红腹锦鸡MHC I类座位的分离及其适应性进化研究
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摘要
红腹锦鸡(Chrysolophus pictus)为我国特有的国家二级保护的近危物种。近些年来,栖息地的严重片段化及过度猎杀,导致红腹锦鸡数量剧降。因此,对该物种的遗传多样性及其在栖息地片段化的胁迫下采取的适应性进化机制的研究是十分必要的。
主要组织相容性复合体(MHC)是脊椎动物的免疫系统中最重要的基因家族之一。多态的MHC功能基因编码的各种糖蛋白分子,主要负责结合并递呈病原体肽段,从而引起适当的免疫反应。MHC基因的多样性会直接影响个体对病原体疾病的抵抗,关乎个体的生存,对提高整个物种对不断变化的外界环境的适应能力也起着关键的作用。它已经成为迄今开展脊椎动物适应性进化研究的最受欢迎的分子标记系统。本文分离并获取了红腹锦鸡全部的MHCⅠ类基因序列,基于经典MHCⅠ类座位的特异性基因型分型,建立了一套完善的分子标记系统,完成了对红腹锦鸡12个野生种群的遗传变异、多态性维持机制、种群分化和种群遗传结构等的研究工作。本研究的主要研究结果及结论如下：
(1)本研究从建库个体中获取6条MHCⅠ类gDNA全长序列,分别命名为A-F,SSCP-HD的复原结果表明已经完全分离出该红腹锦鸡个体的MHCⅠ类序列。跨基因扩增的结果表明A/C和B/D分别属于Chpi-IA1和Chpi-IA2。
(2)通过筛选实验室先前建立的红腹锦鸡BAC文库,得到一个约为80kb的C11BAC克隆,该克隆与之前筛选出的96kb S2BAC克隆形成重叠群。除了Chpi-IA1和Chpi-IA2两个MHCⅠ类基因,这个克隆重叠群还包括序列E和F对应的新的Ⅰ类基因座位,命名为Chpi-IA3。而Chpi-IA3仅存在于C11BAC克隆中。
(3)尽管3个MHCⅠ类基因的cDNA全序列都具有经典MHCⅠ类基因的典型特征,但其组织表达检测表明：Chpi-IA1和Chpi-IA2具有广泛的组织表达,为经典MHCⅠ类基因；Chpi-IA3在已检测的多种组织未表达,且其位于红腹锦鸡MHC-B核心区域之外的位置,为非经典MHCⅠ类基因。
(4)结合PCR-SSCP和测序方法,成功建立了红腹锦鸡两个经典MHC工类基因(Chpi-IA1和Chpi-IA2)exon2和exon3的座位特异性基因型分型方法,并运用这套位点特异扩增体系对红腹锦鸡12个野生种群的334个个体进行多态性调查。2个多态的MHCⅠ类基因共包括41条exon2序列和39条exon3序列：Chpi-IA1-E214条,CChpi-IA1-E211条；Chpi-IA2-E228条,Chpi-IA2-E327条。与Chpi-IA1相比,Chpi-IA2具有更高的氨基酸多态性。
(5)平衡选择维持红腹锦鸡MHCⅠ类基因多态性的主要机制之一。我们的相关证据有：两个多态的MHCⅠ类基因(Chpi-IA1和Chpi-IA2)的PBR较non-PBR具有更高的氨基酸变异；功能结构域α1的抗原结合位点的非同义替换率高于同义替换率；Chpi-IA2α1和α2结构域的10个正选择位点,其中8个来自于其PBR；高频等位基因在所有种群中共享。
(6)重组也是红腹锦鸡MHC Ⅰ类基因的重要的进化模式。根据系统树分析,约有37.0%的Chpi-IA2-E2等位基因与所有的Chpi-IA1-E2等位基因形成独立的进化枝；通过MaXChi2,3Seq和GARD三种方法证实这两个Ⅰ类座位存在基因间的重组,且这些Chpi-IA2-E2等位基因为重组序列。
(7)Ⅰ类基因分化系数表明,秦岭南北麓种群间无明显的分化,但长江以南的种群与长江以北的种群之间的分化显著。根据AMOVA及贝叶斯归类法的分析结果,将红腹锦鸡的12个种群可以划分为2个区域,即{长江以南(LC,HN,QJ,GZ),长江以北(LX,TS,BJ,FP,LN,JQ)},这表明长江的阻隔作用促使这两个区域的种群存在较大的遗传差异。
Golden pheasant(Chysolophus pictus) is a near threatened species endemic to China with national second-class protection. In rencent years, there is a sharp decline in the number of golden pheasants, which is caused by severe fragmentation of habitat and excessive hunting. Hence, it is necessary to investigate the genetic diversity and explore the adaptive evolution mechanism of this species under the stress of habitat fragmentation.
