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Descriptive study of the mitogenome of the diamondback squid ( Thysanoteuthis rhombus Troschel, 1857) and the evolution of mitogenome arrangement in oceanic squids

2021; Wiley; Volume: 59; Issue: 5 Linguagem: Inglês

10.1111/jzs.12478

1439-0469

Yan Tang, Xiaoying Zhang, Yuanyuan Ma, Xiaodong Zheng,

Chemical synthesis and alkaloids

Journal of Zoological Systematics and Evolutionary ResearchVolume 59, Issue 5 p. 981-991 SHORT COMMUNICATION Descriptive study of the mitogenome of the diamondback squid (Thysanoteuthis rhombus Troschel, 1857) and the evolution of mitogenome arrangement in oceanic squids Yan Tang, orcid.org/0000-0003-0564-7279 Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China Key Laboratory of Mariculture, Ocean University of China, Qingdao, ChinaSearch for more papers by this authorXiaoying Zhang, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China Key Laboratory of Mariculture, Ocean University of China, Qingdao, ChinaSearch for more papers by this authorYuanyuan Ma, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China Key Laboratory of Mariculture, Ocean University of China, Qingdao, ChinaSearch for more papers by this authorXiaodong Zheng, Corresponding Author xdzheng@ouc.edu.cn orcid.org/0000-0003-4052-2324 Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China Key Laboratory of Mariculture, Ocean University of China, Qingdao, China Correspondence Xiaodong Zheng, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China. Email: xdzheng@ouc.edu.cnSearch for more papers by this author Yan Tang, orcid.org/0000-0003-0564-7279 Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China Key Laboratory of Mariculture, Ocean University of China, Qingdao, ChinaSearch for more papers by this authorXiaoying Zhang, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China Key Laboratory of Mariculture, Ocean University of China, Qingdao, ChinaSearch for more papers by this authorYuanyuan Ma, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China Key Laboratory of Mariculture, Ocean University of China, Qingdao, ChinaSearch for more papers by this authorXiaodong Zheng, Corresponding Author xdzheng@ouc.edu.cn orcid.org/0000-0003-4052-2324 Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China Key Laboratory of Mariculture, Ocean University of China, Qingdao, China Correspondence Xiaodong Zheng, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China. Email: xdzheng@ouc.edu.cnSearch for more papers by this author First published: 11 May 2021 https://doi.org/10.1111/jzs.12478 Contributing authors Yan Tang (tangyangxmz@163.com), Xiaoying Zhang (zxying2012@126.com), Yuanyuan Ma (myycsd@hotmail.com) Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinked InRedditWechat Abstracten The diamondback squid, Thysanoteuthis rhombus, is the only currently accepted species within the family Thysanoteuthidae. In this study, the mitogenome of T. rhombus was sequenced using the Illumina NovaSeq 6000 platform. Features of the mitogenome were detected, and phylogenetic relationships among the Cephalopoda were reconstructed. Our results indicated that the mitogenome of T. rhombus had six duplicated genes and long non-coding regions. The gene arrangement of T. rhombus was consistent with that of species belonging to Ommastrephidae. Moreover, the most gene rearrangement patterns were found in Oegopsida and Octopoda, whereas only one pattern was detected in Sepioidea. The mitogenome of Myopsida was highly rearranged among the four taxa. The phylogenetic relationship of T. rhombus + (((Dosidicus gigas + Sthenoteuthis oualaniensis) + Ommastrephes bartramii) + (Illex argentines + Todarodes pacificus)) was highly supported by both mitochondrial gene rearrangement analyses and all the phylogenetic analyses. Our study indicated that both gene sequences and arrangements may provide more information on the phylogeny and evolution of diverse mitogenomes in Cephalopoda and contribute to resolving contentious interclass relationships in the future. 抽象的zh 菱鳍鱿鱼 (Thysanoteuthis rhombus) 是目前菱鳍鱿科唯一的物种。本研究利用Illumina NovaSeq 6000平台对菱形鱿鱼的线粒体全基因 组进行了测序,并重建了头足纲的系统发育关系。结果表明,菱鳍鱿鱼的线粒体全基因组有6个重复的基因和长非编码区。菱鳍鱿鱼的基 因排列与柔鱼科物种的基因排列一致。此外,基因重排模式在开眼目和八腕目最多,而在乌贼目中仅发现一种模式。在四大类群中,闭 眼亚目的线粒体基因组高度重排。线粒体基因重排分析和所有的系统发育分析都高度支持了T. rhombus +((Dosidicus gigas + Sthenoteuthis oualaniensis) + Ommastrephes bartramii)) 的系统发育关系。我们的研究表明,无论是基因序列还是排列方式,都 可以为头足类不同线粒体基因组的系统发育和进化提供更多的信息,有助于解决未来有争议的类间关系. Supporting Information Filename Description jzs12478-sup-0001-Supinfo.pdfPDF document, 2.4 MB Figure S1. Predicted motif sequence alignments of long non-coding regions. Figure S2. Rearrangement score (RS) for each species and rearrangement frequency (RF) for each gene among Coleoidea. Figure S3. Bayesian Inference phylogenetic tree of Cephalopoda constructed using amino acids of 13 protein-coding genes (PCGs). Figure S4. Maximum Likelihood phylogenetic tree of Cephalopoda constructed using amino acids of 13 protein-coding genes (PCGs). Figure S5. Evolutionary history of gene rearrangements in Cephalopoda inferred using TreeREx based on data matrix 1. Figure S6. Evolutionary history of gene rearrangements in Oegopsida and Bathyteuthis abyssicola inferred using TreeREx based on data matrix 2. Table S1. Primers information used for amplification of mitogenome of Thysanoteuthis rhombus. Table S2. The list of gene names and abbreviations used in our study. Table S3. The information of cephalopods mitogenome used in constructing phylogenetic tree. Table S4. Best partition scheme and substitution models for the Maximum Likelihood in IQ-TREE and Bayesian Inference in MrBayes. Table S5. Organization of the mitochondrial genome of Thysanoteuthis rhombus. Table S6. The nucleotide composition and skew analysis of Thysanoteuthis rhombus. Table S7. Codon and relative synonymous codon usage (RSCU) of 13 protein-coding genes (PCGs) in the mitogenome of Thysanoteuthis rhombus. jzs12478-sup-0002-AlignmentS1.fasapplication/fas, 638.3 KB Alignment S1. Nucleotide sequence alignment of 13 PCGs and 2 rRNA genes used in this study. jzs12478-sup-0003-AlignmentS2.fasapplication/fas, 175.4 KB Alignment S2. Amino acid sequence alignment of 13 PCGs used in this study. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article. Volume59, Issue5July 2021Pages 981-991 RelatedInformation