{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,10]],"date-time":"2026-02-10T09:37:53Z","timestamp":1770716273048,"version":"3.49.0"},"reference-count":61,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T00:00:00Z","timestamp":1769817600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002322","name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior\u2014Brazil","doi-asserted-by":"crossref","award":["001"],"award-info":[{"award-number":["001"]}],"id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100003593","name":"CNPq","doi-asserted-by":"publisher","award":["303889\/2022-5"],"award-info":[{"award-number":["303889\/2022-5"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Gen\u00f4mica da Biodiversidade Brasileira (GBB) Project"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Diversity"],"abstract":"<jats:p>The marine fish genus Trachinotus (Carangidae: Trachinotinae) comprises species of considerable economic and ecological importance; however, a significant gap in genomic data has limited the understanding of its evolutionary history and systematics. To address this gap, we determined the complete mitochondrial genomes of two key species, Trachinotus goodei (Palometa) and Trachinotus mookalee (Indian Pompano). The mitogenome of T. goodei was sequenced from genomic DNA and assembled de novo, whereas the T. mookalee mitogenome was assembled by mining publicly available RNA-Seq data, demonstrating a cost-effective approach for expanding genomic resources. The resulting mitogenomes were 16,547 bp and 16,545 bp long, respectively, and both presented conserved gene content (13 protein-coding genes, 22 tRNAs, 2 rRNAs) and organization typical of teleost fishes. Phylogenetic analysis incorporating these new genomes with those of four other Trachinotus species was performed via a concatenated dataset of 13 protein-coding genes. Maximum likelihood and Bayesian inference recovered Trachinotus as a strongly supported monophyletic group. The phylogeny revealed a fundamental and deeply divergent split between three major clades, two comprising species from the western Atlantic and the other containing species from the eastern Atlantic\/Mediterranean\/Indo-Pacific. This robust biogeographic partition provides compelling evidence that allopatric speciation is a primary driver of diversification within the genus.<\/jats:p>","DOI":"10.3390\/d18020088","type":"journal-article","created":{"date-parts":[[2026,2,3]],"date-time":"2026-02-03T10:48:01Z","timestamp":1770115681000},"page":"88","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The Complete Mitogenome of Two Trachinotus Species and a Phylogenetic Analysis of the Pompano Subfamily Trachinotinae"],"prefix":"10.3390","volume":"18","author":[{"given":"Oscar David Albito","family":"Balc\u00e1zar","sequence":"first","affiliation":[{"name":"Laborat\u00f3rio de Evolu\u00e7\u00e3o (LEVO), Instituto de Estudos Costeiro (IECOS), Universidade Federal do Par\u00e1 (UFPA), Campus de Bragan\u00e7a, Bragan\u00e7a 68600-000, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1223-8943","authenticated-orcid":false,"given":"Luan","family":"Rabelo","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Evolu\u00e7\u00e3o (LEVO), Instituto de Estudos Costeiro (IECOS), Universidade Federal do Par\u00e1 (UFPA), Campus de Bragan\u00e7a, Bragan\u00e7a 68600-000, Brazil"},{"name":"Instituto Tecnol\u00f3gico Vale (ITV), Bel\u00e9m 66055-090, Brazil"}]},{"given":"Emile Jeane Silva","family":"Menezes","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Evolu\u00e7\u00e3o (LEVO), Instituto de Estudos Costeiro (IECOS), Universidade Federal do Par\u00e1 (UFPA), Campus de Bragan\u00e7a, Bragan\u00e7a 68600-000, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0264-5780","authenticated-orcid":false,"given":"Tib\u00e9rio Cesar Tortola","family":"Burlamaqui","sequence":"additional","affiliation":[{"name":"Instituto Tecnol\u00f3gico Vale (ITV), Bel\u00e9m 66055-090, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7816-9725","authenticated-orcid":false,"given":"Alexandre","family":"Aleixo","sequence":"additional","affiliation":[{"name":"Instituto Tecnol\u00f3gico Vale (ITV), Bel\u00e9m 66055-090, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3571-5183","authenticated-orcid":false,"given":"Jos\u00e9 Augusto Pires","family":"Bitencourt","sequence":"additional","affiliation":[{"name":"Instituto Tecnol\u00f3gico Vale (ITV), Bel\u00e9m 