The forest musk deer(Moschus berezovskii) is one of the most endangered species in China.Over the past decades,extensive hunting and poaching have pushed the forest musk deer to the edge of extinction,and conservation...The forest musk deer(Moschus berezovskii) is one of the most endangered species in China.Over the past decades,extensive hunting and poaching have pushed the forest musk deer to the edge of extinction,and conservation biologists are presently pursuing scientific management plans to rescue this species.The major histocompatibility complex(MHC),a cluster of genes responsible for antigen presentation,is a highly polymorphic genomic region in vertebrates that has become a popular functional marker system for studying adaptive variation.In this study,we developed locus-specific genotyping primers for exon 2 fragments of one DRA gene and one DRB locus of the forest musk deer using a suite of comprehensive methods that included universal primer amplification,genome walking,single-strand conformation polymorphism(SSCP),heteroduplex(HD) profiling,and sequence analysis.Each forest musk deer showed no more than two sequences per locus,confirming the specificity of our primers.Genotyping with these primers allowed us to identify two DRA alleles and six DRB alleles in a captive breeding population of the Sichuan Musk Deer Breeding Institution.For the DRA locus,we found a slightly higher observed heterozygosity(N O =0.154) than expected(N E =0.143).In contrast,the DRB locus showed a significant heterozygote deficiency(N O =0.508;N E =0.761;P<0.05),which was probably due to inbreeding in the captive population.An obvious excess of nonsynonymous substitutions over synonymous was observed at the antigen-binding positions of the DRA and DRB loci,showing the presence of positive selection in the forest musk deer DR genes.Finally,generation of phylogenetic trees for the DRA and DRB sequences of the forest musk deer and other ruminants revealed that the DRA and DRB loci identified in this study had homologous relationships with the known ruminant DRA and DRB genes.Based on this analysis,and to facilitate future studies,we named these novel loci Mobe-DRA and Mobe-DRB3.展开更多
The major histocompatibility complex(MHC) genes play pivotal roles in the immune system of vertebrates against antigens.They are also significant indicators of genetic structure,and are vital to species-level populati...The major histocompatibility complex(MHC) genes play pivotal roles in the immune system of vertebrates against antigens.They are also significant indicators of genetic structure,and are vital to species-level population viability analyses and disease risk assessments.In this study,two DRA and two DQA sequences were isolated from Hainan Eld's deer(Cervus eldi hainanus) using rapid amplification of cDNA ends(RACE) and single-strand conformation polymorphism-heteroduplex(SSCP-HD) analysis.Nucleotide sequence analysis revealed large differences between the two DQA sequences,especially in their exon 2 regions,but only minimal differences between the variants of the DRA gene.Comparison of the predicted amino acid sequences of the Ceel-MHC class Ⅱ A variants with those from six other species revealed that these molecules share high homology among ruminants.A phylogenetic tree of four class Ⅱ A sequences from Hainan Eld's deer and the other species placed the newly identified DQA and DRA genes on two distinct branches(100%-supportively),and further divided the two DQA sequences into 98%-supportive DQA1 and 99%-supportive DQA2 clusters,respectively.Therefore,this study identified monomorphic Ceel-DQA1 and Ceel-DQA2 genes,and one dimorphic Ceel-DRA gene from Hainan Eld's deer.展开更多
基金supported by the National Natural Science Foundation of China (30870362)the State Forestry Administration of Chinathe Fundamental Research Funds for the Central Universities of China
文摘The forest musk deer(Moschus berezovskii) is one of the most endangered species in China.Over the past decades,extensive hunting and poaching have pushed the forest musk deer to the edge of extinction,and conservation biologists are presently pursuing scientific management plans to rescue this species.The major histocompatibility complex(MHC),a cluster of genes responsible for antigen presentation,is a highly polymorphic genomic region in vertebrates that has become a popular functional marker system for studying adaptive variation.In this study,we developed locus-specific genotyping primers for exon 2 fragments of one DRA gene and one DRB locus of the forest musk deer using a suite of comprehensive methods that included universal primer amplification,genome walking,single-strand conformation polymorphism(SSCP),heteroduplex(HD) profiling,and sequence analysis.Each forest musk deer showed no more than two sequences per locus,confirming the specificity of our primers.Genotyping with these primers allowed us to identify two DRA alleles and six DRB alleles in a captive breeding population of the Sichuan Musk Deer Breeding Institution.For the DRA locus,we found a slightly higher observed heterozygosity(N O =0.154) than expected(N E =0.143).In contrast,the DRB locus showed a significant heterozygote deficiency(N O =0.508;N E =0.761;P<0.05),which was probably due to inbreeding in the captive population.An obvious excess of nonsynonymous substitutions over synonymous was observed at the antigen-binding positions of the DRA and DRB loci,showing the presence of positive selection in the forest musk deer DR genes.Finally,generation of phylogenetic trees for the DRA and DRB sequences of the forest musk deer and other ruminants revealed that the DRA and DRB loci identified in this study had homologous relationships with the known ruminant DRA and DRB genes.Based on this analysis,and to facilitate future studies,we named these novel loci Mobe-DRA and Mobe-DRB3.
基金supported by the National Natural Science Foundation of China (30970426)a special grant from the State Forestry Administration of Chinathe Fundamental Research Funds for the Central Universities of China
文摘The major histocompatibility complex(MHC) genes play pivotal roles in the immune system of vertebrates against antigens.They are also significant indicators of genetic structure,and are vital to species-level population viability analyses and disease risk assessments.In this study,two DRA and two DQA sequences were isolated from Hainan Eld's deer(Cervus eldi hainanus) using rapid amplification of cDNA ends(RACE) and single-strand conformation polymorphism-heteroduplex(SSCP-HD) analysis.Nucleotide sequence analysis revealed large differences between the two DQA sequences,especially in their exon 2 regions,but only minimal differences between the variants of the DRA gene.Comparison of the predicted amino acid sequences of the Ceel-MHC class Ⅱ A variants with those from six other species revealed that these molecules share high homology among ruminants.A phylogenetic tree of four class Ⅱ A sequences from Hainan Eld's deer and the other species placed the newly identified DQA and DRA genes on two distinct branches(100%-supportively),and further divided the two DQA sequences into 98%-supportive DQA1 and 99%-supportive DQA2 clusters,respectively.Therefore,this study identified monomorphic Ceel-DQA1 and Ceel-DQA2 genes,and one dimorphic Ceel-DRA gene from Hainan Eld's deer.
