Complete mitochondrial genomes of two catfishes (Siluriformes, Bagridae) and their phylogenetic implications

Abstract

The mitochondrial genome (mitogenome) has been widely used as a molecular marker to investigate phylogenetic analysis and evolutionary history in fish. However, the study of mitogenomes is still scarce in the family Bagridae. In this study, the mitogenomes of Tachysurus brachyrhabdion and T. gracilis were sequenced, annotated, and analyzed. The mitogenomes were found to be 16,532 bp and 16,533 bp, respectively, and each contained 37 typical mitochondrial genes, which are 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. All PCGs begin with the codon ATG, except for the cytochrome c oxidase subunit 1 (COI) gene, while seven PCGs end with an incomplete termination codon. All tRNA genes can fold into their typical cloverleaf secondary structures, except for tRNASer(AGY), which lacks the dihydrouracil arm. The Ka/Ks ratios for all PCGs are far lower than one. Phylogenetic analyses based on Bayesian inference (BI) and maximum likelihood (ML) showed that the two clades in Bagridae excluded Rita rita. The monophyly of Tachysurus supports previous research and the traditional classification that Leiocassis, Pseudobagrus, Pelteobagrus, and Tachysurus belong to one genus (Tachysurus). These findings provide a phylogenetic basis for future phylogenetic and taxonomic studies of Bagridae.

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

“…Eleven PCGs were canonical ATG start codons, while the start codon of the COI gene, and the ND3 gene was a GTG start codon. The non-standard start codon was also found in other fish species [ 4 , 5 ]. Seven PCGs had complete stop codons, while the remaining six PCGs ended with the incomplete stop codons TA or T ( COIII ended with TA and ND2 , COII , ND3 , ND4 , and Cyt b ended with T) ( Table 3 ).…”

“…Fish mtDNA is generally small, ranging from 15–18 kb, which typically contain 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 1 control region (D-loop) [ 2 , 3 ]. In comparison with nuclear DNA, mtDNA has the unique characteristics of maternal inheritance, multiple copies, no introns, a rapid evolution rate, and small molecular size, so it has become an important molecular marker in evolutionary genetics, molecular ecology, species identification, and the conservation biology of fish [ 1 , 4 , 5 ]. In recent years, with the rapid development and application of high-throughput DNA sequencing technologies and bioinformatics analysis, more and more fish mitochondrial genomes have been successfully sequenced and characterized.…”

The Mitochondrial Genome of Linichthys laticeps (Cypriniformes: Cyprinidae): Characterization and Phylogeny

“…The A + T skew and the G + C skew were 0.100 and −0.254, respectively, in the mitogenome of L. laticeps. Fish mitogenomes usually tend to have the characteristics of A + T bias [4,5]. In the L. laticeps mitogenome, there were 14 intergenic spacers ranging from 1 bp to 33 bp in length.…”

“…The mitochondrial genome (mitogenome) is one of the most commonly used molecular markers mainly due to its small size, high copy number, matrilineal inheritance, lack of recombination, and high rate of evolution compared to nuclear genome DNA [1,2]. The mitogenome of fish is typically a double-stranded, looped DNA molecule with a size range of 15-18 kb [3,4]. It generally contains 37 genes (22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and two ribosomal RNA genes (rRNAs)) and one control region (CR) (also known as the D-loop region or the A + T-rich region) [3,4].…”

“…The mitogenome of fish is typically a double-stranded, looped DNA molecule with a size range of 15-18 kb [3,4]. It generally contains 37 genes (22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and two ribosomal RNA genes (rRNAs)) and one control region (CR) (also known as the D-loop region or the A + T-rich region) [3,4]. Fish mitogenomes have been widely used in fish phylogeny, biogeography, and population genetic structure analyses [5].…”