Complete mitochondrial genome of Rhodeus cyanorostris (Teleostei, Cyprinidae): characterization and phylogenetic analysis

Abstract

Rhodeus cyanorostris Li, Liao & Arai, 2020 is a freshwater fish that is endemic to China and restricted to Chengdu City in Sichuan Province. This study is the first to sequence and characterize the complete mitochondrial genome of R. cyanorostris. The mitogenome of R. cyanorostris is 16580 bp in length, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region (D-loop). The base composition of the sequence is 28.5% A, 27.6% C, 26.4% T, and 17.5% G, with a bias toward A+T. The genome structure, nucleotide composition, and codon usage of the mitogenome of R. cyanorostris are consistent with those of other species of Rhodeus. To verify the molecular phylogeny of the genus Rhodeus, we provide new insights to better understand the taxonomic status of R. cyanorostris. The phylogenetic trees present four major clades based on 19 mitogenomic sequences from 16 Rhodeus species. Rhodeus cyanorostris exhibits the closest phylogenetic relationship with R. pseudosericeus, R. amarus, and R. sericeus. This study discloses the complete mitochondrial genome sequence of R. cyanorostris for the first time and provides the most comprehensive phylogenetic reconstruction of the genus Rhodeus based on whole mitochondrial genome sequences. The information obtained in this study will provide new insights for conservation, phylogenetic analysis, and evolutionary biology research.

Complete mitogenome and intra-family comparative mitogenomics showed distinct position of Pama Croaker Otolithoides pama

“…In the mitogenome, a total of 10 intergenic spacer regions (IGS) ranging from 1 -7 bp and nine overlapping regions ranging from 1–10 bp were found among the genes which were typical of most teleosts 39 , 43 , 44 .…”

Complete mitochondrial genome of Rectoris luxiensis (Teleostei, Cyprinidae): characterisation and phylogenetic implications

“…The nucleotide compositions and codon usages of mitogenomes of Cyprinidae were generally similar, but some detectable differences remained. For example, in R. luxiensis , only the COX1 gene started with GTG, but for Rhodeus cyanorostris , both ND1 and COX1 genes started with GTG ( Li et al 2022 ). Whether the diverse usage of start codons amongst different species was generated randomly or with some evolutionarily meaningful preferences, this was an interesting question of selection, but without being given much attention.…”

Complete Mitogenome sequencing of the fish louse Argulus japonicus (Crustacea: Branchiura): Comparative analyses and phylogenetic implications

“…Codon use profiles were examined using MEGA v11 ( 40 ). Additionally, the nucleotide skewness of the A. japonicus mitogenome was assessed through the following formulas: AT skew = (A − T)/(A + T) and GC skew = (G − C)/(G + C) ( 41 ). Alignments of the nucleotide and amino acid sequences of each PCG and concatenated PCGs of A. japonicus and other crustaceans were executed with MEGA.…”