66055-090, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8898-0311","authenticated-orcid":false,"given":"Grazielle","family":"Gomes","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Gen\u00e9tica Aplicada (LAGA), Instituto de Estudos Costeiro (IECOS), Universidade Federal do Par\u00e1 (UFPA), Campus de Bragan\u00e7a, Bragan\u00e7a 68600-000, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6468-6158","authenticated-orcid":false,"given":"Nils Edvin","family":"Asp Neto","sequence":"additional","affiliation":[{"name":"Instituto de Estudos Costeiro (IECOS), Universidade Federal do Par\u00e1 (UFPA), Campus de Bragan\u00e7a, Bragan\u00e7a 68600-000, Brazil"}]},{"given":"Iracilda","family":"Sampaio","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Evolu\u00e7\u00e3o (LEVO), Instituto de Estudos Costeiro (IECOS), Universidade Federal do Par\u00e1 (UFPA), Campus de Bragan\u00e7a, Bragan\u00e7a 68600-000, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3465-3830","authenticated-orcid":false,"given":"Marcelo","family":"Vallinoto","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Evolu\u00e7\u00e3o (LEVO), Instituto de Estudos Costeiro (IECOS), Universidade Federal do Par\u00e1 (UFPA), Campus de Bragan\u00e7a, Bragan\u00e7a 68600-000, Brazil"},{"name":"CIBIO-InBIO, Centro de Investiga\u00e7\u00e3o em Biodiversidade and Recursos Gen\u00e9ticos, Universidade do Porto, 4485-661 Vair\u00e3o, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,31]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"e13058","DOI":"10.1111\/jeu.13058","article-title":"Ultrastructural and Molecular Characterization of Glugea sp. (Microsporidia), a Parasite of the Red Sea Fish Carangoides bajad (Carangidae)","volume":"71","author":"Aboelhadid","year":"2024","journal-title":"J. Eukaryot. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1111\/jfb.13509","article-title":"Multi-gene Phylogeny of Jacks and Pompanos (Carangidae), Including Placement of Monotypic Vadigo Campogramma glaycos","volume":"92","author":"Damerau","year":"2018","journal-title":"J. Fish Biol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"20230657","DOI":"10.1098\/rspb.2023.0657","article-title":"Widespread Sympatry in a Species-Rich Clade of Marine Fishes (Carangoidei)","volume":"290","author":"Glass","year":"2023","journal-title":"Proc. R. Soc. B Biol. Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1111\/jfb.15596","article-title":"Interdecadal Changes in Ichthyofauna in a Tropical Bay with High Anthropogenic Influences: Functional Stability despite Turnover Predominance","volume":"104","year":"2024","journal-title":"J. Fish Biol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1111\/j.1749-7345.1985.tb00190.x","article-title":"Culture of Fishes of the Genus Trachinotus (Carangidae) in the Western Atlantic: Prospests and Problems","volume":"16","author":"Jory","year":"1985","journal-title":"J. World Maric. Soc."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1080\/00222936208651283","article-title":"The Nomenclature of the European Fishes of the Subfamily Trachinotinae","volume":"5","author":"Wheeler","year":"1962","journal-title":"Ann. Mag. Nat. Hist."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1247","DOI":"10.1111\/jfb.14828","article-title":"Age, Growth and Maturity for Two Highly Targeted Jack Species: Caranx ignobilis and Caranx melampygus","volume":"99","author":"Pardee","year":"2021","journal-title":"J. Fish Biol."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Langlois, J., Guilhaumon, F., Baletaud, F., Casajus, N., De Almeida Braga, C., Fleur\u00e9, V., Kulbicki, M., Loiseau, N., Mouillot, D., and Renoult, J.P. (2022). The Aesthetic Value of Reef Fishes Is Globally Mismatched to Their Conservation Priorities. PLoS Biol., 20.","DOI":"10.1371\/journal.pbio.3001640"},{"key":"ref_9","first-page":"1","article-title":"Indo-West Pacific Species of Trachinotus with Spots on Their Sides as Adults, with Description of a New Species Endemic to the Marquesas Islands (Teleostei: Carangidae)","volume":"4651","author":"Walsh","year":"2019","journal-title":"Zootaxa"},{"key":"ref_10","first-page":"26","article-title":"Age, Growth, and Reproduction of Permit (Trachinotus falcatus) in Florida Waters","volume":"100","author":"Crabtree","year":"2002","journal-title":"Fish. Bull."