The complete mitochondrial genome of Microphysogobio elongatus (Teleostei, Cyprinidae) and its phylogenetic implications

Abstract

Mitochondria are important organelles with independent genetic material of eukaryotic organisms. In this study, we sequenced and analyzed the complete mitogenome of a small cyprinid fish, Microphysogobio elongatus (Yao & Yang, 1977). The mitogenome of M. elongatus is a typical circular molecule of 16,612 bp in length containing 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a 930 bp control region. The base composition of the M. elongatus mitogenome is 30.8% A, 26.1% T, 16.7% G, and 26.4% C. All PCGs used the standard ATG start codon with the exception of COI. Six PCGs terminate with complete stop codons, whereas seven PCGs (ND2, COII, ATPase 6, COIII, ND3, ND4, and Cyt b) terminate with incomplete (T or TA) stop codons. All tRNA genes exhibited typical cloverleaf secondary structures with the exception of tRNASer(AGY), for which the dihydrouridine arm forms a simple loop. The phylogenetic analysis divided the subfamily Gobioninae in three clades with relatively robust support, and that Microphysogobio is not a monophyletic group. The complete mitogenome of M. elongatus provides a valuable resource for future studies about molecular phylogeny and/or population genetics of Microphysogobio.

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

“…Twenty-one tRNA genes showed the typical cloverleaf secondary structure (Suppl. material 1, 2), while the tRNA-Ser AGY gene lacked the dihydrouracil (DHU) arm as noted in other fish species (Zhang and Wang 2018;Zhang et al 2021). The low Ka/Ks value for each PCG indicated that they were all under strong purifying selection.…”

“…Most of the PCGs of these two species had ATG as the start codon except COI that had GTG as the start codon. The COI gene usually uses GTG as the start codon in other fishes, such as Lateolabrax, Sinocyclocheilus multipunctatus, and Microphysogobio elongatus (Shan et al 2016;Zhang and Wang 2018;Zhang et al 2021). The PCGs of these two bagrid catfishes had an incomplete stop codon that was automatically filled by post-transcriptional polyadenylation (Ojala et al 1981).…”

“…material 3). PCR amplification were performed as described previously (Zhang et al 2021). The PCR products were fractionated by electrophoresis through 1% agarose gel electrophoresis.…”

“…Similar to other vertebrates, fish mitochondrial DNA (mtDNA) is a circular double-stranded molecule, and it is independent of the nuclear genome (Xiao and Zhang 2000). Fish mtDNA is generally small (15-18 kb), containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding region (D-loop) (Brown 2008;Zhang and Wang 2018;Zhang et al 2021). The mitochondrial genome has been used to study fish species identification, genome evolution, and phylogenetic studies because of the advantages of its small size, multiple copies, maternal inheritance, rapid evolution rate, and lack of introns (Boore 1999;Xiao and Zhang 2000;Zhang and Wang 2018;Zhang et al 2021).…”

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

“…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.…”