Complete mitochondrial genome sequencing of Anchisquilla fasciata and phylogenetic analysis of the Squillidae
-
摘要: 条尾近虾蛄（Anchisquilla fasciata）属于虾蛄科Squillidae（Latreille, 1802）。在本研究中，通过二代测序技术得到了条尾近虾蛄的线粒体全基因组，对基因组基本结构特点做了分析，发现共含有37个基因，包含13个蛋白质编码基因（PCGs），2个rRNA，22个tRNA。对碱基含量分析发现A碱基含量最高为35.42%，G碱基最低为12.83%，选择了虾蛄科11个物种的线粒体基因组进行选择压力分析发现所有PCGs都受到纯化选择。另外通过结合软甲纲下2个亚纲的线粒体基因组的13个PCGs构建了系统发育树，结果发现虾蛄科为单系群，科内物种能够形成一个独立的分支，与其他相关的掠虾亚纲动物（如琴虾蛄科等）有明显的分化。对软甲纲的线粒体基因重排进行比较发现口足目未表现出重排现象。从重建的掠虾亚纲的分歧时间的年代图谱，得到现存物种的分化最早发生在中生代白垩纪期，在新生代物种大量分化。这些结果将更好地帮助人们理解不同虾蛄科物种的亲缘关系，以及软甲纲内各亚纲之间的进化地位与关系。Abstract: Anchisquilla fasciata belongs to the Squillidae (Latreille, 1802). In this study, the complete mitochondrial genome of Anchisquilla fasciata was obtained through next-generation sequencing technology. Analysis of the basic structural characteristics of the genome revealed that it contains a total of 37 genes, including 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes. Analysis of nucleotide composition showed that A had the highest content at 35.42%, while G had the lowest content at 12.83%. Selection pressure analysis was conducted on the mitochondrial genomes of 11 species within the Squillidae, and it was found that all PCGs were under purifying selection. Additionally, a phylogenetic tree was constructed using the 13 PCGs of mitochondrial genomes from two subclasses of Malacostraca, revealing that the Squillidae forms a monophyletic group with species within the family branching off into a distinct clade, showing clear differentiation from other related Hoplocarida (such as the Lysiosquillidae). Comparison of mitochondrial gene rearrangements within Malacostraca showed that the Stomatopoda did not exhibit any rearrangements. The reconstructed chronogram of divergence times within the Hoplocarida indicated that the earliest diversification of existing species occurred during the Cretaceous period of the Mesozoic era, with a significant diversification of species in the Cenozoic era. These results will provide better insights into the phylogenetic relationships among different species of Squillidae and the evolutionary positions and relationships among subclasses within Malacostraca.
-
Key words:
- Squillidae /
- Stomatopod /
- mitochondrial genome /
- phylogenetic analysis /
- divergence time
-
图 2 条尾近虾蛄tRNA二级结构
Fig. 2 Secondary structure of the tRNA genes in the mitogenome of Anchisquilla fasciata
图 3 条尾近虾蛄线粒体基因组的氨基酸组成（a）及同义密码子使用频率（b）
Fig. 3 Amino acid composition (a) and relative synonymous codon usage frequencies (b) of Anchisquilla fasciata
图 5 基于软甲纲两个亚纲的13个蛋白编码基因构建的系统发育树
a. ML树的拓扑结构（红色虚线框标记了BI树和ML树结果之间的差异） b. 贝叶斯树中的不同结果；每个节点前的数字表示最大似然法树的支持率，本研究中的条尾近虾蛄已用红色圆形标记。“/”代表该物种无中文名
Fig. 5 The phylogenetic was constructed based on 13 PCGs of two subclasses in Malacostraca
a. The topological structure of the ML tree (the diferences between BI tree and ML tree results are marked with red dashed boxes) b. the diferentresults in the Bl tree; The number in front of each node indicate the support rate of the ML tree, the Anchisquilla fasciata in this study has been marked by a red circle. The “/” indicates that the species lacks a Chinese name
图 6 祖先甲壳类动物(泛甲壳纲基本模式)、口足目、等足目和短尾次目(十足目)基因顺序对比
