De Novo Assembly Of Mitochondrial Genomes Provides Insights Into Genetic Diversity And Molecular Evolution In European And Asian Pigs

Pig domestication has a long history,which is also an important part of human civilization.The study of its domestication history and molecular evolution requires the comprehensive use of molecular biology and population genetics methods to analyze modern and ancient porcine DNA.Mitochondrial DNA,as a classical tool for population genetics research,is of vital importance for revealing the domestication and origin of pigs.However,the existing swine mitochondrial sequences on public databases have problems such as short length,few complete sequences,and scarcity of wildboar samples,which hinders us from understanding the maternal genetic structure,diversity and molecular evolution rate before and after pig domestication.In this study,PCR amplification and sequencing,next-generation high-throughput sequencing and chip-capture sequencing were performed to evaluate the genetic structure,nucleotide polymorphism,and selection efficiency of Eastern and Western pigs.The results obtained are as follows:(1)Compared with traditional methods of PCR amplification and sequencing splicing to obtain full mitochondrial sequences,the use of second-generation high-throughput sequencing data to de novo assemble mitochondrial genomes is more time-and labor-saving,which can efficiently mine maternal genetic information of wild boars and domestic pigs.(2)Phylogenetic analysis shows that there are obvious maternally inherited structural differences between Eurasian domestic and wild pigs.Compared with European pigs,the domestication history of Asian pigs is much more complicated.At the same times,we also detect a small fraction of maternal introgression(about 5%),of which impacts of such individuals needs careful analysis.(3)The genetic diversity of mitochondrial genome in both European and Asian pigs are markedly reduced since domestication.Compared to other areas on mitochondrial DNA,the nucleotide polymorphisms in the D-loop region varied most significantly,which can be used as a molecular marker to identify individuals.(4)The mitochondrial sequences of Eurasian domestic and wild pigs are under purifying selection(Ka/Ks less than 1).The branch model test showed that the mitochondrial genomes of Eurasian domestic and wild pigs differed with their own evolutionary patterns.Besides,the natural selection efficiency of European and Asian domestic pigs is declined by 200%compared to the wild boars,probably due to the natural selection of relaxation after domestication and the change of effective maternal population size.(5)Our preliminary analysis of ancient DNA,despite the limitation of the quality of the extracted DNA,chip enrichment,can increase the mitochondrial sequencing coverage to 26-89 times compared with the traditional sequencing technology,indicating that chip capture and sequencing is an effective method to detect genetic information hidden in ancient samples.The above results illustrate the important changes in mitochondrial genome genetic diversity and selection efficiency since the domestication of Eurasian pigs.In the future,more comprehensive technical tools will be used to further produce abundant mitochondrial sequences and dig deep into important genetic information in ancient DNA to deepen our understanding of the maternal genetic history of animal domestication,and to lay a scientific foundation for our better germplasm conservation of genetic resources pigs.