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

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.

Novel Gene Rearrangement in the Mitochondrial Genome of Three Garra and Insights Into the Phylogenetic Relationships of Labeoninae

Complete mitochondrial genomes (mitogenomes) can provide valuable information for phylogenetic relationships, gene rearrangement, and molecular evolution. Here, we report the mitochondrial whole genomes of three Garra species and explore the mechanisms of rearrangements that occur in their mitochondrial genomes. The lengths of the mitogenomes’ sequences of Garra dengba, Garra tibetana, and Garra yajiangensis were 16,876, 16,861, and 16,835, respectively. They contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genomes of three Garra species were rearranged compared to other fish mitochondrial genomes. The tRNA-Thr, tRNA-Pro and CR (T-P-CR) genes undergo replication followed by random loss of the tRNA-Thr and tRNA-Pro genes to form tRNA-Thr, CR1, tRNA-Pro and CR2 (T-CR-P-CR). Tandem duplication and random loss best explain this mitochondrial gene rearrangement. These results provide a foundation for future characterization of the mitochondrial gene arrangement of Labeoninae and further phylogenetic studies.

Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes)

The cyprinid tribe Labeonini (sensuRainboth, 1991) is a large group of freshwater fishes containing around 40 genera and 400 species. They are characterized by an amazing diversity of modifications to their lips and associated structures. In this study, a total of 34 genera and 142 species of putative members of this tribe, which represent most of the generic diversity and more than one third of the species diversity of the group, were sampled and sequenced for four nuclear genes and five mitochondrial genes (totaling 9465bp). Phylogenetic relationships and subdivision of this tribe were investigated and the placement and status of most genera are discussed. Partitioned maximum likelihood analyses were performed based on the nuclear dataset, mitochondrial dataset, combined dataset, and the dataset for each nuclear gene. Inclusion of the genera Paracrossochilus, Barbichthys, Thynnichthys, and Linichthys in the Labeonini was either confirmed or proposed for the first time. None of the genera Labeo, Garra, Bangana, Cirrhinus, and Crossocheilus are monophyletic. Taxonomic revisions of some genera were made: the generic names Gymnostomus Heckel, 1843, Ageneiogarra Garman, 1912 and Gonorhynchus McClelland, 1839 were revalidated; Akrokolioplax Zhang and Kottelat, 2006 becomes a junior synonym of Gonorhynchus; the species Osteochilus nashii was found to be a member of the barbin genus Osteochilichthys. Five historical hypotheses on the classification of the Labeonini were tested and rejected. We proposed to subdivide the tribe, which is strongly supported as monophyletic, into four subtribes: Labeoina, Garraina, Osteochilina, and Semilabeoina. The taxa included in each subtribe were listed and those taxa that need taxonomic revision were discussed.