蓝色方框代表蛋白编码基因，肉色方框核糖体RNA基因，而绿色方框代表转运RNA基因。红色方框为与祖先甲壳类动物基因顺序不同之处，“CR”代表控制区域
Fig. 6 Comparison of gene order among Ancestral Crustaceans (basic pattern of Pancrustacea), Stomatopoda, Isopoda, and Brachyura (Decapoda)
The blue boxes represent protein-coding genes, the flesh-colored boxes represent rRNA genes, and the green boxes represent tRNA genes. Red boxes indicate differences in gene order compared to ancestral crustaceans, “CR” stands for control region
图 7 基于掠虾亚纲13个蛋白编码基因的分歧时间估计（中*代表中新世）
Fig. 7 Estimation of divergence time based on 13 PCGs of Hoplocarida (“中*” represents the Miocene)
表 1 用于系统发育分析的软甲纲物种及其GenBank登录号列表
Tab. 1 List of Malacostraca species for phylogenetic analysis with their GenBank accession numbers
亚纲 目 科 种 长度/bp 登录号 叶虾亚纲 Phyllocarida — — — — — 掠虾亚纲 Hoplocarida 口足目 Stomatopoda 虾蛄科 Squillidae *条尾近虾蛄 Anchisquilla fasciata 16 200 PQ672624 猛虾蛄 Harpiosquilla harpax 15 714 AY699271 / Kempella mikado 15 217 PP761318 螳虾蛄 Squilla mantis 15 994 AY639936 / Alima pacifica 15 678 MW867307 脊条褶虾蛄 Lophosquilla costata 15 771 MT276143 瘦拟虾蛄 Squilloides leptosquilla 16 376 KR095170 口虾蛄 Oratosquilla oratoria 15 783 GQ292769 指虾蛄科 Gonodactylidae 螳螂虾 Neogonodactylus oerstedii 16 327 MW867303 小虾蛄科 Nannosquillidae / Coronis scolopendra 16 201 PP761317 仿虾蛄科 Parasquillidae / Faughnia profunda 14 979 PP761314 齿指虾蛄科 Odontodactylidae 哈瓦那齿指虾蛄 Odontodactylus havanensis 16 035 MW867300 原虾蛄科 Protosquillidae 东方裂虾蛄 Chorisquilla orientalis 15 880 MT672286 琴虾蛄科 Lysiosquillidae 斑琴虾蛄 Lysiosquilla maculata 16 325 DQ191683 真软甲亚纲 Eumalacostraca 十足目 Decapoda 拟鳌虾科 Parastacidae 双齿螯虾 Cherax bicarinatus 15 890 OQ955828 关公蟹科 Dorippidae 颗粒拟关公蟹 Paradorippe granulata 15 084 PQ645161 日本平家蟹 Heikeopsis japonica 15 979 OQ434093 沙蟹科 Leucosiidae 圆十一刺栗壳蟹 Arcania novemspinosa 15 713 PP405211 / Myra affinis 15 349 MW192449 / Pyrhila pisum 15 516 KU343210 溪蟹科 Potamidae 将乐龙溪蟹 Longpotamon jianglense 17 622 OR771088 / Tenuipotamon xinpingense 17 814 OR497828 鳃刺华石蟹 Sinolapotamon anacoluthon 14 923 PP999690 娄底华溪蟹 Longpotamon loudiense 18 544 OQ376288 无鞭黔桂溪蟹 Qianguimon aflagellum 16 929 OQ612632 阔螯华南溪蟹 Huananpotamon koatenense 15 528 OQ091257 细肢非拟溪蟹 Aparapotamon gracilipedum 17 969 OP526650 长臂虾科 Palaemonidae 佩林氏螯虾 Palaemon peringueyi 15 923 PQ474315 罗氏沼虾 Macrobrachium rosenbergii 15 766 PQ213808 寄居蟹科 Paguridae 拉氏寄居蟹 Pagurus rathbuni 16 466 OR523820 石蟹科 Lithodidae 无刺窄颚蟹 Oedignathus inermis 16 584 OR523819 / Hapalogaster dentata 16 607 OR523818 梭子蟹科 Portunidae 蓝蟹 Callinectes sapidus 16 263 PQ436349 鼓虾科 Alpheidae 优美鼓虾 Alpheus euphrosyne 15 866 PQ468956 藻虾科 Hippolytidae 古根双鞭虾 Lysmata kuekenthali 17 540 PQ043512 瓷蟹科 Porcellanidae / Pisidia striata 15 357 PQ010714 枪虾科 Rhynchocinetidae / Rhynchocinetes brucei 16 158 OR095174 匙指虾科 Atyidae 网球虾 Atyopsis moluccensis 15 933 OP618117 磷虾目 Euphausiacea 磷虾科 Euphausiidae 南极磷虾 Euphausia superba 18 926 PQ217826 冰磷虾 Euphausia crystallorophias 17 291 OR478165 中华假磷虾 Pseudeuphausia sinica 16 192 MK579299 端足目 Amphipoda 钩虾科 Gammaridae 日本大鳃溞 Gammarus nipponensis 16 429 OR268765 地钩虾科 Caprelloidea 双棘戴奥多溞 Dyopedos bispinis 14 836 PQ037584 山虾目 Anaspidacea 山虾科 Anaspididae / Paranaspides williamsi 17 320 OQ721894 / Anaspides tasmaniae 15 475 OQ721893 / Anaspides swaini 15 514 OQ721883 / Allanaspides hickmani 15 568 OQ721881 / Allanaspides helonomus 15 309 OQ721879 / Paranaspides lacustris 15 779 OQ721878 注：新测序的条尾近虾蛄用*标记；“/”代表该物种无中文名。 
