The complete mitochondrial DNA sequence of Yimeng black pig (Sus Scrofa)

Abstract

Yimeng black pig is a national breed of geographical indication in China. The complete mitochondrial genome sequence of Yimeng black pig was first determined in this study (Accession number MN624263). The mitogenome (16,771 bp) consists of 22 tRNA genes, 13 protein-coding genes, 2 ribosomal RNA genes, and 1 control region (D-loop region). The complete mitochondrial genome sequence of the Yimeng black pig enriches data resource for further study in genetic mechanism and classification.

Keywords:

• Yimeng black pig
• Sus Scrofa
• mitochondria genome

Yimeng black pig (Sus Scrofa), an indigenous breed of Shangdong province in Eastern China, is characterized by a special tolerance of cold, well adaptability to coarse feed, good meat quality, and high slaughter percentage (Zhang 1986). In this study, the complete mitochondrial genome of Yimeng black pig was sequenced and characterized in detail. Sample was collected from Mengyin City (35°43′N, 117°57′E), Shandong Province, China in September 2019. The specimen of Yimeng black pig, named as YimengBP-01 was stored in the College of Life Sciences, Linyi University, Linyi, China. Total genomic DNA was extracted from Yimeng black pig muscle according to Liu et al. (2012, 2014). The complete mitochondrial genome was sequenced using a shotgun approach and assembly. DNA sequence was analyzed using MEGA 7.0 (Kumar et al. 2016). Protein-coding genes were analyzed by ORF Finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html) using the vertebrate mitochondrial code. The tRNA genes were identified by ARWEN (Laslett and Canback 2008) and tRNA-scan SE (Lowe and Eddy 1997).

The complete mitochondrial genome of Yimeng black pig (Accession number MN296708) was 16,771bp in length, of which 15,378 nucleotides are coding DNA, and 1393 nucleotides are non-coding DNA. It consists of 22 tRNA genes, 13 protein-coding genes, 2 ribosomal RNA genes, and 1 control region (D-loop region). The distribution and composition of the mitochondrial genome is also comparable to the case of other vertebrates (Xu et al. 2015; Shan and Liu 2016; Shen et al. 2016; Liu et al. 2016; Li, Liu, Sui et al. 2019; Li, Liu, Zhang et al. 2019). A neighbor-joining phylogenetic tree constructed from the complete mitochondrial genomes of 11 Chinese indigenous pig breeds and 3 foreign pig species is shown in Figure 1. There are 11 overlapping regions (total 104 bp) and 11 intergenic spacers (total 59 bp) among the genes. The total base composition of the mitochondrial genome is 34.61% A, 25.78% T, 26.21% C and 13.40% G, and an A + T (60.39%)-rich feature occurs in the Yimeng black pig. To investigate the nucleotide bias, skew for a given strand was calculated as (A-T)/(A + T) or (G-C)/(G + C) (Perna and Kocher 1995). The AT and GC skews for the Yimeng Black pig mitochondrial genome were 0.146 and −0.323, respectively; this finding indicated that the strand that encoded genes contained more A and C than T and G, and this skew was evidence of codon usage bias. The total length of 13 protein-coding genes is 11,438 bp. ND2, ND3 and ND5 protein-coding genes used the start codon ATA, ND4L used GTG, while other nine protein-coding genes used the start codon ATG. When it comes to stop codons, six genes (COX1, ATPase8, ATPase6, ND4L, ND5 and ND6) terminated with TAA, whereas Cytb terminated with AGA. In addition, other six genes (ND1, ND2, COX2, COX3, ND3 and ND4) terminated with incomplete stop codon T–– that is the 5′ terminal of the adjacent gene, which presumptively formed a complete stop codon by post-transcriptional polyadenylation (Anderson et al. 1981). All the mitogenome genes were encoded on the H strand except for ND6 and eight tRNA genes (tRNA^Gln, tRNA^Ala, tRNA^Asn, tRNA^Cys, tRNA^Tyr, tRNA^Ser, tRNA^Pro and tRNA^Glu). The 12S rRNA (963 bp) gene and 16S rRNA (1572 bp) gene were located between the tRNA^Phe and tRNA^Leu genes and separated by the tRNA^Val gene, and the result was the same as the other mammals. The 22 tRNA genes ranged in length from 59 to 75 bp. The D-loop region locates between tRNA^Pro and tRNA^Phe with a length of 1334 bp. Moreover, the small non-coding region, a putative origin of the light-strand replication, was located between tRNA^Asn and tRNA^Cys genes in the length of 33 bp. The data would facilitate further investigations of phylogenetic relationships within Sus Scrofa.

Figure 1. Neighbor-joining tree based on combining the complete mitochondrial genome sequences of 18 species by using MEGA 7.0. Bootstrap values based on 1000 replicates are shown at branch nodes.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This work was supported by the Key Research and Development Program in Shandong Province [2019YYSP026], the National Natural Science Foundation of China [31560719], and the High-level Talent Introduction Project of Linyi University [LYDX2018BS032].