{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T17:16:13Z","timestamp":1788282973763,"version":"build-2803163510"},"reference-count":83,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32403085"],"award-info":[{"award-number":["32403085"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"award":["32403085"],"award-info":[{"award-number":["32403085"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Science and Technology Program of Xinjiang Uyghur Autonomous Region","award":["2023B02012"],"award-info":[{"award-number":["2023B02012"]}]},{"name":"Science and Technology Program of Xinjiang Uyghur Autonomous Region","award":["2025B02020"],"award-info":[{"award-number":["2025B02020"]}]},{"name":"Xinjiang Agricultural University\u2019s Undergraduate Innovation Project","award":["DXSCX2026131"],"award-info":[{"award-number":["DXSCX2026131"]}]},{"award":["DXSCX2026131"],"award-info":[{"award-number":["DXSCX2026131"]}],"id":[{"id":"https:\/\/ror.org\/04qjh2h11","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Codon usage bias (CUB) is a useful indicator of evolutionary forces shaping mitochondrial genomes. Codon usage bias in mitochondrial genomes of Diphyllobothriidae and especially in Ligula intestinalis was characterized. The roles of natural selection and mutation pressure in framing this bias were evaluated on the basis of 12 protein-coding genes in Diphyllobothriidae. The complete mitogenome (13,725 bp) of L. intestinalis comprises 12 protein-coding genes (PCGs), 22 tRNAs, and two rRNAs, all positioned on the heavy strand, and contains an overall AT content of 66.15%. The mean CAI (0.176), CBI (\u22120.105), and ENC (45.33) and an evident preference for U-ending codons observed in all examined genes indicate weak CUB. Neutrality, ENC, and PR2 plots consistently demonstrate that natural selection is the predominant force driving CUB and contributes approximately 56% in L. intestinalis and 83% in other Diphyllobothriidea species, with mutation pressure playing a secondary role. Phylogenetic reconstruction supported the monophyly of Diphyllobothriidea, confirmed the paraphyly of Diphyllobothrium as traditionally defined, and placed Ligula and Digramma as sister taxa. These findings clarify the evolutionary constraints governing codon usage in cestode mitogenomes and provide practical resources for codon optimization in heterologous gene expression and genetic studies of this economically important parasite.<\/jats:p>","DOI":"10.3390\/ani16172723","type":"journal-article","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T16:28:22Z","timestamp":1788280102000},"page":"2723","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Natural Selection Drives Codon Usage Bias in the Mitochondrial Genome of Ligula intestinalis (Linnaeus, 1758) Gmelin, 1790 (Cestoda: Diphyllobothriidea): Insights from Comparative Genomics and Optimal Codon Identification"],"prefix":"10.3390","volume":"16","author":[{"given":"Shun-Jie","family":"Wang","sequence":"first","affiliation":[{"name":"College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Shi-Min","family":"Zeng","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"given":"Feng-Cheng","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Jin-Nan","family":"Hu","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Shun-Hai","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"given":"Li","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheng","family":"Yue","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2320-4324","authenticated-orcid":false,"given":"Cui-Lan","family":"Hao","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China"},{"name":"Xinjiang Regional Key Laboratory of Clinical Veterinary Medicine Research, Urumqi 830052, China"},{"name":"Xinjiang Key Laboratory of New Drug Research and Development for Herbivorous Animals, Urumqi 830052, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1767","DOI":"10.1093\/nar\/27.8.1767","article-title":"Animal mitochondrial genomes","volume":"27","author":"Boore","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/S0378-1119(01)00807-1","article-title":"Mitochondrial DNA in metazoa: Degree of freedom in a frozen event","volume":"286","author":"Saccone","year":"2002","journal-title":"Gene"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/S0074-7696(08)62066-5","article-title":"Animal mitochondrial DNA: Structure and evolution","volume":"141","author":"Wolstenholme","year":"1992","journal-title":"Int. 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