下载: 导出CSV
表 2 条尾近虾蛄的线粒体全基因组组成
Tab. 2 Organization of the mitogenome of Anchisquilla fasciata
基因 位置 编码链 大小 密码子 反密码子 间隔长度/bp 开始 结束 长度/bp 氨基酸 起始密码子 终止密码子 trnI 0 69 + 69 GAT 2 trnQ 67 135 − 69 TTG −15 trnM 150 218 + 69 CAT −1 nad2 219 1 220 + 1 002 334 ATT TAA − 1 trnW 1 219 1 287 + 69 TCA −5 trnC 1 292 1 358 − 67 GCA −4 trnY 1 362 1 428 − 67 GTA −4 cox1 1 432 2 967 + 1 536 512 CGA TAA − 4 trnL2 2 963 3 029 + 67 TAA −4 cox2 3 033 3 740 + 708 236 ATG TAA − 19 trnK 3 721 3 788 + 68 TTT −4 trnD 3 792 3 859 + 68 GTC −1 atp8 3 860 4 018 + 159 53 ATC TAA − 6 atp6 4 012 4 689 + 678 226 ATG TAA − 0 cox3 4 689 5 477 + 789 263 ATG TAG − 0 trnG 5 477 5 543 + 67 TCC −4 nad3 5 547 5 897 + 351 117 ATT TAA − −1 trnA 5 898 5 962 + 65 TGC −5 trnR 5 967 6 031 + 65 TCG −3 trnN 6 034 6 103 + 70 GTT −1 trnS1 6 104 6 171 + 68 ACT −2 trnE 6 173 6 241 + 69 TTC −1 trnF 6 242 6 308 − 67 GAA −1 nad5 6 309 8 018 − 1 710 570 ATA TAA − −19 trnH 8 037 8 103 − 67 GTG 0 nad4 8 103 9 443 − 1 341 447 ATG TAA − 6 nad4l 9 437 9 736 − 300 100 ATG TAA − −3 trnT 9 739 9 807 + 69 TGT −1 trnP 9 808 9 873 − 66 TGG −57 nad6 9 930 10 433 + 504 168 ATT TAA − 37 cob 10 396 11 532 + 1 137 379 ATG TAA − 0 trnS2 11 532 11 601 + 70 TGA −32 nad1 11 633 12 571 − 939 313 ATG TAA − −1 trnL1 12 572 12 636 − 65 TAG 39 rrnL 12 597 13 987 − 1 391 − −2 trnV 13 989 14 059 − 71 TAC 1 rrnS 14 058 14 896 − 839 − 0
下载: 导出CSV
表 3 条尾近虾蛄线粒体基因组碱基组成比较
Tab. 3 Base content in the mitogenome of Anchisquilla fasciata
基因 A含量/% T含量/% C含量/% G含量/% （A + T）含量/% （G + C）含量/% AT-skew GC-skew mito 35.42 33.31 18.44 12.83 68.73 31.27 0.0307 − 0.1794 cox1 26.7 35.9 19.6 17.8 62.6 37.4 − 0.1470 − 0.0481 cox2 31.4 34.5 16.9 17.2 65.9 34.1 − 0.0470 0.0088 atp8 37.1 38.4 17.6 6.9 75.5 24.5 − 0.0172 − 0.4367 atp6 29.4 36.7 21.5 12.4 66.1 33.9 − 0.1104 − 0.2684 nad5 26.9 41.8 11.6 19.7 68.7 31.3 − 0.2169 0.2588 nad4 25 43.9 9.6 21.5 68.9 31.1 − 0.2743 0.3826 nad4l 23.3 44 11 21.7 67.3 32.7 − 0.3076 0.3272 cob 26.6 36.9 20.2 16.3 63.5 36.5 − 0.1622 − 0.1068 nad6 33.3 41.1 16.1 9.5 74.4 25.6 − 0.1048 − 0.2578 nad1 22.9 43.3 12.1 21.6 66.2 33.7 − 0.3082 0.2819 cox3 27.6 34.3 20.3 17.7 61.9 38 − 0.1082 − 0.0684 nad3 29.6 38.7 17.7 14 68.3 31.7 − 0.1332 − 0.1167 nad2 28.7 38 20.7 12.6 66.7 33.3 − 0.1394 − 0.2432
下载: 导出CSV
-
[1] 王春琳, 徐善良, 梅文骧, 等. 口虾蛄的生物学基本特征[J]. 浙江水产学院学报, 1996, 17(1): 60−62.Wang Chunlin, Xu Shanliang, Mei Wenxiang, et al. A biological basic character of the Oratosquilla oratoria[J]. Journal of Zhejiang College of Fisheries, 1996, 17(1): 60−62. [2] 魏崇德. 浙江动物志·甲壳类[M]. 杭州: 浙江科学技术出版社, 1991.Wei Chongde. Fauna of Zhejiang: Crustacea[M]. Hangzhou: Zhejiang Science and Technology Press, 1991. [3] 任中杰. 全长转录组揭示口虾蛄复眼识别圆偏振光的分子特征[D]. 烟台: 烟台大学, 2024.Ren Zhongjie. Full-length transcriptome reveals the molecular characteristic of the compound eye of Oratosquilla oratoria in recognition of circularly polarization light[D]. Yantai: Yantai University, 2024. [4] 杜欣蔚. 中国东部近海口虾蛄群体遗传多样性研究[D]. 舟山: 浙江海洋大学, 2016.Du Xinwei. Genetic population genetic variation of Oratosquilla oratoria in eastern coastal waters of China[D]. Zhoushan: Zhejiang Ocean University, 2016. [5] 隋宥珍, 刘连为, 徐开达, 等. 