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"102970","DOI":"10.1016\/j.ecoinf.2024.102970","article-title":"DataFishing: An Efficient Python Tool and User-Friendly Web-Form for Mining Mitochondrial and Chloroplast Sequences, Taxonomic, and Biodiversity Data","volume":"85","author":"Rabelo","year":"2025","journal-title":"Ecol. Inform."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1300\/J028v07n02_06","article-title":"Effects of Feeding Four Formulated Diets on Growth of Juvenile Palometa, Trachinotus goodei","volume":"7","author":"Cole","year":"1997","journal-title":"J. Appl. Aquac."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1111\/jfb.14227","article-title":"Seasonal Occupancy and Connectivity amongst Nearshore Flats and Reef Habitats by Permit Trachinotus falcatus: Considerations for Fisheries Management","volume":"96","author":"Brownscombe","year":"2020","journal-title":"J. Fish Biol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"100648","DOI":"10.1016\/j.mgene.2020.100648","article-title":"Mitochondrial Genome to Aid Species Delimitation and Effective Conservation of the Sharpnose guitarfish (Glaucostegus granulatus)","volume":"24","author":"Johri","year":"2020","journal-title":"Meta Gene"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Xu, C., Bi, W., Ma, R., Li, P., Liu, F., and Liu, Z. (2025). Assembly and Comparative Analysis of the Complete Mitochondrial of Spodiopogon sagittifolius, an Endemic and Protective Species from Yunnan, China. BMC Plant Biol., 25.","DOI":"10.1186\/s12870-025-06341-z"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"128571","DOI":"10.1016\/j.ijbiomac.2023.128571","article-title":"Assembly and Comparative Analysis of the First Complete Mitochondrial Genome of a Traditional Chinese Medicine Angelica biserrata (Shan et Yuan) Yuan et Shan","volume":"257","author":"Wang","year":"2024","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Alvarenga, M., D\u2019Elia, A.K.P., Rocha, G., Arantes, C.A., Henning, F., de Vasconcelos, A.T.R., and Sol\u00e9-Cava, A.M. (2024). Mitochondrial Genome Structure and Composition in 70 Fishes: A Key Resource for Fisheries Management in the South Atlantic. BMC Genom., 25.","DOI":"10.1186\/s12864-024-10035-5"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"2185","DOI":"10.1007\/s11033-021-07037-x","article-title":"Genome Survey of Misgurnus anguillicaudatus to Identify Genomic Information, Simple Sequence Repeat (SSR) Markers, and Mitochondrial Genome","volume":"49","author":"Huang","year":"2022","journal-title":"Mol. Biol. Rep."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"108895","DOI":"10.1016\/j.foodcont.2022.108895","article-title":"DNA Barcoding as an Approach for Species Traceability and Labeling Accuracy of Fish Fillet Products in Thailand","volume":"136","author":"Panprommin","year":"2022","journal-title":"Food Control"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1038\/s41576-023-00657-y","article-title":"Genomics for Monitoring and Understanding Species Responses to Global Climate Change","volume":"25","author":"Bernatchez","year":"2024","journal-title":"Nat. Rev. Genet."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1590\/S1415-47572012005000062","article-title":"Inclusion of South American Samples Reveals New Population Structuring of the Blacktip Shark (Carcharhinus limbatus) in the Western Atlantic","volume":"35","author":"Souza","year":"2012","journal-title":"Genet Mol. Biol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"31541","DOI":"10.1038\/s41598-024-83196-8","article-title":"Deep Genetic Divergences and Few Morphological Changes Support the Cryptic Speciation in Larimus breviceps (Sciaenidae, Acanthuriformes) from the Western South Atlantic","volume":"14","author":"Alencar","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"4773","DOI":"10.1016\/j.cub.2021.08.062","article-title":"Overfishing Drives over One-Third of All Sharks and Rays toward a Global Extinction Crisis","volume":"31","author":"Dulvy","year":"2021","journal-title":"Curr. Biol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1007\/s13127-024-00648-9","article-title":"Diagnostic Applicability of Mitogenomics in Uncovering Intraspecific Carangid Diversifications: Insights into Phylogeny, Divergence Time, and Characterization of Two Cryptic Selaroides leptolepis Mitogenomes","volume":"24","author":"Halasan","year":"2024","journal-title":"Org. Divers. Evol."