| Capra contain one domestic species and nine endangered wild species,which are distributed widely and can adapt to extreme environments.During the period from the appearance of the earliest caprine in the late Miocene to livestock breeding currently,the differences between goat and its wild relatives were caused by two stages of evolution and selection,which are(1)the adaptive evolution and selection from ancestors to wild species more than two million years ago,(2)and the artificial selection and breeding from wild species to domesticated species since ten thousand years ago.The progress of natural or artificial selection contains the increase of genotype frequency whose alleles are more adapted to the natural or artificial selection environment and fixed within the population eventually.Through the analyses of the fixed allelic differences between domestic goats and their relatives,the changes between domestic goat and its wild relatives over millions of years could be represented.Due to the rareness of the wild species,it is difficult to obtain its live sample,especially the transcriptome data of wild individuals.In this study,the domestic goat and one of its wild relatives,Siberian ibex(Capra sibirica)were selected.The genomes of ibex and domestic goat were used for the comparative genomics analysis.Combined with the transcriptome data of the hybrid offsprings of domestic goat and Siberian ibex,allele specific expression and splicing were analyzed.This study tried to explain the differences between them for millions of years from the genomic and transcriptome levels.The results are as following:The analyses of positive selection and rapidly evolution were performed for the Capra sibirica and goat genome,respectively.A total of 74 positive selection genes and 410 rapidly evolution genes were found in ibex genome.These genes are enriched in the immune system and olfactory receptors related pathway.And a total of 96 positive selection genes enriched in the immune system and 396 rapidly evolution genes were found in goat genome.The enriched pathway of rapidly evolution genes were signal transduction,olfactory signaling pathway,metabolism,neuronal system,muscle contraction,and so on;According to the ASE analysis of 13 hybrids,897 genes were detected,accounting for 3.1% of the whole genome genes.And the functional enrichment showed a gathering of the immune-related pathways,including TLR family-related pathways,immune cell immune factor-related pathways,disease pathways and immune system pathways.And based on the ASS analysis,617 genes with alternative splicing were defined in all,accounting for 2.1% of the total gene.And it’s mainly functional enrichments are immune-related pathways,including TLR family-related pathways,immune cell immune factor-related pathways,disease pathways and immune system pathways.Considering the comprehensive transcriptome analysis of hybrids,the TLR family and its related pathways were significant in the analyses of adaptive evolution,ASE and ASS.The TLR family plays a fundamental role in the activation of immune response,with the function recognizing pathogens.Through the analysis of the adaptive evolution of Siberian Ibex and goat genomes,and the transcriptome analysis of the hybrids of Siberian Ibex and goat,we found that the changes in immune system were one of important differential phenotypes.In addition,the fixed divergence sites between Siberian Ibex and goat could influence a large proportion of transcriptome varieties by regulating the gene expression or splicing through cis-regulatory.This provides an insight for the analysis of genomic changes in closely related species during the adaptive evolution process,and a basis for demonstrating the genetic basis of the differences between Siberian Ibex and goat in immune system. |
PDF Full Text Request