基于线粒体Cytb基因的口虾蛄种群遗传结构研究[J]. 大连海洋大学学报, 2019, 34(3): 355−361.Sui Youzhen, Liu Lianwei, Xu Kaida, et al. Population genetic structure of mantis shrimp Oratosquilla oratoria based on the partial mitochondrial DNA cytochrome b gene[J]. Journal of Dalian Ocean University, 2019, 34(3): 355−361. [6] 沙忠利, 王永良, 程娇. 基于线粒体COI序列的DNA条形码在中国海口足类物种鉴定中的应用分析[J]. 中国水产科学, 2018, 25(4): 858−866. doi: 10.3724/SP.J.1118.2018.17338Sha Zhongli, Wang Yongliang, Cheng Jiao. Application of mitochondrial COI-based DNA barcoding for the identification of stomatopod species (Crustacea, Stomatopoda) in the China seas[J]. Journal of Fishery Sciences of China, 2018, 25(4): 858−866. doi: 10.3724/SP.J.1118.2018.17338 [7] Hamano T, Matsuura S. Egg laying and egg mass nursing behaviour in the Japanese mantis shrimp[J]. Nippon Suisan Gakkaishi, 1984, 50(12): 1969−1973. doi: 10.2331/suisan.50.1969 [8] Hamano T, Matsuura S. Egg size, duration of incubation, and larval development of the Japanese mantis shrimp in the laboratory[J]. Nippon Suisan Gakkaishi, 1987, 53(1): 23−39. doi: 10.2331/suisan.53.23 [9] Hamano T. Mating behavior of Oratosquilla oratoria (De Haan, 1844) (Crustacea: stomatopoda)[J]. Journal of Crustacean Biology, 1988, 8(2): 239−244. doi: 10.2307/1548315 [10] Hamano T, Matsuura S. Food habits of the Japanese mantis shrimp in the benthic community of Hakata Bay[J]. Nippon Suisan Gakkaishi, 1986, 52(5): 787−794. doi: 10.2331/suisan.52.787 [11] Hamano T. Growth of the stomatopod crustacean Oratosquilla oratoria in Hakata Bay[J]. Nippon Suisan Gakkaishi, 1990, 56(9): 1529. doi: 10.2331/suisan.56.1529 [12] Manning R B. Stomatopoda from the collection of his majesty the emperor of Japan[J]. Crustaceana, 1965, 9(3): 249−262. doi: 10.1163/156854065X00037 [13] Manning R B. A revision of the family Squillidae (Crustacea, Stomatopoda), with the description of eight new genera[J]. Bulletin of marine Science, 1968, 18(1): 105−142. [14] Manning R B. Stomatopod Crustacea from Madagascar[J]. Proceedings of the United States National Museum, 1968, 124: 1−6. [15] Manning R B. Stomatopod crustacea of vietnam: the legacy of raoul Serène[J]. Crustacean Research, 1995, 1995(4): 1−339. [16] Manning R B. Keys to the species of Oratosquilla (Crustacea: stomatopoda), with descriptions of two new species[J]. Smithsonian Contributions to Zoology, 1971, 71: 1−16. [17] Manning R B. Further observations on Oratosquilla, with accounts of two new genera and nine new species (Crustacea: stomatopoda: squillidae)[J]. Smithsonian Contributions to Zoology, 1978, 272: 1−44. [18] Moosa K M. Marine biodiversity of the South China Sea: a checklist of stomatopod Crustacea[J]. The Raffles Bulletin of Zoology, 2000(S8): 405−457. [19] Martin J W, Davis G E. An Updated Classification of the recent Crustacea[M]. Los Angeles, Calif: Natural History Museum of Los Angeles County Los Angeles, 2001. [20] Ahyong S T. Phylogenetic analysis of the Squilloidea (Crustacea: Stomatopoda)[J]. Invertebrate Systematics, 2005, 19(3): 189−208. doi: 10.1071/IS04037 [21] Kodama K, Yamakawa T, Shimizu T, et al. Age estimation of the wild population of Japanese mantis shrimp Oratosquilla oratoria (Crustacea: stomatopoda) in Tokyo Bay, Japan, using lipofuscin as an age marker[J]. Fisheries Science, 2005, 71(1): 141−150. doi: 10.1111/j.1444-2906.2005.00941.x [22] Ahyong S T. Phylogenetic analysis of the Stomatopoda (Malacostraca)[J]. Journal of Crustacean Biology, 1997, 17(4): 695−715. doi: 10.1163/193724097X00134 [23] Audo D, Kawai T, Letenneur C, et al. Crayfishes from the Jehol biota[J]. Geodiversitas, 2023, 45(24): 689−719. [24] 宋晓阳. 