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

Abstract

Mitochondrial genomes (mitogenomes) have been widely used in phylogenetic analysis and evolutionary biology. The Labeoninae is the largest subfamily of Cypriniformes and has great economic importance and ecological value. In this study, we sequenced, annotated, and characterized the complete mitogenome of Linichthys laticeps and then constructed the phylogenetic tree with previously published Labeoninae mitogenomes. The mitogenome of L. laticeps was 16,593 bp in length, with an A + T content of 57.1%. The mitogenome contained a standard set of 37 genes and a control region with the same order and orientation of genes as most fish mitogenomes. Each protein-coding gene (PCG) was initiated by an initial ATG codon, excluding COI, that began with a GTG codon. Furthermore, most of the PCGs were terminated by a conventional stop codon (TAA/TAG), while an incomplete termination codon (TA/T) was detected in 7 of the 13 PCGs. Most tRNA genes in L. laticeps were predicted to fold into the typical cloverleaf secondary structures. The Ka/Ks (ω) values for all PCGs were below one. The phylogenetic relationships of 96 Labeoninae mitogenomes indicated that Labeoninae was not a monophyletic group and L. laticeps was closely related to the genera Discogobio and Discocheilus. Overall, our study provided the first complete annotated mitogenome of L. laticeps, which filled a knowledge gap in Labeoninae and extended the understanding of the taxonomy and mitogenomic phylogeny of the subfamily Labeoninae.

The New Mitochondrial Genome of Hemiculterella wui (Cypriniformes, Xenocyprididae): Sequence, Structure, and Phylogenetic Analyses

“…It implies that ATPase 8 might evolve more rapidly than other mitochondrial protein coding genes. Even under different selection pressures, the evolutionary patterns of 13 PCGs in Xenocyprididae were similar to those of Sinocyclocheilus (Fang, 1936) fishes [23] and Labeoninae [9]. Furthermore, the average Ka/Ks ratios of all PCGs were much lower than one, indicating that these genes were all under a strong purifying selection.…”

“…Next-generation sequencing was performed at the DNA Stories Bioinformatics Center (Chengdu, Sichuan, China). Library construction and Illumina sequencing were carried out according to Zhang et al [9].…”

“…The minimum overlap region was located between tRNA Thr and tRNA Pro (1 bp), and the maximum overlap region was located between ATPase 8 and ATPase 6, ND4L and ND4 (7 bp). Mitochondrial gene overlap and gene spacers were common phenomena in teleost species [9,21]. There were 13 intergenic spacers found in the H. wui mitochondrial genome.…”