Complete mitochondrial genome of Chrysolophus pictus (Galliformes: Phasianidae), a national protected wild pheasant in China.

The complete mitochondrial genome (mitogenome) of golden pheasant Chrysolophus pictus from North China was sequenced by the shotgun genome skimming methods. The mitogenome of C. pictus was 16,678 bp in length, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one non-coding control region (D-loop). Its overall base composition was 30.4% A, 24.8% T, 31.2% C and 13.6% G. All protein-coding genes had a typical ATG initiation codon except COX1 with GTG and terminated with a TAN codon, whereas COX1 terminated with a codon of AGG, COX3, ND2 and ND4 terminated with a single T. The ML phylogenetic tree constructed using 13 protein-coding genes showed that Chrysolophus species formed a monophyletic group, which was sister to the clade clustered by the two genera Crossoptilon and Lophura.

The golden pheasant or Chinese pheasant Chrysolophus pictus is a gamebird of the order Galliformes (Gallinaceous birds) and the family Phasianidae (Pheasants) (Jobling 2010). The species is endemic in China, and its core distribution area is at Gansu and Qinling area (Zhao 2001). The National Forestry Administration of China listed the species into ‘Red Book of Endangered Animals of China’ as the protected wild animal level: Level 2 and also listed in IUCN Red List of Threatened Species ver. 3.1 regarded as ‘Least Concern’ (2012). The previous studies on C. pictus mainly focused on possible evolutionary significance of egg-white proteins, egg production performance and nutritional value (Baker 1965; Gao et al. 2016; Kullu et al. 2017). Genetic characteristics are very important in species conservation, however, there is no more reports on the mitogenome of the golden-pheasant C. pictus in North China. We here performed the complete mitogenome sequencing of C. pictus for the purpose of better understanding the pheasant genomic structure, function and genetic variation.

The feather material from a healthy adult individual of Chrysolophus pictus by undamaged method in Manghe National Nature Reserve (112°22′10″E, 35°12′30″N, altitude 310 m), Shanxi, China, and the total genomic DNA (Voucher No. Ren-Z17) was stored at the Zoology Herbarium of School of Life Science in Shanxi University. The mitogenomic sequence was obtained using the shotgun genome skimming method on an Illumina HiSeq4000 platform (Zimmer and Wen 2015), and was then de novo assembled by SPAdes v. 3.7.1 (Bankevich et al. 2012).

The complete mitochondrial genome of Chrysolophus pictus is 16,678 bp in length (GenBank Accession No. MN857545), and consists of 30.4% A, 24.8% T, 31.2% C and 13.6% G with a little higher A + T content (55.2%) than that of G + C (44.8%), which is basically consistent with those of other Phasianidae species. The complete mitogenome of C. pictus totally included 13 protein-coding genes (ND1-6, ND4L; COX1-3; ATP6 and ATP8; and Cyt B), 22 tRNA genes, two rRNA genes (12S and 16S rRNA) and one non-coding control region (D-loop). All the protein-coding genes had a typical ATG initiation codon except COX1 with GTG. Most genes terminated with TAA codons except ND6 and Cyt B had TAG termination codons, and COX1 with AGG codon, whereas, COX3, ND2 and ND4 each terminated with a single T. The genetic variation among the four Chrysolophus pictus individuals is much lower with average similarity 99.6%.

We downloaded the complete mitogenomic sequences of Phasianidae species from GenBank with three Odontophoridae species as outgroups to construct the phylogenetic relationship of Chrysolophus pictus and other Phasianidae species in RAxML program under the GTRGAMMA model with 1000 bootstrap replicates (Stamatakis 2014). The phylogenetic analyses indicated that Chrysolophus is sister to Phasianus but with poor support, and they are close to the clade clustered by the two genera Crossoptilon and Lophura (Figure 1). In conclusion, our study contributes to understand the structure and composition of the complete mitogenome of C. pictus and the evolutionary history and genetic resource conservation of Phasianidae.

Figure 1.

Maximum likelihood phylogenetic tree of Chrysolophus pictus and other Phasianidae species based on 13 protein-coding genes. Numbers associated with branches are BS > 75, and “★” represents nodes with 100% BS.