The complete mitochondrial genome of Kele pig ( Sus scrofa ) using next-generation deep sequencing
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TECHNICAL NOTE
The complete mitochondrial genome of Kele pig (Sus scrofa) using next-generation deep sequencing Ya Tan1,2 · Kai‑zhi Shi1 · Jing Wang1 · Chun‑lin Du1 · Chun‑ping Zhao1 · Xiong Zhang1 · Li Zhu2 · Yi‑shun Shang1
Received: 17 June 2017 / Accepted: 22 June 2017 © Springer Science+Business Media B.V. 2017
Abstract Kele pig (Sus scrofa), a semi-captive native breed in the Southwest of China, have a range of light to dark brown shades phenotype, just like the coat color of Duroc in some way, and also are well known for their good meat quality. However, Kele pigs decreased dramatically in recent years. The first complete mitochondrial genome of Kele pig was sequenced by next-generation sequencing in order to develop the mitogenome data for genus S. scrofa. The total length of the mitogenome is 16,828 bp, which contains 1 control region, 2 ribosomal RNA genes, 13 protein-coding genes and 22 transfer RNA genes. Phylogenetic analyses based on the complete sequences from several breeds were analyzed by neighbor-joining methods and showed that Kele pigs have closer relationships with domestic pigs in southwest region of China. These results are useful for pig phylogenetic study and evolution study of pig genomes. Keywords Kele pig · Mitochondrial genome · Deep sequencing
Ya Tan and Kai-zhi Shi contributed equally to this work. * Li Zhu [email protected] * Yi‑shun Shang [email protected] 1
Institute of Animal Husbandry and Veterinary, Guizhou Academy of Agricultural Science, Guiyang 550005, Guizhou, China
2
College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
Chinese indigenous pig breeds are well-known for their unique reproductive and lactation performance, good meat quality, strong adaptability and disease resistance traits (Wang et al. 2010). Kele pig, a valuable local breed in Guizhou Province of China, is famous for its excellent meat quality and strong adaption to the harsh local environment. However, Kele pigs have been in direct competition with western breeds (e.g. Landrace and Large White) with higher growth rate and higher lean content, and this breed is in danger of extinction. To preserve this genetic resource and thus contribute to its conservation, we reported the first mitochondrial genome sequence of endangered Kele pig. For studying the complete mitochondrial genome of Kele pig, the blood was collected from an adult Kele pig in Guizhou province of China. The genome DNA was extracted by using TruSeq DNA sample Preparation kit (Illumina, Inc) following the manufacturer’s instructions. An Illumina TruSeq library was generated from the genomic DNA with the verification of DNA quality, and then the library was sequenced on a full run of Illumina Hiseq2500 platform. Reads from the library were assembled and annotated using mitoMaker (http://sourceforge.net/projects/mitomaker/) with Sus scrofa reference mitogenome in NCBI (Genebank number NC_000845.1). The circular map of Kele mitogenome sequence was drawn with CGView (Grant and Sto
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