Abstract
Domestic pig (Sus scrofa domesticus) is one of the important farm animal contributing 7% of the country’s total animal protein sources in India. In the present study, random hexamer primer was used to amplify the complete mitochondrial genome of Central Indian domestic pig and resolved the complete mitochondrial sequence by shotgun sequencing followed by de novo assembly in MIRA version 4.0.5. The sequence assembly revealed to be 15,827 bp mitogenome of pig (accession no. KT965278). The mitogenome in the present study has 99% homology with previously reported mitogenome of pigs from different parts of the world. The present study is the first report of complete sequence of mitogenome of pig from Indian subcontinent. Mitogenome analysis by MITOS web server revealed similarity of gene order, organization with the other pig breeds and vertebrates, comprising of 13 protein-coding genes, 22 tRNAs, 2 rRNAs and a control region. It was concluded that modified random hexamer can be successfully used for whole mitogenome sequencing using NGS without designing mitogenome-specific primer, thereby reducing cost and labor.
Highlights
Pig (Sus scrofa domesticus) is domesticated since 8000 years, yet the origin and evolution of domestic pigs of India has not been established
We have resolved the complete mitogenome of a domestic pig from Central India using PGM Ion torrent next-generation sequencing (NGS) technology
The ancestral history of Central Indian (CI) domestic pig was derived from GenBank, which retrieved 59 complete mitogenome sequences of pig and Phacochoerus africanus (NC 008830) as out group using MEGA 6 (Tamura et al 2013)
Summary
KEYWORDS Sus scrofa domesticus; mitogenome; nextgeneration sequencing; PGM Ion torrent Pig (Sus scrofa domesticus) is domesticated since 8000 years, yet the origin and evolution of domestic pigs of India has not been established. The introgression of exotic genome under state sponsored programs to upgrade the local population using semen or live animals of exotic breeds has diluted the gene pool of local breeds, breed specification of the local domestic pig remains questionable. Most studies on Indian domestic pig mitochondrial DNA (MtDNA) are restricted to capillary electrophoresis (CE)-derived short sequence fragments analysis of cytocgrome b, 12S rRNA (Jadav et al 2014a,b), D-loop region of mitogenome (Srivastava et al 2014).
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