Characterization of the complete mitochondrial genome of slaty bunting Emberiza siemsseni (Passeriformes: Fringillidae)
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Characterization of the complete mitochondrial genome of slaty bunting Emberiza siemsseni (Passeriformes: Fringillidae) Qiang Shi1,2 · Yang Liu2 · Hong-Feng Zhao1,2
Received: 20 September 2016 / Accepted: 4 October 2016 © Springer Science+Business Media Dordrecht 2016
Abstract The slaty bunting Emberiza (formerly Latoucheornis) siemsseni is a protected species of bird within the family Fringillidae, and is endemic to central and southeastern China. To facilitate its conservation genetic studies, its complete mitochondrial genome has been assembled and characterized from Illumina sequencing reads. The circular genome of E. siemsseni is 16,780 bp in size with an asymmetric base composition (28.9 % A, 33.5 % C, 15.1 % G & 22.5 % T; light strand), and harbors the typical set of 37 mitochondrial genes (i.e. 13 PCGs, 22 tRNAs and two rRNAs) and the non-coding control region. The 13 PCGs are initiated with the typical ATA/ATG/GTG codons, and are terminated with the complete AGA/AGG/TAA/TAG or the incomplete TA(a)/T(aa) codons. Phylogenetic analysis supported the inclusion of E. siemsseni within the genus Emberiza, and suggested that the two subfamilies Carduelinae and Drepanidinae are not monophyletic. Keywords Assembly by reduced complexity (ARC) · Bird · Illumina sequencing · Mitochondrial genome · Mitogenomics
Electronic supplementary material The online version of this article (doi:10.1007/s12686-016-0632-x) contains supplementary material, which is available to authorized users.
Hong-Feng Zhao [email protected] 1
Co-Innovation Center for Qinba Regions’ Sustainable Development, Shaanxi Normal University, Xi’an, Shaanxi 710119, People’s Republic of China
2
College of Life Sciences, Shaanxi Normal University, 620 Western Chang’an Street, Xi’an, Shaanxi 710119, People’s Republic of China
The slaty bunting Emberiza (formerly Latoucheornis) siemsseni is a species of bird within the family Fringillidae, and is endemic to central and southeastern China, mainly occurring in secondary forests and shrubs(Zhang et al. 2013). This species has long been listed among the protected species by the central government (State Forestry Administration of the People’s Republic of China 2000). To facilitate its genetic assays and thus contribute to its conservation, we assembled and characterized its complete mitochondrial genome from high-throughput Illumina sequencing data. The annotated mitogenomic sequence has been deposited into GenBank under the Accession Number KX809695. An individual of E. siemsseni was collected from Zhouzhi County, Shaanxi Province, China (33°51′16″N, 107°50′30″E; 20/10/2010). A voucher specimen (H089) was stored in the specimen room of the College of Life Sciences, Shaanxi Normal University (Xi’an, Shaanxi Province, China). Total genomic DNA was extracted from muscle tissue using an Ezup Column Animal Genomic DNA Extraction Kit (Sangon Biotech, Shanghai, China). The shotgun library preparation and high-throughput sequencing was carried out following the manufacturer’s protocol
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