geothelphusa dehaani (Crustacea: Brachyura): evidence for its evolution via gene duplication[J]. Gene, 2005, 355: 28−39. doi: 10.1016/j.gene.2005.05.020 [51] Ji Yongkun, Wang An, Lu Xiuling, et al. Mitochondrial genomes of two brachyuran crabs (Crustacea: Decapoda) and phylogenetic analysis[J]. Journal of Crustacean Biology, 2014, 34(4): 494−503. doi: 10.1163/1937240X-00002252 [52] Lavrov D V, Boore J L, Brown W M. The complete mitochondrial DNA sequence of the horseshoe crab Limulus polyphemus[J]. Molecular Biology and Evolution, 2000, 17(5): 813−824. doi: 10.1093/oxfordjournals.molbev.a026360 [53] Conrad I, Craft A, Thurman C L, et al. The complete mitochondrial genome of the red-jointed brackish-water fiddler crab Minuca minax (LeConte 1855) (Brachyura: Ocypodidae): new family gene order, and purifying selection and phylogenetic informativeness of protein coding genes[J]. Genomics, 2021, 113(1): 565−572. doi: 10.1016/j.ygeno.2020.09.050 [54] Xie Zhuofang, Fazhan H, Li Xincang, et al. Identification of the complete mitochondrial genome of Monomia gladiator (Decapoda: Brachyura: Portunidae) and its phylogenetic relationship[J]. Mitochondrial DNA Part B, 2018, 3(1): 200−201. doi: 10.1080/23802359.2018.1437827 [55] Huang Y H, Shih H T. Diversity in the Taiwanese swimming crabs (Crustacea: Brachyura: Portunidae) estimated through DNA barcodes, with descriptions of 14 new records[J]. Zoological Studies, 2021, 60: e60. [56] Zhong Shengping, Zhao Yanfei, Zhang Qin. The complete mitochondrial genome of Thalamita sima (Decapoda: Portunidae)[J]. Mitochondrial DNA Part B, 2018, 3(2): 723−724. doi: 10.1080/23802359.2018.1483777 [57] Lu Xinting, Gong Li, Zhang Ying, et al. The complete mitochondrial genome of Calappa bilineata: the first representative from the family Calappidae and its phylogenetic position within Brachyura[J]. Genomics, 2020, 112(3): 2516−2523. doi: 10.1016/j.ygeno.2020.02.003 [58] Duan Xinbing, Dong Xiangli, Li Jiji, et al. The complete mitochondrial genome of Pilumnopeus makianus (Brachyura: Pilumnidae), novel gene rearrangements, and phylogenetic relationships of Brachyura[J]. Genes, 2022, 13(11): 1943. doi: 10.3390/genes13111943 [59] Hall R. Cenozoic geological and plate tectonic evolution of SE Asia and the SW Pacific: computer-based reconstructions, model and animations[J]. Journal of Asian Earth Sciences, 2002, 20(4): 353−431. doi: 10.1016/S1367-9120(01)00069-4 [60] Schubart C D, Reuschel S. A proposal for a new classification of Portunoidea and Cancroidea (Brachyura: Heterotremata) based on two independent molecular phylogenies[M]//Martin J W, Crandall K A, Felder D L. Decapod Crustacean Phylogenetics. Boca Raton: CRC Press, 2009: 533-549. [61] Evans N. Molecular phylogenetics of swimming crabs (Portunoidea Rafinesque, 1815) supports a revised family-level classification and suggests a single derived origin of symbiotic taxa[J]. PeerJ, 2018, 6: e4260. doi: 10.7717/peerj.4260 [62] Spiridonov V A. An update of phylogenetic reconstructions, classification and morphological characters of extant Portunoidea Rafinesque, 1815 (Decapoda, Brachyura, Heterotremata), with a discussion of their relevance to fossil material[J]. Geologija, 2020, 63(1): 133−166. doi: 10.5474/geologija.2020.014 [63] Yang Jinshu, Lu Bo, Chen Dianfu, et al. When did decapods invade hydrothermal vents? Clues from the Western Pacific and Indian Oceans[J]. Molecular Biology and Evolution, 2012, 30(2): 305−309. doi: 10.1093/molbev/mss224 [64] Ellison J C, Stoddart D R. Mangrove ecosystem collapse during predicted sea-level rise: Holocene analogues and implications[J]. Journal of Coastal Research, 1991, 7(1): 151−165. [65] Niu Jiaojiao, Hu Xuelei, Ip J C H, et al. Multi-omic approach provides insights into osmoregulation and osmoconformation of the crab Scylla paramamosain[J]. Scientific Reports, 2020, 10(1): 21771. doi: 10.1038/s41598-020-78351-w [66] Woodruff D S. Biogeography and conservation in Southeast Asia: how 2.7 million years of repeated environmental fluctuations affect today’s patterns and the future of the remaining refugial-phase biodiversity[J]. Biodiversity and Conservation, 2010, 19(4): 919−941. doi: 10.1007/s10531-010-9783-3 -
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