Analysis of the complete organellar genomes of the Streaked Rosefinch Carpodacus rubicilloides on the Tibet Plateau

Abstract

The Streaked Rosefinch (Carpodacus rubicilloides) is a poorly-known bird species distributed in China and Himalayas. In this paper, we described the whole mitochondrial genome of the Streaked Rosefinch. The entire mitochondrial sequences were determined using long-range PCR and conserved primer walking approaches. The results demonstrated that the whole mitochondrial genome of C. rubicilloides was 16,805 bp in length with 53.9% A + T content; the genome harbored the same gene order as that of other passerine birds, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 non-coding control region. The control region (D-loop) of C. rubicilloides was located between tRNA-Gln and tRNA-Phe with 1228 bp length. Phylogenetic analysis indicated that the genome of Carpodacus species clustered within a clade and is closer related to other Fringillidae species than Anatidae species. These mitochondrial data are potentially important for the further studies on molecular evolution and conservation genetics in true finch species.

Keywords:

• Rosefinch
• mitochondrial genome
• passerine
• Carpodacus
• Tibet Plateau

The streaked rosefinch Carpodacus rubicilloides is a true finch species and it commonly occurs in southwest China and the Himalayas (Zheng 2005; Clement 2018). The typical habitat of this species is shrubland at high altitudes and its altitudinal range varies from 3000 m to even more than 5000 m above sea level (Martens and Trautmann 2008; Clement 2018). Currently, the Streaked Rosefinch is still poorly understood and the knowledge on its natural history is mainly based on simple descriptions from species accounts (Martens and Trautmann 2008; Clement 2018). In this study, we described the whole mitochondrial genome of Carpodacus rubicilloides based on next-generation sequencing. The newly sequenced complete mitochondrial genome sequence will provide basic data for further studies on this poorly-known species.

Blood sample of the Streaked Rosefinch was collected by puncturing the brachial vein from a female individual (id cr_1702) caught by mist nets, on 16 June 2017 at Tianjun County (37°18′ N, 99° 01′ E; 3416 m a.s.l.), northeastern of Tibet Plateau. The sample was quickly stored in TES buffer (50 mM EDTA, 1% SDS, 50 mM Tris). Genomic DNA was extracted from blood samples according to the protocol of TIANamp Genomic DNA kits (Tiangen, Beijing). The remaining blood sample is now stored in Room 315 of College of Life Science at Yangtze University. The complete sequence of the Streaked Rosefinch mitochondrial genome was determined by long-range PCR and conserved primer walking approaches.

The results revealed that the entire mitochondrial genome of the Streaked Rosefinch comprised 16,805 bp nucleotides in length, which exhibited the typical mitochondrial structure of passerine birds (Li et al. 2016; Cao et al. 2017), including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a non-coding control region. The overall nucleotide composition includes A (29.93%), T (23.96%), G (14.92%), and C (31.19%), with a total A and T content of 53.88%. The entire mitochondrial sequence has been deposited in GenBank with accession number of MH363715.

Among the 37 genes, 28 genes were encoded on heavy strand and the remaining genes on the light strand (Table 1). All protein-coding genes of the Carpodacus rubicilloides mitochondrial genome started with ATG codon, except for ND3 with ATA. For terminate codon usage, most of the genes terminate with TAA or TAG, ND5 and ND1 terminated with AGA, COX1 with AGG, and the COX3 and ND4 genes had an incomplete termination codon T (Table 1). The control region of C. rubicilloides was located between tRNA-Gln and tRNA-Phe with 1228 bp length, which contained several conserved sequences involved in the replication and transcription of mitochondrial genome.

Phylogenetic analyses were conducted with mitochondrial data of this study and 26 other bird species from the GenBank database. The topology of the tree was inferred using Neighbor-Joining analyses in the program MEGA7 (Kumar et al. 2016). Execution model was statistically well supported by high bootstrap values at most nodes (Figure 1). The phylogenetic tree revealed that four Carpodacus species clustered in a clad and were closer related to Fringillidae species than Anatidae. All the clades were consistent with the traditional morphology-based taxonomies and recent molecular taxonomies (Gill and Donsker 2018). Currently, most of Carpodacus species are poorly known about their natural history and genetic information (Xiao et al. 2017; Gill and Donsker 2018), and only three complete mitochondrial genomes of Carpodacus species have released in Genebank (Figure 1). The additional complete mitochondrial genome of the Streaked Rosefinch could provide fundamental information for further molecular phylogenetic studies on Carpodacus species.

Figure 1. Evolutionary relationships of 27 taxa were inferred using the Neighbor-Joining method based on their complete mitochondrial genome (the genbank accession number in parentheses; data from this study were marked with a triangle; numbers at branches indicate bootstrap values from 1000 replications.

Acknowledgment

We appreciate the help from Bao Gang, Zhuoma Linzhen, Le Yang and Jicuo Dou in the field.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This study was supported by National Natural Sciences Foundation of China [Grant 31501869].