{"title":"Mitochondrial Genome and Phylogenetic Analysis of Rhinogobius virgigena.","authors":"Yi-Jing Zhan, Wei Hu, Kai-Rui Zhang, Cheng-He Sun","doi":"10.1007/s10528-025-11171-7","DOIUrl":null,"url":null,"abstract":"<p><p>Rhinogobius virgigena is a fish species of the family Gobiidae, order Perciformes. This study aims to better understand the phylogenetic status of R. virgigena within Gobiidae and the phylogenetic relations in this family. Mitochondrial DNA is maternally inherited and does not recombine; therefore, mitochondrial genomes simplify genealogical tracing and reveal phylogenetic relationships among species more clearly than nuclear genomes. Therefore, we used high-throughput sequencing to obtain a complete mitochondrial genome sequence of R. virgigena and conducted phylogenetic analyses. The R. virgigena mitochondrial genome is 16,491 bp long and its base composition shows AT preference. It comprises 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a D loop. Protein-coding genes account for 69.3% of the complete genome. Leucine is the most abundant amino acid, whereas cysteine is the least abundant. tRNA genes account for 9.4% of the genome. Twenty-one tRNAs have a typical cloverleaf secondary structure, whereas tRNA-Ser1 lacks the dihydrouracil arm. The two rRNA genes are separated by tRNA-Val. A mitochondrial genome contains seven overlaps and 11 gaps, indicating a tight arrangement. Two phylogenetic trees constructed based on the nucleotide sequences of 13 protein-coding genes from 54 Gobiidae species using the maximum likelihood method and Bayesian inference revealed that R. virgigena is the most closely related to Rhinogobius duospilus.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":1.6000,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Biochemical Genetics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1007/s10528-025-11171-7","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Rhinogobius virgigena is a fish species of the family Gobiidae, order Perciformes. This study aims to better understand the phylogenetic status of R. virgigena within Gobiidae and the phylogenetic relations in this family. Mitochondrial DNA is maternally inherited and does not recombine; therefore, mitochondrial genomes simplify genealogical tracing and reveal phylogenetic relationships among species more clearly than nuclear genomes. Therefore, we used high-throughput sequencing to obtain a complete mitochondrial genome sequence of R. virgigena and conducted phylogenetic analyses. The R. virgigena mitochondrial genome is 16,491 bp long and its base composition shows AT preference. It comprises 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a D loop. Protein-coding genes account for 69.3% of the complete genome. Leucine is the most abundant amino acid, whereas cysteine is the least abundant. tRNA genes account for 9.4% of the genome. Twenty-one tRNAs have a typical cloverleaf secondary structure, whereas tRNA-Ser1 lacks the dihydrouracil arm. The two rRNA genes are separated by tRNA-Val. A mitochondrial genome contains seven overlaps and 11 gaps, indicating a tight arrangement. Two phylogenetic trees constructed based on the nucleotide sequences of 13 protein-coding genes from 54 Gobiidae species using the maximum likelihood method and Bayesian inference revealed that R. virgigena is the most closely related to Rhinogobius duospilus.
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Biochemical Genetics welcomes original manuscripts that address and test clear scientific hypotheses, are directed to a broad scientific audience, and clearly contribute to the advancement of the field through the use of sound sampling or experimental design, reliable analytical methodologies and robust statistical analyses.
Although studies focusing on particular regions and target organisms are welcome, it is not the journal’s goal to publish essentially descriptive studies that provide results with narrow applicability, or are based on very small samples or pseudoreplication.
Rather, Biochemical Genetics welcomes review articles that go beyond summarizing previous publications and create added value through the systematic analysis and critique of the current state of knowledge or by conducting meta-analyses.
Methodological articles are also within the scope of Biological Genetics, particularly when new laboratory techniques or computational approaches are fully described and thoroughly compared with the existing benchmark methods.
Biochemical Genetics welcomes articles on the following topics: Genomics; Proteomics; Population genetics; Phylogenetics; Metagenomics; Microbial genetics; Genetics and evolution of wild and cultivated plants; Animal genetics and evolution; Human genetics and evolution; Genetic disorders; Genetic markers of diseases; Gene technology and therapy; Experimental and analytical methods; Statistical and computational methods.
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