The complete mitochondrial genome of the Odorrana schmackeri (Anura, Ranidae)

Abstract The complete mitochondrial genome of O. schmackeri has been sequenced and characterized in this study. The mitogenome is a circular molecule of 18 610 bp in length, containing 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 21 transfer RNA (tRNA) genes and a non-coding D-loop region (control region). Its gene arrangements are identical to the typical neobatrachian-type except for the loss of tRNAHis gene. Our data provide a useful resource for the phylogenetic studies of genus Odorrana.

The Chinese piebald odorous frog (Odorrana schmackeri) is widely distributed in southern and south-central China at 200-1400 m elevation (Frost 2015). The specimen of O. schmackeri was captured from Huangshan, Anhui province in China (30 06 0 N, 118 09 0 E; 595 m elevation) and stored in Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources from Anhui Normal University. Total genomic DNA was extracted from O. schmackeri muscle tissue using the standard phenol-chloroform protocol, as described by Sambrook and   Russell (2001), and the complete mtDNA of O. schmackeri was amplified and sequenced using 17 primer pairs.
In this study, we determined the complete mitochondrial genome sequence of O. schmackeri, which is 18 610 bp in size (GenBank accession no. KP732086). The circular mitogenome contains 36 genes, including 13 typical protein-coding genes, 21 tRNA genes (tRNA His gene lacked), two rRNA (12S rRNA and 16S rRNA) genes and a control region. Most genes were encoded on the heavy strand (H-strand) except for ND6 gene and eight tRNA genes (tRNA Pro , tRNA Gln , tRNA Ala , tRNA Asn , tRNA Cys , tRNA Tyr , tRNA Ser(UCN) and tRNA Glu ) which were encoded on the L-strand.
The non-coding regions in the O. schmackeri mtDNA included the control region and some intergenic spacers. The control region was located between Cyt b and tRNA Leu (CUN) genes, with a 2769 bp length. Two long (167 bp and 229 bp) and several short (1-67 bp) non-coding sequences are dispersed in the O. schmackeri mtDNA. The putative origin of light-strand replication (OL) (30 bp) is situated between the tRNA Ala and tRNA Asn genes instead of between tRNA Asn and tRNA Cy as in most vertebrates in the WANCY tRNA cluster (Su et al. 2007;Jiang et al. 2015;Sun et al. 2015;Yan et al. 2016).
The 13 identified PCGs were 11 299 bp in total length (168-1794 bp). Nine of the 13 protein-coding genes initiated with ATG as the start codon, while COI and ATP6 began with ATA, and ND2 and ND4L started with ATT. Stop codons were variable for all protein-coding genes. Six genes (ATP8, ND4L, ND4, Cyt b, ND2 and ND5) used the common TAA and TAG as the stop codon, whereas, COI and COII ended with AGA, and ND6 stopped with AGG. Incomplete stop codons (T--) were found in ND1, ATP6, ND3 and COIII.
The 21 tRNA genes ranged in size from 64 bp (tRNA Cys ) to 73 bp (tRNA Asn and tRNA Leu (UUR) ). In the new mitogenome, the notable feature is the loss of tRNA His , we were unable to find the potential tRNA His gene at any other location in the mitogenome of O. schmackeri. In contrast to the PCGs, loss of tRNA genes is relatively more frequent during the evolution of animal mtDNAs (Zhang et al. 2009). Nevertheless, the loss of tRNA His gene was discovered for the first time in anurans. The predominant explanation for the mitochondrial gene loss is the gene replacement hypothesis (Adams & Palmer 2003).
The complete mitogenomes sequences of O. schmackeri and other individuals belonging to Ranidae were used for phylogenetic analysis, with setting Microhyla ornata as outgroup (Figure 1). Maximum-likelihood method (ML) was used to examine the phylogenetic position of O. schmackeri applying RAxML (7.2.6) (Stamatakis 2007). It appeared that O. schmackeri, O. tormotus, O. margaretae and O. ishikawae formed a monophyletic group. These data provide a powerful tool for systematic analysis of genus Odorrana and family Ranidae.