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The mitogenome totals 16,621 bp and encodes 37 vertebrate mitochondrial genes: 13 protein-coding genes, 22 tRNAs, two rRNAs, and a non-coding D-loop. Codon usage, termination patterns, and A+T bias (54.1%) are reported. Phylogenetic analyses using 44 Cichlidae mitogenomes recover key monophyletic tribes while resolving Astronotinae as polyphyletic, clarifying B. cupido’s evolutionary position and informing cichlid phylogeny.",{"@graph":69,"@context":123},[70,84,106],{"@type":71,"itemListElement":72},"BreadcrumbList",[73,77,79,82],{"item":74,"name":75,"@type":76,"position":8},"https://docshare.wps.com","Home","ListItem",{"item":78,"name":9,"@type":76,"position":14},"https://docshare.wps.com/document/",{"item":80,"name":40,"@type":76,"position":81},"https://docshare.wps.com/document/research-report/",3,{"item":83,"name":65,"@type":76,"position":19},"https://docshare.wps.com/document/the-first-complete-mitochondrial-genome-of-biotodoma-cupido-cichiliformes-cichlidae-and-its-phylogeny/156494/",{"url":83,"name":65,"@type":85,"image":86,"author":91,"headline":65,"publisher":94,"fileFormat":97,"inLanguage":63,"description":67,"dateModified":98,"datePublished":99,"encodingFormat":97,"isAccessibleForFree":100,"interactionStatistic":101},"DigitalDocument",{"url":87,"@type":88,"width":89,"height":90},"https://docshare.wps.com/thumbnails/the-first-complete-mitochondrial-genome-of-biotodoma-cupido-cichiliformes-cichlidae-and-its-phylogeny/156494.png","ImageObject",300,407,{"name":92,"@type":93},"Evangeline","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-10-22","2026-08-28",true,{"@type":102,"interactionType":103,"userInteractionCount":105},"InteractionCounter",{"@type":104},"ViewAction",12,{"@type":107,"mainEntity":108},"FAQPage",[109,115,119],{"name":110,"@type":111,"acceptedAnswer":112},"What is the main contribution of this study about Biotodoma cupido?","Question",{"text":113,"@type":114},"The study reports the first complete mitochondrial genome of Biotodoma cupido and uses it to infer its phylogenetic position within New World cichlids.","Answer",{"name":116,"@type":111,"acceptedAnswer":117},"How long is the complete mitochondrial genome and what genes does it contain?",{"text":118,"@type":114},"The mitochondrial genome is 16,621 bp long and encodes 37 genes: 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one non-coding control region (D-loop).",{"name":120,"@type":111,"acceptedAnswer":121},"Which phylogenetic results clarify the evolutionary relationships among cichlid tribes?",{"text":122,"@type":114},"Maximum likelihood and Bayesian trees consistently recover Geophaginae, Cichlasomatinae, and Cichlinae as monophyletic, while Astronotinae is recovered as polyphyletic.","https://schema.org",{"og:url":83,"og:type":125,"og:title":65,"og:site_name":95,"og:description":67},"article",{"robots":127,"canonical":83},"index,follow",{"doc_id":129,"site_id":62},156494,1787960956,{"code":4,"msg":5,"data":132},{"doc_id":129,"user_id":133,"nickname":92,"user_avatar":134,"doc_module":4,"category_id":39,"category_name":40,"doc_title":65,"doc_description":67,"doc_content":135,"file_id":136,"file_url":137,"file_type":138,"file_size":139,"view_count":105,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":105,"language":140,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":141,"faqs":142,"seo_title":143,"seo_description":67,"update_tm":130,"read_time":41,"preview_page_count":4},13056703019662,"https://ap-avatar.wpscdn.com/avatar/be000253a8e92610077?_k=1778726343310543188","TYPE Original Research PUBLISHED 29 August 2025  \nDOI 10.3389/fgene.2025.1623517  \nOPEN ACCESS  \nEDITED BY  \nSuxu Tan,  \nQingdao University, China  \nREVIEWED BY  \nOmar Mejía,  \nNational Polytechnic Institute, Mexico Nélida Rodríguez-Osorio, Universidad de la República, Uruguay  \n*CORRESPONDENCE  \nCheng-He Sun,  \n [sunchenghe@njfu.edu.cn](sunchenghe@njfu.edu.cn)  \nRECEIVED 06 May 2025  \nACCEPTED 15 August 2025  \nPUBLISHED 29 August 2025  \nCITATION  \nZhang X, Jia S-X and Sun C-H (2025) The first complete mitochondrial genome of Biotodoma cupido (Cichiliformes: Cichlidae) and its phylogeny.  \nFront. Genet. 16:1623517 .  \ndoi: 10.3389/fgene.2025.1623517  \nCOPYRIGHT  \n© 2025 Zhang, Jia and Sun. This is an openaccess article distributed under the terms of the Creative Commons Attribution License (CC BY) . The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.  \nThe first complete mitochondrial genome of Biotodoma cupido (Cichiliformes: Cichlidae) and its phylogeny  \nXiaoli Zhang 1, Shuang-Xi Jia 2 and Cheng-He Sun 2*  \n1College of Environment and Life Health, Anhui Vocational and Technical College, Hefei, China, 2College of Life Sciences, Nanjing Forestry University, Nanjing, China  \nTraditional classifications of New World cichlids have been subject to persistent controversy. Within the genus Biotodoma, only two species are currently recognized; however, complete mitochondrial sequences for these taxa have remained unavailable. In the present study, we sequenced and characterized the complete mitochondrial genome of Biotodoma cupido. This mitogenome has a total length of 16,621 bp and encodes the standard 37 genes found in vertebrate mitochondria: 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one non-coding control region (D-loop) . Among the PCGs, only Cox1 gene utilizes GTG as its start codon, while the remaining 12 PCGs start with ATG. Observed termination codons included TAA, AGA, TAG, and the incomplete codons TA and T. The overall base composition of the B. cupido mitochondrial sequence exhibits an A + T bias, with a combined A + T content of 54 . 1% . In this study, the high mitogenome similarity observed among several species in this study resulted from interspecific hybridization rather than synonymy or taxonomic misidentification. Maximum likelihood and Bayesian inference evolutionary trees were constructed using mitochondrial genome sequences from 44 Cichlidae species. Phylogenetic analyses consistently recovered the tribes Geophaginae, Cichlasomatinae, and Cichlinae as monophyletic groups. In contrast, the tribe Astronotinae was recovered as polyphyletic. These results clarify the evolutionary position of B. cupido within New World cichlids and will contribute to elucidating the complex phylogenetic relationships among cichlid species.  \nKEYWORDS  \nBiotodoma cupido, cichlidae fish species, hybridization, mitochondrial genome, phylogenetic analysis  \n1 Introduction  \nBiotodoma cupido (Heckel, 1840) belongs to the order Cichliformes and the family Cichlidae. Its distribution encompasses much of the Amazon Basin, extending from the Ucayali River system in Peru eastwards through the Brazilian Amazon to the Tocantins drainage, which flows into the Atlantic Ocean alongside the Amazon Delta. The southern limit of its range appears to be the Río Mamoré in Bolivia, a tributary of the Rio Guaporé, and the northern limit is the Essequibo basin, Guyana (Cichocki, 1977; Morey et al., 2019; Morey et al., 2024). This South American cichlid, reaching approximately 15 cm in length, is valued as an ornamental species. B. cupido exhibits a mild temperament and omnivorous feeding habits, consuming water worms, snails, ","cbCaieBHmQzdt617","https://ap.wps.com/l/cbCaieBHmQzdt617","pdf",2362328,"English","# Introduction\n## Species background and distribution\n## Significance of molecular methods and mtDNA\n## Mitochondrial markers and phylogenetic rationale","[{\"question\":\"What is the main contribution of this study about Biotodoma cupido?\",\"answer\":\"The study reports the first complete mitochondrial genome of Biotodoma cupido and uses it to infer its phylogenetic position within New World cichlids.\"},{\"question\":\"How long is the complete mitochondrial genome and what genes does it contain?\",\"answer\":\"The mitochondrial genome is 16,621 bp long and encodes 37 genes: 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one non-coding control region (D-loop).\"},{\"question\":\"Which phylogenetic results clarify the evolutionary relationships among cichlid tribes?\",\"answer\":\"Maximum likelihood and Bayesian trees consistently recover Geophaginae, Cichlasomatinae, and Cichlinae as monophyletic, while Astronotinae is recovered as polyphyletic.\"}]","The first complete mitochondrial genome of Biotodoma cupido (Cichiliformes: Cichlidae) and its phylogeny | PDF"]