Mitochondrial genomes (mitogenomes) are widely used in scientific studies on phylogenetic relationships, molecular evolution and population genetics. Here, we sequenced and analysed the mitogenome of Rectoris luxiensis, a Yangtze River drainage endemic, but threatened cyprinid fish of Labeoninae. The complete mitogenome of R. luxiensis was 16,592 bp in length, encoding 13 protein coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a control region. The mitogenome showed a high A+T content (58.2%) and a positive AT-skew (0.10) and negative GC-skew (–0.25) base composition pattern. All the 13 PCGs were found to start with ATG codons, except for the COXI, in which GTG was the start codon. The ratio of non-synonymous and synonymous substitutions (Ka/Ks) of all the 13 PCGs were less than 1, indicating negative or purifying selection evolved in these genes. Comparatively speaking, the evolutionary rate of ATP8 was the fastest and ND4L was the slowest. All tRNAs could fold into a typical cloverleaf secondary structure, except tRNASer1 that lacked a dihydrouridine arm. Phylogenetic relationships, based on the PCGs dataset of 91 mitogenomes of Labeoninae, showed that R. luxiensis grouped with Rectoris posehensis and they formed a monophyletic Rectoris. However, many non-monophyletic genera were revealed in labeoninae fishes, such as Cirrhinus, Decorus, Garra, Labeo and Pseudocrossocheilus, which indicated that the validities of some traditional genera required a further check. This study reported the complete mitogenome of R. luxiensis for the first time, which provided valuable data for future molecular evolution and conservation related studies of Rectoris and other species in Labeoninae.

The mustache toads Leptobrachium boringii and Leptobrachium liui are two attractive species in Megophryidae, in which adult males have mustache-like keratinized nuptial spines on their upper lip. However, both are under threat due to multiple factors, of which scientific studies are still very limited. In this study, two new complete mitochondrial genomes of L. boringii and L. liui were sequenced, assembled, and annotated based on next-generation sequencing. The mitogenome lengths of L. boringii and L. liui were found to be 17,100 and 17,501 bp, respectively, with both containing 13 protein coding genes, 23 tRNAs, 2 rRNAs, and 1 non-coding control region. Nucleotide diversity analyses indicate that atp8, atp6, and nad2 showed higher nucleotide diversity than cox1, cox3, and cytb. The intraspecific genetic distances among three different populations of L. boringii exceed 4%, and those between two populations of L. liui reach 7%. Phylogenetic relationships support their division into two subfamilies of Megophryidae (Leptobrachiinae and Megophryinae) as well as two species groups within Leptobrachium, corresponding to the number of keratinized nuptial spines (10–48 in the L. boringii species group vs. 2–6 in the L. liui species group). The two new mitogenomes reported in this study provide valuable data for future molecular evolutionary and conservation studies of the genus Leptobrachium and other Megophryidae toads.