The major histocompatibility complex (MHC) is one of the most important gene family in the vertebrate immune system, encoding diverse glycoprotein molecules, which responsible for binding and presenting pathogen peptides to T cells in order to trigger an appropriate immune response. The diversity of MHC genes may directly influence the survival of individuals against pathogen disease and it also plays a key role in the adaptation of species to the changing environment. It becomes a popular molecular marker system in the adaptive evolutionary study of vertebrates. In this study, we isolated all the MHC I gene sequences in the golden pheasant, then developed locus-specific genotying primers and finally set up a good molecular marker system of classical MHC I loci for this endangerd bird. We investigated the genetic variability, analysed the maintenance mechanisms of MHC polymorphism, and discussed population structuring in twelve wild golden pheasant populations. The main results and conclusions are listed below.
(1) We isolated all the MHC I genes and got six full-length genomic sequences from the same individual and designated them A-F according to an alphabetical order. The results of cross-locus amplication showed A/C and B/D belonged to Chpi-IA1and Chpi-IA2respectively.
(2) We isolated a positve BAC clone C11, which is about80kb in length, and forms a contig with the previously published S2BAC clone (96kb). There were three MHC I genes inclued in this contig:the former two genes Chpi-IA1and Chpi-IA2, and the new identified gene Chpi-IA3. The novel MHC Ⅰ gene was comprised of sequences E and F and was only found in C11.
(3) Analysis of tissue expression revealed that IA1and IA2could be regarded as classical loci due to their extensive tissue expression while IA3appeared to be nonclassical one without expression patterns, though the predicted cDNA full-length sequences had normal exonic structures and typical characteristics of classical class MHC I genes.
(4) Combining the PCR-SSCP and sequencing methods, we succeeded in establishment of locus-specific genotyping techniques for exon2and exon3for the two classical MHC class I genes (Chpi-IA1and Chpi-IA2). Then we investigated genetic polymorphisms of334individuals from12wild population of the golden pheasant and identified41exon-2alleles and39exon-3ones across the two polymorphic MHC class I genes:Chpi-IA1-E2(14), Chpi-IA1-E2(11), Chpi-IA2-E2(28) and Chpi-IA2-E3(27).
(5) We found evidences of balancing selection in the MHC class I genes of the golden pheasant; showing much higher amino acid substibutions in the PBR than the non-PBR, having an exccess of nonsynonymous nucleotide substitution over synonymous nucleotide substitution at the PBR sites of al domain in both polymorphic MHC class I genes, presenting eight out of ten positively selective sites in the PBR, observing sharing of alleles in high frequencies over all the populations.
(6) Recombination is also an important evolutionary mechanism of MHC class I genes in the golden pheasant. The phylogenetic tree showed that about37.0%Chpi-IA2-E2alleles and all Chpi-IA1-E2alleles were grouped together. The three methods (MaxChi2,3Seq and GARD), all verificated that the inter-gene recombination existed between Chpi-IA2-E2and Chpi-IA1-E2, and found that those Chpi-IA2-E2alleles might be recombinants.
(7) Class I gene-based differentiation coefficients revealed there were no significant genetic divergence between the populations of the south and those of the north of Qinling Mountain, while significant differentiation between populations of south to the Yangtze River and all populations of north to the Yangtze River. Combined with the AMOVA and Bayesian clustering results, it supported twelve populations could be divided into two regions,{(LC, HN, QJ, GZ)(LX, TS, BJ, FP, LN, JQ)}.There were much genetic divergence between the two geographic regions due to the seperation of Yangtze River.
