Cargando…

The Complete Mitochondrial Genome of the Freshwater Fish Onychostoma ovale (Cypriniformes, Cyprinidae): Genome Characterization and Phylogenetic Analysis

In this study, we sequenced and characterized the complete mitochondrial genome (mitogenome) of Onychostoma ovale. The mitogenome of O. ovale was 16,602 bp in length with 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region. The nucleotide...

Descripción completa

Detalles Bibliográficos
Autores principales: Zhang, Renyi, Zhu, Tingting, Luo, Qi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10298739/
https://www.ncbi.nlm.nih.gov/pubmed/37372406
http://dx.doi.org/10.3390/genes14061227
_version_ 1785064192518127616
author Zhang, Renyi
Zhu, Tingting
Luo, Qi
author_facet Zhang, Renyi
Zhu, Tingting
Luo, Qi
author_sort Zhang, Renyi
collection PubMed
description In this study, we sequenced and characterized the complete mitochondrial genome (mitogenome) of Onychostoma ovale. The mitogenome of O. ovale was 16,602 bp in length with 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region. The nucleotide composition of the O. ovale mitogenome was 31.47% A, 24.07% T, 15.92% G, and 28.54% C, with a higher A + T content (55.54%) than G + C content (44.46%). All PCGs began with the standard ATG codon, except for the cytochrome c oxidase subunit 1 (COX1) gene and the NADH dehydrogenase 3 (ND3) gene with GTG, while six PCGs ended with incomplete termination codons (TA or T). The Ka/Ks ratios of 13 PCGs were all less than one, indicating that they were under purifying selection. All tRNA genes were folded into the typical cloverleaf secondary structures with the exception of tRNA(Ser(AGY)), whose dihydrouridine (DHU) arm was absent. The phylogenetic trees showed that Onychostoma and Acrossocheilus were classified into three clades. There was a mosaic relationship between Onychostoma and Acrossocheilus. Moreover, the phylogenetic tree analysis showed that O. rarum was the closest species to O. ovale. This study can provide a useful resource for further phylogeny and population genetic analyses of Onychostoma and Acrossocheilus.
format Online
Article
Text
id pubmed-10298739
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-102987392023-06-28 The Complete Mitochondrial Genome of the Freshwater Fish Onychostoma ovale (Cypriniformes, Cyprinidae): Genome Characterization and Phylogenetic Analysis Zhang, Renyi Zhu, Tingting Luo, Qi Genes (Basel) Article In this study, we sequenced and characterized the complete mitochondrial genome (mitogenome) of Onychostoma ovale. The mitogenome of O. ovale was 16,602 bp in length with 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region. The nucleotide composition of the O. ovale mitogenome was 31.47% A, 24.07% T, 15.92% G, and 28.54% C, with a higher A + T content (55.54%) than G + C content (44.46%). All PCGs began with the standard ATG codon, except for the cytochrome c oxidase subunit 1 (COX1) gene and the NADH dehydrogenase 3 (ND3) gene with GTG, while six PCGs ended with incomplete termination codons (TA or T). The Ka/Ks ratios of 13 PCGs were all less than one, indicating that they were under purifying selection. All tRNA genes were folded into the typical cloverleaf secondary structures with the exception of tRNA(Ser(AGY)), whose dihydrouridine (DHU) arm was absent. The phylogenetic trees showed that Onychostoma and Acrossocheilus were classified into three clades. There was a mosaic relationship between Onychostoma and Acrossocheilus. Moreover, the phylogenetic tree analysis showed that O. rarum was the closest species to O. ovale. This study can provide a useful resource for further phylogeny and population genetic analyses of Onychostoma and Acrossocheilus. MDPI 2023-06-06 /pmc/articles/PMC10298739/ /pubmed/37372406 http://dx.doi.org/10.3390/genes14061227 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Zhang, Renyi
Zhu, Tingting
Luo, Qi
The Complete Mitochondrial Genome of the Freshwater Fish Onychostoma ovale (Cypriniformes, Cyprinidae): Genome Characterization and Phylogenetic Analysis
title The Complete Mitochondrial Genome of the Freshwater Fish Onychostoma ovale (Cypriniformes, Cyprinidae): Genome Characterization and Phylogenetic Analysis
title_full The Complete Mitochondrial Genome of the Freshwater Fish Onychostoma ovale (Cypriniformes, Cyprinidae): Genome Characterization and Phylogenetic Analysis
title_fullStr The Complete Mitochondrial Genome of the Freshwater Fish Onychostoma ovale (Cypriniformes, Cyprinidae): Genome Characterization and Phylogenetic Analysis
title_full_unstemmed The Complete Mitochondrial Genome of the Freshwater Fish Onychostoma ovale (Cypriniformes, Cyprinidae): Genome Characterization and Phylogenetic Analysis
title_short The Complete Mitochondrial Genome of the Freshwater Fish Onychostoma ovale (Cypriniformes, Cyprinidae): Genome Characterization and Phylogenetic Analysis
title_sort complete mitochondrial genome of the freshwater fish onychostoma ovale (cypriniformes, cyprinidae): genome characterization and phylogenetic analysis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10298739/
https://www.ncbi.nlm.nih.gov/pubmed/37372406
http://dx.doi.org/10.3390/genes14061227
work_keys_str_mv AT zhangrenyi thecompletemitochondrialgenomeofthefreshwaterfishonychostomaovalecypriniformescyprinidaegenomecharacterizationandphylogeneticanalysis
AT zhutingting thecompletemitochondrialgenomeofthefreshwaterfishonychostomaovalecypriniformescyprinidaegenomecharacterizationandphylogeneticanalysis
AT luoqi thecompletemitochondrialgenomeofthefreshwaterfishonychostomaovalecypriniformescyprinidaegenomecharacterizationandphylogeneticanalysis
AT zhangrenyi completemitochondrialgenomeofthefreshwaterfishonychostomaovalecypriniformescyprinidaegenomecharacterizationandphylogeneticanalysis
AT zhutingting completemitochondrialgenomeofthefreshwaterfishonychostomaovalecypriniformescyprinidaegenomecharacterizationandphylogeneticanalysis
AT luoqi completemitochondrialgenomeofthefreshwaterfishonychostomaovalecypriniformescyprinidaegenomecharacterizationandphylogeneticanalysis