口虾蛄池塘育苗及立体养殖技术[J]. 中国水产, 2023(3): 77−78.Song Xiaoyang. Pond seed production and integrated aquaculture techniques for Oratosquilla oratoria[J]. China Fisheries, 2023(3): 77−78. [25] de Haan W. Crustacea. Fauna japonica, sive, Descriptio animalium, quae in itinere per Japoniam, jussu et auspiciis, superiorum, qui summum in India Batava imperium tenent, suscepto, annis 1823−1830[M]. Lugduni Batavorum: Apud Auctorem, 1833−1850. [26] Schram F R. Checklist of marine biota of China Seas[J]. Journal of Crustacean Biology, 2010, 30(2): 339−339. doi: 10.1651/09-3228.1 [27] Aljanabi S M, Martinez I. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques[J]. Nucleic Acids Research, 1997, 25(22): 4692−4693. doi: 10.1093/nar/25.22.4692 [28] Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads[J]. EMBnet Journal, 2011, 17(1): 10−12. doi: 10.14806/ej.17.1.200 [29] 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 [30] 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 [31] Koga C, Rouse G W. Mitogenomics and the phylogeny of mantis shrimps (Crustacea: Stomatopoda)[J]. Diversity, 2021, 13(12): 647. doi: 10.3390/d13120647 [32] Xia Xuhua. DAMBE7: new and improved tools for data analysis in molecular biology and evolution[J]. Molecular Biology and Evolution, 2018, 35(6): 1550−1552. doi: 10.1093/molbev/msy073 [33] Hassanin A, Léger N, Deutsch J. Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of Metazoa, and consequences for phylogenetic inferences[J]. Systematic Biology, 2005, 54(2): 277−298. doi: 10.1080/10635150590947843 [34] Kumar S, Stecher G, Li M, et al. MEGA X: molecular evolutionary genetics analysis across computing platforms[J]. Molecular Biology and Evolution, 2018, 35(6): 1547−1549. doi: 10.1093/molbev/msy096 [35] 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 [36] Zhang Dong, Gao Fangluan, Jakovlić I, et al. PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies[J]. Molecular Ecology Resources, 2020, 20(1): 348−355. doi: 10.1111/1755-0998.13096 [37] 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 [38] Katoh K, Standley D M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability[J]. Molecular Biology and Evolution, 2013, 30(4): 772−780. doi: 10.1093/molbev/mst010 [39] Ranwez V, Douzery E J P, Cambon C, et al. MACSE v2: toolkit for the alignment of coding sequences accounting for frameshifts and stop codons[J]. Molecular Biology and Evolution, 2018, 35(10): 2582−2584. doi: 10.1093/molbev/msy159 [40] Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments[J]. Systematic Biology, 2007, 56(4): 564−577. doi: 10.1080/10635150701472164 [41] Kalyaanamoorthy S, Minh B Q, Wong T K F, et al. ModelFinder: fast model selection for accurate phylogenetic estimates[J]. Nature Methods, 2017, 14(6): 587−589. doi: 10.1038/nmeth.4285 [42] Ronquist F, Teslenko M, Van Der Mark P, et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space[J]. Systematic Biology, 2012, 61(3): 539−542. doi: 10.1093/sysbio/sys029 [43] Nguyen L T, Schmidt H A, Von Haeseler A, et al. