De novo assembly of mitochondrial genomes provides insights into genetic diversity and molecular evolution in wild boars and domestic pigs

• Published in: Genetica Vol. 146; no. 3; pp. 277 - 285
• Main Authors: Ni, Pan, Bhuiyan, Ali Akbar, Chen, Jian-Hai, Li, Jingjin, Zhang, Cheng, Zhao, Shuhong, Du, Xiaoyong, Li, Hua, Yu, Hui, Liu, Xiangdong, Li, Kui
• Format: Journal Article
• Language: English
• Published: Cham Springer International Publishing 01-06-2018; Springer Nature B.V
• Subjects: Animal Genetics and Genomics; Bayesian analysis; Biological evolution; Biomedical and Life Sciences; Divergence; Domestic animals; Domestication; Evolutionary Biology; Gene sequencing; Genetic diversity; Genetic relationship; Genomes; Hogs; Human Genetics; Life Sciences; Microbial Genetics and Genomics; Mitochondria; Mitochondrial DNA; Molecular chains; Molecular evolution; Nucleotides; Original Paper; Plant Genetics and Genomics; Population number; Suidae; Swine; Genetic diversity; Genetic structure; Selection; Mitochondrial genomes; Sus scrofa
• ISSN: 0016-6707; 1573-6857
• DOI: 10.1007/s10709-018-0018-y

Up to date, the scarcity of publicly available complete mitochondrial sequences for European wild pigs hampers deeper understanding about the genetic changes following domestication. Here, we have assembled 26 de novo mtDNA sequences of European wild boars from next generation sequencing (NGS) data and downloaded 174 complete mtDNA sequences to assess the genetic relationship, nucleotide diversity, and selection. The Bayesian consensus tree reveals the clear divergence between the European and Asian clade and a very small portion (10 out of 200 samples) of maternal introgression. The overall nucleotides diversities of the mtDNA sequences have been reduced following domestication. Interestingly, the selection efficiencies in both European and Asian domestic pigs are reduced, probably caused by changes in both selection constraints and maternal population size following domestication. This study suggests that de novo assembled mitogenomes can be a great boon to uncover the genetic turnover following domestication. Further investigation is warranted to include more samples from the ever-increasing amounts of NGS data to help us to better understand the process of domestication.