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Muhala, V., Guimar\u00e3es-Costa, A., Macate, I.E., Rabelo, L.P., Bessa-Silva, A.R., Watanabe, L., dos Santos, G.D., Sambora, L., Vallinoto, M., and Sampaio, I. (2024). DNA Barcoding for the Assessment of Marine and Coastal Fish Diversity from the Coast of Mozambique. PLoS ONE, 19.","DOI":"10.1371\/journal.pone.0293345"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1134\/S1995425518030022","article-title":"Phylogeny of Salmonoid Fishes (Salmonoidei) Based on MtDNA COI Gene Sequences (Barcoding)","volume":"11","author":"Artamonova","year":"2018","journal-title":"Contemp. Probl. Ecol."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"de Sousa, R.P.C., Bessa-Brito, C.D., Guimar\u00e3es-Costa, A., Evangelista-Gomes, G., Sampaio, I., de Oliveira, E.H.C., and Vallinoto, M. (2022). Exploring the Diversity of Elopidae (Teleostei; Elopiformes) Using DNA Barcoding Analysis. Diversity, 14.","DOI":"10.3390\/d14111008"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1651\/08-3020.1","article-title":"\u201cCOI-like\u201d Sequences Are Becoming Problematic in Molecular Systematic and DNA Barcoding Studies","volume":"29","author":"Buhay","year":"2009","journal-title":"J. Crustac. Biol."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Bingpeng, X., Heshan, L., Zhilan, Z., Chunguang, W., Yanguo, W., and Jianjun, W. (2018). DNA Barcoding for Identification of Fish Species in the Taiwan Strait. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0198109"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"bbaa429","DOI":"10.1093\/bib\/bbaa429","article-title":"MITGARD: An Automated Pipeline for Mitochondrial Genome Assembly in Eukaryotic Species Using RNA-Seq Data","volume":"22","author":"Nachtigall","year":"2021","journal-title":"Brief. Bioinform."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: An Ultra-Fast All-in-One FASTQ Preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Chen, S. (2023). Ultrafast One-pass FASTQ Data Preprocessing, Quality Control, and Deduplication Using Fastp. iMeta, 2.","DOI":"10.1002\/imt2.107"},{"key":"ref_33","first-page":"e18","article-title":"NOVOPlasty: De Novo Assembly of Organelle Genomes from Whole Genome Data","volume":"45","author":"Dierckxsens","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Rabelo, L.P., Sodr\u00e9, D., de Sousa, R.P.C., Watanabe, L., Gomes, G., Sampaio, I., and Vallinoto, M. (2024). SynGenes: A Python Class for Standardizing Nomenclatures of Mitochondrial and Chloroplast Genes and a Web Form for Enhancing Searches for Evolutionary Analyses. BMC Bioinform., 25.","DOI":"10.1186\/s12859-024-05781-y"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast Gapped-Read Alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"3088","DOI":"10.1093\/gbe\/evx232","article-title":"Genetic Drift and Indel Mutation in the Evolution of Yeast Mitochondrial Genome Size","volume":"9","author":"Xiao","year":"2017","journal-title":"Genome Biol. Evol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve Years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1093\/bioinformatics\/btv566","article-title":"Qualimap 2: Advanced Multi-Sample Quality Control for High-Throughput Sequencing Data","volume":"32","author":"Okonechnikov","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"msad035","DOI":"10.1093\/molbev\/msad035","article-title":"MitoFish, MitoAnnotator, and MiFish Pipeline: Updates in 10 Years","volume":"40","author":"Zhu","year":"2023","journal-title":"Genome Biol. Evol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1016\/j.ympev.2012.08.023","article-title":"MITOS: Improved de Novo Metazoan Mitochondrial Genome Annotation","volume":"69","author":"Bernt","year":"2013","journal-title":"Mol. Phylogenetics Evol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"W54","DOI":"10.1093\/nar\/gkw413","article-title":"TRNAscan-SE On-Line: Integrating Search and Context for Analysis of Transfer RNA Genes","volume":"44","author":"Lowe","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"3377","DOI":"10.1093\/bioinformatics\/btv372","article-title":"Forna (Force-Directed RNA): Simple and Effective Online RNA Secondary Structure Diagrams","volume":"31","author":"Kerpedjiev","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms","volume":"35","author":"Kumar","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_44","first-page":"348","article-title":"PhyloSuite: An Integrated and Scalable Desktop Platform for Streamlined Molecular Sequence Data Management and Evolutionary Phylogenetics Studies","volume":"20","author":"Zhang","year":"2020","journal-title":"Mol. Biol. Resour."