Ke, Z.; Zhou, K.; Hou, M.; Luo, H.; Li, Z.; Pan, X.; Zhou, J.; Jing, T.; Ye, H. Characterization of the Complete Mitochondrial Genome of the Elongate Loach and Its Phylogenetic Implications in Cobitidae. Animals2023, 13, 3841.
Ke, Z.; Zhou, K.; Hou, M.; Luo, H.; Li, Z.; Pan, X.; Zhou, J.; Jing, T.; Ye, H. Characterization of the Complete Mitochondrial Genome of the Elongate Loach and Its Phylogenetic Implications in Cobitidae. Animals 2023, 13, 3841.
Ke, Z.; Zhou, K.; Hou, M.; Luo, H.; Li, Z.; Pan, X.; Zhou, J.; Jing, T.; Ye, H. Characterization of the Complete Mitochondrial Genome of the Elongate Loach and Its Phylogenetic Implications in Cobitidae. Animals2023, 13, 3841.
Ke, Z.; Zhou, K.; Hou, M.; Luo, H.; Li, Z.; Pan, X.; Zhou, J.; Jing, T.; Ye, H. Characterization of the Complete Mitochondrial Genome of the Elongate Loach and Its Phylogenetic Implications in Cobitidae. Animals 2023, 13, 3841.
Abstract
Elongate loach (Leptobotia elongata) is an endemic fish in China. Previous studies have provided some insights into the mitochondrial genome composition, and the phylogenetic relationships of L. elongata inferred using protein-coding genes (PCGs). However, the detailed information about is limited. Therefore, in this study, we sequenced the complete mitochondrial genome of L. elongata and analyzed its structural characteristics. The PCGs and mitochondrial genome were used for selective stress analysis and genomic comparative analysis respectively. The complete mitochondrial genome of the L. elongata, together with those of 36 Cyprinidae species, was used to infer the phylogenetic relationships of the Cobitidae family through maximum likelihood (ML) reconstruction. The results showed that the genome sequence has a full length of 16,591 bp, which includes 13 PCGs, 22 transfer RNA genes (tRNA), two ribosomal RNA genes (rRNA), and two non-coding regions (CR D-loop and light chain sub-chain replication origin OL). Overall, L. elongata shared the same gene arrangement and composition of the mitochondrial genes with other teleost fishes. The Ka/Ks ratios of all mitochondrial PCGs were less than 1, indicating that all the PCGs were evolving under purifying selection. Genome comparison analyses showed a significant sequence homology of species of Leptobotia. A significant identity between L. elongata and the other 5 Leptobotia species was observed in the visualization result, except for L. mantschurica, which lacked the tRNA-Arg gene and had a shorter tRNA-Asp gene. The phylogenetic tree revealed that the Cobitidae species examined here can be grouped into two clades, with L. elongata forming a sister relationship with L. microphthalma. This study could provide additional inferences for a better understanding of the phylogenetic relationships among Cobititdae species.
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