Mitochondrial genome of Acheilognathus barbatulus (Cypriniformes, Cyprinidae, Acheilognathinae): characterisation and phylogenetic analysis
Acheilognathus barbatulus is distributed in Yangtze River, Yellow River and Pearl River systems in China. Genome data can help to understand the phylogenetic relationships of A. barbatulus, but its complete mitochondrial genome has not been published. We determined the complete mitochondrial genome...
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| Format: | Article |
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Pensoft Publishers
2023-02-01
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| Series: | Biodiversity Data Journal |
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| Online Access: | https://bdj.pensoft.net/article/93947/download/pdf/ |
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| author | Jinhui Yu Xin Chen Ruyao Liu Yongtao Tang Guoxing Nie Chuanjiang Zhou |
| author_facet | Jinhui Yu Xin Chen Ruyao Liu Yongtao Tang Guoxing Nie Chuanjiang Zhou |
| author_sort | Jinhui Yu |
| collection | DOAJ |
| description | Acheilognathus barbatulus is distributed in Yangtze River, Yellow River and Pearl River systems in China. Genome data can help to understand the phylogenetic relationships of A. barbatulus, but its complete mitochondrial genome has not been published. We determined the complete mitochondrial genome structure and characteristics of this species and constructed a comprehensive phylogenetic tree, based on mitochondrial genome data of several species of Acheilognathus, Rhodeus and Pseudorasbora parva. The complete length of the mitochondrial genome of A. barbatulus is 16726 bp. The genome is a covalently closed double-stranded circular molecule containing 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, a D-loop and a light strand replication initiation region. The base composition of the complete mitochondrial genome is A (29.33%) > T (27.6%) > C (26.12%) > G (16.95%), showing a strong AT preference and anti-G bias. All 13 PCGs have different degrees of codon preference, except for cytochrome c oxidase 1, which uses GTG as the start codon. All the PCGs use ATG as the start codon and the stop codon is dominated by TAG. The encoded amino acids Leu and Ser exist in two types, whereas the rest are all present as one type, except for tRNASer (GCT), which lacks the D-arm and has an incomplete secondary structure, all other tRNAs can be folded to form a typical cloverleaf secondary structure. Based on the 13 PCG tandems, the Maximum Likelihood and Bayesian trees were constructed, based on the concatenated sequence of 13 PCGs for the genera Acheilognathus and Rhodeus, with Pseudorasbora parva as the outgroup. Acheilognathus barbatulus, Acheilognathus tonkinensis and Acheilognathus cf. macropterus were clustered together and the most closely related. The results of this study enrich the mitochondrial genomic data of Acheilognathus and provide molecular and genetic base information for species conservation, molecular identification and species evolution of Acheilognathinae. |
| first_indexed | 2024-04-10T07:51:52Z |
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| id | doaj.art-45cf1681152047ca9a2dd399f2ab846d |
| institution | Directory Open Access Journal |
| issn | 1314-2828 |
| language | English |
| last_indexed | 2024-04-10T07:51:52Z |
| publishDate | 2023-02-01 |
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| record_format | Article |
| series | Biodiversity Data Journal |
| spelling | doaj.art-45cf1681152047ca9a2dd399f2ab846d2023-02-23T09:11:03ZengPensoft PublishersBiodiversity Data Journal1314-28282023-02-011112310.3897/BDJ.11.e9394793947Mitochondrial genome of Acheilognathus barbatulus (Cypriniformes, Cyprinidae, Acheilognathinae): characterisation and phylogenetic analysisJinhui Yu0Xin Chen1Ruyao Liu2Yongtao Tang3Guoxing Nie4Chuanjiang Zhou5College of Fisheries, Henan Normal UniversityCollege of Fisheries, Henan Normal UniversityCollege of Fisheries, Henan Normal UniversityCollege of Fisheries, Henan Normal UniversityCollege of Fisheries, Henan Normal UniversityCollege of Life sciences, Henan Normal UniversityAcheilognathus barbatulus is distributed in Yangtze River, Yellow River and Pearl River systems in China. Genome data can help to understand the phylogenetic relationships of A. barbatulus, but its complete mitochondrial genome has not been published. We determined the complete mitochondrial genome structure and characteristics of this species and constructed a comprehensive phylogenetic tree, based on mitochondrial genome data of several species of Acheilognathus, Rhodeus and Pseudorasbora parva. The complete length of the mitochondrial genome of A. barbatulus is 16726 bp. The genome is a covalently closed double-stranded circular molecule containing 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, a D-loop and a light strand replication initiation region. The base composition of the complete mitochondrial genome is A (29.33%) &gt; T (27.6%) &gt; C (26.12%) &gt; G (16.95%), showing a strong AT preference and anti-G bias. All 13 PCGs have different degrees of codon preference, except for cytochrome c oxidase 1, which uses GTG as the start codon. All the PCGs use ATG as the start codon and the stop codon is dominated by TAG. The encoded amino acids Leu and Ser exist in two types, whereas the rest are all present as one type, except for tRNASer (GCT), which lacks the D-arm and has an incomplete secondary structure, all other tRNAs can be folded to form a typical cloverleaf secondary structure. Based on the 13 PCG tandems, the Maximum Likelihood and Bayesian trees were constructed, based on the concatenated sequence of 13 PCGs for the genera Acheilognathus and Rhodeus, with Pseudorasbora parva as the outgroup. Acheilognathus barbatulus, Acheilognathus tonkinensis and Acheilognathus cf. macropterus were clustered together and the most closely related. The results of this study enrich the mitochondrial genomic data of Acheilognathus and provide molecular and genetic base information for species conservation, molecular identification and species evolution of Acheilognathinae.https://bdj.pensoft.net/article/93947/download/pdf/<i>Acheilognathus barbatulus</i>mitochondrial ge |
| spellingShingle | Jinhui Yu Xin Chen Ruyao Liu Yongtao Tang Guoxing Nie Chuanjiang Zhou Mitochondrial genome of Acheilognathus barbatulus (Cypriniformes, Cyprinidae, Acheilognathinae): characterisation and phylogenetic analysis Biodiversity Data Journal <i>Acheilognathus barbatulus</i> mitochondrial ge |
| title | Mitochondrial genome of Acheilognathus barbatulus (Cypriniformes, Cyprinidae, Acheilognathinae): characterisation and phylogenetic analysis |
| title_full | Mitochondrial genome of Acheilognathus barbatulus (Cypriniformes, Cyprinidae, Acheilognathinae): characterisation and phylogenetic analysis |
| title_fullStr | Mitochondrial genome of Acheilognathus barbatulus (Cypriniformes, Cyprinidae, Acheilognathinae): characterisation and phylogenetic analysis |
| title_full_unstemmed | Mitochondrial genome of Acheilognathus barbatulus (Cypriniformes, Cyprinidae, Acheilognathinae): characterisation and phylogenetic analysis |
| title_short | Mitochondrial genome of Acheilognathus barbatulus (Cypriniformes, Cyprinidae, Acheilognathinae): characterisation and phylogenetic analysis |
| title_sort | mitochondrial genome of acheilognathus barbatulus cypriniformes cyprinidae acheilognathinae characterisation and phylogenetic analysis |
| topic | <i>Acheilognathus barbatulus</i> mitochondrial ge |
| url | https://bdj.pensoft.net/article/93947/download/pdf/ |
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