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies[J]. Molecular Biology and Evolution, 2015, 32(1): 268−274. doi: 10.1093/molbev/msu300 [44] Guindon S, Dufayard J F, Lefort V, et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0[J]. Systematic Biology, 2010, 59(3): 307−321. doi: 10.1093/sysbio/syq010 [45] Xie Jianmin, Chen Yuerong, Cai Guanjing, et al. Tree visualization by one table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees[J]. Nucleic Acids Research, 2023, 51(W1): W587−W592. doi: 10.1093/nar/gkad359 [46] Bouckaert R, Vaughan T G, Barido-Sottani J, et al. BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis[J]. PLoS Computational Biology, 2019, 15(4): e1006650. doi: 10.1371/journal.pcbi.1006650 [47] 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 [48] Lowe T M, Chan P P. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes[J]. Nucleic Acids Research, 2016, 44(W1): W54−W57. doi: 10.1093/nar/gkw413 [49] Chan P P, Lowe T M. tRNAscan-SE: searching for tRNA genes in genomic sequences[J]. Methods in Molecular Biology, 2019, 1962: 1−14. [50] 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 [51] Liu Yuan, Cui Zhaoxia. The complete mitochondrial genome of the mantid shrimp Oratosquilla oratoria (Crustacea: malacostraca: stomatopoda): novel non-coding regions features and phylogenetic implications of the Stomatopoda[J]. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 2010, 5(3): 190−198. doi: 10.1016/j.cbd.2010.04.001 [52] Boore J L, Lavrov D V, Brown W M. Gene translocation links insects and crustaceans[J]. Nature, 1998, 392(6677): 667−668. doi: 10.1038/33577 [53] Kilpert F, Podsiadlowski L. The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel gene order and unusual control region features[J]. BMC Genomics, 2006, 7: 241. doi: 10.1186/1471-2164-7-241 [54] Kilpert F, Held C, Podsiadlowski L. Multiple rearrangements in mitochondrial genomes of Isopoda and phylogenetic implications[J]. Molecular Phylogenetics and Evolution, 2012, 64(1): 106−117. doi: 10.1016/j.ympev.2012.03.013 [55] Wang Zhengfei, Zheng Yuqiang, Zhao Xinyue, et al. Molecular phylogeny and evolution of the Tuerkayana (Decapoda: Brachyura: Gecarcinidae) genus based on whole mitochondrial genome sequences[J]. Biology, 2023, 12(7): 974. doi: 10.3390/biology12070974 [56] Sun Hongying, Zhou Kaiya, Song Daxiang. Mitochondrial genome of the Chinese mitten crab Eriocheir japonica sinenesis (Brachyura: Thoracotremata: Grapsoidea) reveals a novel gene order and two target regions of gene rearrangements[J]. Gene, 2005, 349: 207−217. doi: 10.1016/j.gene.2004.12.036 [57] 李玥. 亚洲特有种卵圆扁蝼蛄虾鳃虱 (等足目: 寄生下目: 鳃虱科) 全线粒体基因组序列的分析研究[D]. 太原: 山西师范大学, 2017.Li Yue. The study of the complete mitochondrial genome of the Asian endemic species Gyge ovalis (Shiino, 1939) (Isopoda: Epicaridea: Bopyridae)[D]. Taiyuan: Shanxi Normal University, 2017. [58] 张瑞. 基于线粒体基因组数据探究潮虫亚目(甲壳动物亚门: 等足目)的系统演化关系[D]. 