主要组织相容性复合体(MHC)是脊椎动物的免疫系统中最重要的基因家族之一。多态的MHC功能基因编码的各种糖蛋白分子,主要负责结合并递呈病原体肽段,从而引起适当的免疫反应。MHC基因的多样性会直接影响个体对病原体疾病的抵抗,关乎个体的生存,对提高整个物种对不断变化的外界环境的适应能力也起着关键的作用。它已经成为迄今开展脊椎动物适应性进化研究的最受欢迎的分子标记系统。本文分离并获取了红腹锦鸡全部的MHCⅠ类基因序列,基于经典MHCⅠ类座位的特异性基因型分型,建立了一套完善的分子标记系统,完成了对红腹锦鸡12个野生种群的遗传变异、多态性维持机制、种群分化和种群遗传结构等的研究工作。本研究的主要研究结果及结论如下：
(1)本研究从建库个体中获取6条MHCⅠ类gDNA全长序列,分别命名为A-F,SSCP-HD的复原结果表明已经完全分离出该红腹锦鸡个体的MHCⅠ类序列。跨基因扩增的结果表明A/C和B/D分别属于Chpi-IA1和Chpi-IA2。
(2)通过筛选实验室先前建立的红腹锦鸡BAC文库,得到一个约为80kb的C11BAC克隆,该克隆与之前筛选出的96kb S2BAC克隆形成重叠群。除了Chpi-IA1和Chpi-IA2两个MHCⅠ类基因,这个克隆重叠群还包括序列E和F对应的新的Ⅰ类基因座位,命名为Chpi-IA3。而Chpi-IA3仅存在于C11BAC克隆中。
(3)尽管3个MHCⅠ类基因的cDNA全序列都具有经典MHCⅠ类基因的典型特征,但其组织表达检测表明：Chpi-IA1和Chpi-IA2具有广泛的组织表达,为经典MHCⅠ类基因；Chpi-IA3在已检测的多种组织未表达,且其位于红腹锦鸡MHC-B核心区域之外的位置,为非经典MHCⅠ类基因。
(4)结合PCR-SSCP和测序方法,成功建立了红腹锦鸡两个经典MHC工类基因(Chpi-IA1和Chpi-IA2)exon2和exon3的座位特异性基因型分型方法,并运用这套位点特异扩增体系对红腹锦鸡12个野生种群的334个个体进行多态性调查。2个多态的MHCⅠ类基因共包括41条exon2序列和39条exon3序列：Chpi-IA1-E214条,CChpi-IA1-E211条；Chpi-IA2-E228条,Chpi-IA2-E327条。与Chpi-IA1相比,Chpi-IA2具有更高的氨基酸多态性。
(5)平衡选择维持红腹锦鸡MHCⅠ类基因多态性的主要机制之一。我们的相关证据有：两个多态的MHCⅠ类基因(Chpi-IA1和Chpi-IA2)的PBR较non-PBR具有更高的氨基酸变异；功能结构域α1的抗原结合位点的非同义替换率高于同义替换率；Chpi-IA2α1和α2结构域的10个正选择位点,其中8个来自于其PBR；高频等位基因在所有种群中共享。
(6)重组也是红腹锦鸡MHC Ⅰ类基因的重要的进化模式。根据系统树分析,约有37.0%的Chpi-IA2-E2等位基因与所有的Chpi-IA1-E2等位基因形成独立的进化枝；通过MaXChi2,3Seq和GARD三种方法证实这两个Ⅰ类座位存在基因间的重组,且这些Chpi-IA2-E2等位基因为重组序列。
(7)Ⅰ类基因分化系数表明,秦岭南北麓种群间无明显的分化,但长江以南的种群与长江以北的种群之间的分化显著。根据AMOVA及贝叶斯归类法的分析结果,将红腹锦鸡的12个种群可以划分为2个区域,即{长江以南(LC,HN,QJ,GZ),长江以北(LX,TS,BJ,FP,LN,JQ)},这表明长江的阻隔作用促使这两个区域的种群存在较大的遗传差异。
Golden pheasant(Chysolophus pictus) is a near threatened species endemic to China with national second-class protection. In rencent years, there is a sharp decline in the number of golden pheasants, which is caused by severe fragmentation of habitat and excessive hunting. Hence, it is necessary to investigate the genetic diversity and explore the adaptive evolution mechanism of this species under the stress of habitat fragmentation.