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"W484","DOI":"10.1093\/nar\/gkad326","article-title":"Proksee: In-Depth Characterization and Visualization of Bacterial Genomes","volume":"51","author":"Grant","year":"2023","journal-title":"Nucleic Acids Resour."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"TrimAl: A Tool for Automated Alignment Trimming in Large-Scale Phylogenetic Analyses","volume":"25","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1093\/oxfordjournals.molbev.a026334","article-title":"Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis","volume":"17","author":"Castresana","year":"2000","journal-title":"Mol. Biol. Evol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1093\/sysbio\/syv033","article-title":"Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference","volume":"64","author":"Tan","year":"2015","journal-title":"Syst. Biol."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Sun, P., Yang, Y., Yuan, M., and Tang, Q. (2025). CamITree: A Streamlined Software for Phylogenetic Analysis of Viral and Mitochondrial Genomes. BMC Bioinform., 26.","DOI":"10.1186\/s12859-025-06034-2"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1093\/sysbio\/sys029","article-title":"MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space","volume":"61","author":"Ronquist","year":"2012","journal-title":"Syst. Biol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/nar\/27.2.573","article-title":"Tandem Repeats Finder: A Program to Analyze DNA Sequences","volume":"27","author":"Benson","year":"1999","journal-title":"Nucleic Acids Resour."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"3358","DOI":"10.1038\/s41598-024-52979-4","article-title":"Comparative Mitochondrial Genome Brings Insights to Slight Variation in Gene Proportion and Large Intergenic Spacer and Phylogenetic Relationship of Mudskipper Species","volume":"14","author":"Muhala","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.ympev.2016.01.017","article-title":"Recovering Complete Mitochondrial Genome Sequences from RNA-Seq: A Case Study of Polytomella Non-Photosynthetic Green Algae","volume":"98","author":"Tian","year":"2016","journal-title":"Mol. Phylogenetics Evol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"33465","DOI":"10.1038\/srep33465","article-title":"Application of RNA-Seq for Mitogenome Reconstruction, and Reconsideration of Long-Branch Artifacts in Hemiptera Phylogeny","volume":"6","author":"Song","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Li, Z., Li, M., Xu, S., Liu, L., Chen, Z., and Zou, K. (2020). Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21134685"},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Li, B., Wang, H., Yang, L., Liu, S., and Zhuang, Z. (2021). Complete Mitochondrial Genome of Pseudocaranx dentex (Carangidae, Perciformes) Provides Insight into Phylogenetic and Evolutionary Relationship among Carangidae Family. Genes, 12.","DOI":"10.3390\/genes12081234"},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Zhao, F., Xian, L., Zhu, K., Zhang, N., Guo, H., Liu, B., Yang, J., Liu, B., and Zhang, D. (2025). Mitochondrial genome of eight Carangidae and phylogenetic analysis in the family. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0326619"},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Li, A., An, C., Wang, H., Che, S., Liu, S., and Zhuang, Z. (2025). DNA Barcode and Correct Scientific Name of Golden Pompano, an Important Marine Aquaculture Fish Species in China. Fishes, 10.","DOI":"10.3390\/fishes10030129"},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Harrington, R.C., Faircloth, B.C., Eytan, R.I., Smith, W.L., Near, T.J., Alfaro, M.E., and Friedman, M. (2016). Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye. BMC Evol. Biol., 16.","DOI":"10.1186\/s12862-016-0786-x"}],"container-title":["Diversity"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1424-2818\/18\/2\/88\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,9]],"date-time":"2026-02-09T14:21:45Z","timestamp":1770646905000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1424-2818\/18\/2\/88"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,31]]},"references-count":61,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2026,2]]}},"alternative-id":["d18020088"],"URL":"https:\/\/doi.org\/10.3390\/d18020088","relation":{},"ISSN":["1424-2818"],"issn-type":[{"value":"1424-2818","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,31]]}}}