太原: 山西师范大学, 2020.Zhang Rui. Phylogeny of subfamily Oniscidea (Crustacea: Isopoda) based on the mitochondrial genome[D]. Taiyuan: Shanxi Normal University, 2020. [59] Zhang Daizhen, Sun Xiaoli, Chen Lianfu, et al. The chromosome-level genome provides insights into the adaptive evolution of the visual system in Oratosquilla oratoria[J]. BMC Biology, 2025, 23(1): 38. doi: 10.1186/s12915-025-02146-6 [60] Xu Tao, Bravo H, Van Der Meij S E T. Phylomitogenomics elucidates the evolution of symbiosis in Thoracotremata (Decapoda: Cryptochiridae, Pinnotheridae, Varunidae)[J]. PeerJ, 2023, 11: e16217. doi: 10.7717/peerj.16217 [61] Wu Ruiwen, Guo Rongxiu, Xi Qianqian, et al. Phylogenetic position of Bopyroides hippolytes, with comments on the rearrangement of the mitochondrial genome in isopods (Isopoda: Epicaridea: Bopyridae)[J]. BMC Genomics, 2022, 23(1): 253. doi: 10.1186/s12864-022-08513-9 [62] Shen Xin, Tian Mei, Yan Binlun, et al. Phylomitogenomics of Malacostraca (Arthropoda: Crustacea)[J]. Acta Oceanologica Sinica, 2015, 34(2): 84−92. doi: 10.1007/s13131-015-0583-1 [63] Zhang Yazhou, Bi Yuanxin, Feng Meiping. The complete mitochondrial genome of Lophosquillia costata (Malacostraca: Stomatopoda) from China and phylogeny of stomatopods[J]. Mitochondrial DNA Part B, 2020, 5(3): 2495−2497. doi: 10.1080/23802359.2020.1780170 [64] Kang H E, Kim J N, Yoon T H, et al. Total mitochondrial genome of mantis shrimp, Squilloides leptosquilla (Brooks, 1886) (Crustacea: Stomatopoda: Squillidae) in Korean waters[J]. Mitochondrial DNA Part A, 2015, 27(4): 2842−2843. [65] Ahyong S T, Jarman S N. Stomatopod interrelationships: preliminary results based on analysis of three molecular loci[J]. Arthropod Systematics & Phylogeny, 2009, 67(1): 91−98. [66] Tang R W K, Yau C, Ng W C. Identification of stomatopod larvae (Crustacea: Stomatopoda) from Hong Kong waters using DNA barcodes[J]. Molecular Ecology Resources, 2010, 10(3): 439−448. doi: 10.1111/j.1755-0998.2009.02794.x [67] Harling C. Reexamination of eye design in the classification of stomatopod crustaceans[J]. Journal of Crustacean Biology, 2000, 20(1): 172−185. doi: 10.1163/20021975-99990026 [68] Ahyong S T, Harling C. The phylogeny of the stomatopod Crustacea[J]. Australian Journal of Zoology, 2000, 48(6): 607−642. doi: 10.1071/ZO00042 [69] Porter M L, Zhang Yunfei, Desai S, et al. Evolution of anatomical and physiological specialization in the compound eyes of stomatopod crustaceans[J]. Journal of Experimental Biology, 2010, 213(20): 3473−3486. doi: 10.1242/jeb.046508 [70] Barber P H, Erdmann M V. Molecular systematics of the Gonodactylidae (Stomatopoda) using mitochondrial cytochrome oxidase C (subunit 1) DNA sequence data[J]. Journal of Crustacean Biology, 2000, 20(5): 20−36. doi: 10.1163/1937240X-90000004 [71] Cheng Jiao, Chan T Y, Zhang Nan, et al. Mitochondrial phylogenomics reveals insights into taxonomy and evolution of Penaeoidea (Crustacea: Decapoda)[J]. Zoologica Scripta, 2018, 47(5): 582−594. doi: 10.1111/zsc.12298 [72] Bracken H D, De Grave S, Felder D L, et al. Phylogeny of the infraorder Caridea based on mitochondrial and nuclear genes (Crustacea: Decapoda)[M]//Martin J W, Crandall K A, Felder D L. Decapod Crustacean Phylogenetics. Boca Raton: CRC Press, 2009, 18: 274-298. [73] 张阳. 口虾蛄不同地理群体线粒体DNA控制区和转录组变异研究[D]. 