Mitochondrial genome of Stachyris ruficeps (Aves, Passeriformes, Timaliidae).

Stachyris ruficeps are commonly found in the eastern Himalayas and south China. In our study, we reported the complete mitogenome and obtain basic genetic information of S. ruficeps for the first time. The complete mitochondrial genomes of S. ruficeps (16 885bp in length) had 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes (12S rRNA and 16S rRNA) and 2 control regions. All of the 13 PCGs were initiated by ATG. All the genes in S. ruficeps were distributed on the H-strand, except for the ND6 gene and eight tRNA genes which were encoded on the L-strand.

Stachyris ruficeps (Aves, Passeriformes, Timaliidae) was first discovered in India (Blyth 1847), Rufous-Capped Babbler are commonly found in the eastern Himalayas and south China (Liu et al. 2012). Stachyris ruficeps is a non-migration oriental bird, it always inhabited broadleaf evergreen forests from 200 to 2500 m (Qu et al. 2015). The length of S. ruficeps body was 11cm, the whole body was pale olive, and the back of top head was red brown, throat with thin vertical stripes, chest and central of the abdomen both were yellow-white. The S. ruficeps mitochondrial genome could provide the molecular data for the species diversity, genetic diversity and ecological diversity study.

Total mitochondrial genome of S. ruficeps was extracted from the muscle tissue by the traditional phenol-chloroform method (Sambrook & Russell 2001). The muscle sample of S. ruficeps was collected from Ya'an (N30°01′, E103°02′) and stored at the Wildlife Conservation Laboratory, Sichuan Agricultural University, Sichuan province, China. Twenty-one primer pairs were designed according to Garrulax cineraceus (GeneBank number: NC024553) for amplification and sequencing. The complete mitochondrial genomes of S. ruficeps has been submitted to GenBank and the accession number: KU362930 has been obtained.

The complete mitochondrial genome of S. ruficeps (16 885bp in length) had 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes (12S rRNA and 16S rRNA) and 2 control regions. The nucleotide composition of S. ruficeps mitogenome was 30.70% for A, 31.37% for C, 23.43% for T and 14.50% for G (C > A> T > G). The compact arrangement of S. ruficeps sequence was similar to the typical avian mitochondrial genome (Huan et al. 2015; Zhou et al. 2015). All of 13 PCGs were initiated by ATG. Nine of 13 PCGs used complete (TAA) or incomplete (TA– or T––) stop codons. ND1 and ND5 regarded AGA as the stop codon, COX1 ended with AGG, and ND6 used TAG as stop codon. Twelve PCGs, 2 rRNAs, and 14 tRNAs were encoded on the H-strand, whereas the ND6 and 8 tRNAs (tRNA, tRNA, tRNA, tRNA, tRNA, tRNA, tRNA, tRNA) were encoded on the L-strand. The two control regions of the S. ruficeps mitochondrial genome were D-loop1 (1092 bp) and D-loop2 (231 bp). 12SrRNA (974bp) and 16SrRNA (1601bp) were located between tRNA and tRNA(UUR) and were separated by tRNA.

In order to analyse the phylogenetic relationships of S. ruficeps, we constructed a phylogenetic tree using MrBayes (Huelsenbeck 2001). In Figure 1, the phylogenetic tree showed that Macronous and Stachyris were clustered in a clade and Stachyris rufifrons was the nearest sister to S. ruficeps. This result was consistent with Cibois et al. (2002) and Moyle et al. (2012).

Figure 1.

Bayesian tree based on cytb sequence of 13 Timaliidae and one Paradoxornis birds. The Bayesian tree was reconstructed with general-time-reversible (GTR) model, and the Markov chains for 1 000 000 generations. Numbers on branches represent bootstrap supports (1000 replicates). Paradoxornis webbianus were used as outgroup.