The major histocompatibility complex (MHC) is one of the most important gene family in the vertebrate immune system, encoding diverse glycoprotein molecules, which responsible for binding and presenting pathogen peptides to T cells in order to trigger an appropriate immune response. The diversity of MHC genes may directly influence the survival of individuals against pathogen disease and it also plays a key role in the adaptation of species to the changing environment. It becomes a popular molecular marker system in the adaptive evolutionary study of vertebrates. In this study, we isolated all the MHC I gene sequences in the golden pheasant, then developed locus-specific genotying primers and finally set up a good molecular marker system of classical MHC I loci for this endangerd bird. We investigated the genetic variability, analysed the maintenance mechanisms of MHC polymorphism, and discussed population structuring in twelve wild golden pheasant populations. The main results and conclusions are listed below.
(1) We isolated all the MHC I genes and got six full-length genomic sequences from the same individual and designated them A-F according to an alphabetical order. The results of cross-locus amplication showed A/C and B/D belonged to Chpi-IA1and Chpi-IA2respectively.
(2) We isolated a positve BAC clone C11, which is about80kb in length, and forms a contig with the previously published S2BAC clone (96kb). There were three MHC I genes inclued in this contig:the former two genes Chpi-IA1and Chpi-IA2, and the new identified gene Chpi-IA3. The novel MHC Ⅰ gene was comprised of sequences E and F and was only found in C11.
(3) Analysis of tissue expression revealed that IA1and IA2could be regarded as classical loci due to their extensive tissue expression while IA3appeared to be nonclassical one without expression patterns, though the predicted cDNA full-length sequences had normal exonic structures and typical characteristics of classical class MHC I genes.
(4) Combining the PCR-SSCP and sequencing methods, we succeeded in establishment of locus-specific genotyping techniques for exon2and exon3for the two classical MHC class I genes (Chpi-IA1and Chpi-IA2). Then we investigated genetic polymorphisms of334individuals from12wild population of the golden pheasant and identified41exon-2alleles and39exon-3ones across the two polymorphic MHC class I genes:Chpi-IA1-E2(14), Chpi-IA1-E2(11), Chpi-IA2-E2(28) and Chpi-IA2-E3(27).
(5) We found evidences of balancing selection in the MHC class I genes of the golden pheasant; showing much higher amino acid substibutions in the PBR than the non-PBR, having an exccess of nonsynonymous nucleotide substitution over synonymous nucleotide substitution at the PBR sites of al domain in both polymorphic MHC class I genes, presenting eight out of ten positively selective sites in the PBR, observing sharing of alleles in high frequencies over all the populations.
(6) Recombination is also an important evolutionary mechanism of MHC class I genes in the golden pheasant. The phylogenetic tree showed that about37.0%Chpi-IA2-E2alleles and all Chpi-IA1-E2alleles were grouped together. The three methods (MaxChi2,3Seq and GARD), all verificated that the inter-gene recombination existed between Chpi-IA2-E2and Chpi-IA1-E2, and found that those Chpi-IA2-E2alleles might be recombinants.
(7) Class I gene-based differentiation coefficients revealed there were no significant genetic divergence between the populations of the south and those of the north of Qinling Mountain, while significant differentiation between populations of south to the Yangtze River and all populations of north to the Yangtze River. Combined with the AMOVA and Bayesian clustering results, it supported twelve populations could be divided into two regions,{(LC, HN, QJ, GZ)(LX, TS, BJ, FP, LN, JQ)}.There were much genetic divergence between the two geographic regions due to the seperation of Yangtze River.
引文
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