舟山: 浙江海洋大学, 2018.Zhang Yang. Genetic variation analysis of different population mantis shrimp Oratosquilla oratoria based on mitochondrial DNA control region and transcriptome[D]. Zhoushan: Zhejiang Ocean University, 2018. [74] Jakovlić I, Zou Hong, Chen Jianhai, et al. Slow crabs - fast genomes: locomotory capacity predicts skew magnitude in crustacean mitogenomes[J]. Molecular Ecology, 2021, 30(21): 5488−5502. doi: 10.1111/mec.16138 [75] Hof C H J. Fossil stomatopods (Crustacea: Malacostraca) and their phylogenetic impact[J]. Journal of Natural History, 1998, 32(10/11): 1567−1576. [76] Schram F R. Upper Pennsylvanian arthropods from black shales of Iowa and Nebraska[J]. Journal of Paleontology, 1984, 58(1): 197−209. [77] 宋海军, 童金南. 二叠纪-三叠纪之交生物大灭绝与残存[J]. 地球科学, 2016, 41(6): 901−918.Song Haijun, Tong Jinnan. Mass extinction and survival during the Permian-Triassic Crisis[J]. Earth Science, 2016, 41(6): 901−918. [78] Guo Zhen, Flannery-Sutherland J T, Benton M J, et al. Bayesian analyses indicate bivalves did not drive the downfall of brachiopods following the Permian-Triassic mass extinction[J]. Nature Communications, 2023, 14(1): 5566. doi: 10.1038/s41467-023-41358-8 [79] Benton M J, Wu Feixiang. Triassic revolution[J]. Frontiers in Earth Science, 2022, 10: 899541. doi: 10.3389/feart.2022.899541 [80] Van Valen L M. A resetting of Phanerozoic community evolution[J]. Nature, 1984, 307(5946): 50−52. doi: 10.1038/307050a0 [81] 张武文. 地学概论[M]. 北京: 中国林业出版社, 2000.Zhang Wuwen. Introduction to Geological Sciences[M]. Beijing: China Forestry Publishing House, 2000. [82] 列昂捷夫O K, 朱大奎. 关于中生代—新生代世界洋面的变化[J]. 海洋通报, 1974(1): 70−77.Leontev O K, Zhu Dakui. On the changes of the world ocean surface during the Mesozoic-Cenozoic[J]. Marine Science Bulletin, 1974(1): 70−77. [83] 姜建军. 古生代、中生代海平面变化研究状况[J]. 海洋学报, 1991, 13(5): 715−720.Jiang Jianjun. Research status of sea-level changes during the Paleozoic and Mesozoic Eras[J]. HaiYang Xuebao, 1991, 13(5): 715−720. [84] 李枢强, 赵喆, 侯仲娥. 特提斯海变迁对全球动物分布的影响[J]. 河北大学学报(自然科学版), 2021, 41(5): 551−564.Li Shuqiang, Zhao Zhe, Hou Zhong'e. Tethyan changes shaped global animal distribution[J]. Journal of Hebei University (Natural Science Edition), 2021, 41(5): 551−564. [85] Dames W. Ueber einige crustaceen aus den kreideablagerungen des libanon[J]. Zeitschrift der Deutschen Geologischen Gesellschaft, 1886, 38(3): 551−575. [86] Van Der Wal C, Ahyong S T, Adams M W D, et al. Total-evidence phylogenetic analysis resolves the evolutionary timescale of mantis shrimps (Stomatopoda) and provides insights into their molecular and morphological evolutionary rates[J]. Molecular Phylogenetics and Evolution, 2025, 207: 108346. doi: 10.1016/j.ympev.2025.108346 [87] Sun Yuman, Liu Wanting, Chen Jian, et al. Sequence comparison of the mitochondrial genomes of five caridean shrimps of the infraorder Caridea: phylogenetic implications and divergence time estimation[J]. BMC Genomics, 2024, 25(1): 968. doi: 10.1186/s12864-024-10775-4 [88] 鹿博. 西太平洋和印度洋海底热液口十足目系统发育及其演化关系的研究[D]. 杭州: 浙江大学, 2013.Lu Bo. Phylogeny and evolution of hydrothermal vent decapods in West Pacific and Indian Oceans[D]. Hangzhou: Zhejiang University, 2013. -
图(7) / 表(3)
计量
- 文章访问数: 112
- HTML全文浏览量: 77
- PDF下载量: 8
- 被引次数: 0
