SLAⅠ类经典基因多态性及正选择检验分析
摘要
主要组织相容性复合体(Major Histocompatibility Complex,MHC)指集中于某一染色体、编码与免疫应答直接相关的一类细胞膜糖蛋白基因群。MHCⅠ类基因主要编码MHCⅠ类分子,负责内源性抗原递呈,与动物机体的免疫应答密切相关,在移植排斥反应中起重要作用,在人和鼠上已经开展了大量研究。本文以从江香猪及大花白猪为研究对象,运用RT-PCR、克隆菌液PCR-SSCP、挑选克隆子测序等方法研究了三个SLAⅠ类基因外显子2、3的多态性,并在此基础上分析其进化选择机制。通过SLAⅠ类基因单个氨基酸位点正选择检验分析来推测可能存在的ARS位点,为SLAⅠ类基因多态性、适应性进化及抗原递呈功能性的研究提供理论基础,主要结果如下:
1.通过与网上已有的SLAⅠ类基因对比分析,在从江香猪及大花白猪测序得到的222条序列中共发现53个SLA-1新等位基因,30个SLA-2新等位基因,31个SLA-3新等位基因,GenBank上有12个等位基因在本试验得到验证。按照国际动物遗传学会(ISAG)2004年制定的SLAⅠ类基因系统命名法要求进行了系统命名,建立了等位基因间系统进化树。
2.三个SLA经典Ⅰ类基因的外显子2、3具有高度多态性,在氨基酸水平从江香猪SLA-1、SLA-2完整外显子2、大部分外显子3编码的169个氨基酸序列中变异位点分别有71个(57P+14S)、64个(50P+14S),SLA-3完整外显子2、3编码的182个氨基酸序列中变异位点有75个(55P+20S)。SLA-3~*0702dh01在CDS序列第238、239位间有9个碱基的插入(AGTGGCAGG);SLA-3~*05dh01在CDS序列第881、882位间有3个碱基的插入(TGT);未发现如等位基因SLA-3~*04sc19(AY135586)在CDS序列第507、511位间有3个碱基缺失的情况。大花白猪中发现有第6外显子缺失SLA-1等位基因;从江香猪和大花白猪都发现有第6外显子缺失的SLA-3等位基因。
3.三个基因外显子2、3核苷酸含量高低都依次为G＞C＞A＞T,三个基因间第一、二、三位密码子的碱基含量相近,第三位密码子偏向富含GC,G+C的含量(87.6%)远远高于A+T的含量(12.4%)。三个基因总体上来看颠换大于转换,4种颠换T—A、T—G、A—C、C—G发生的次数相近,而C—T转换数明显小于A—G转换数。三个SLA经典Ⅰ类基因外显子2、3各位密码子碱基替换情况不同,SLA-1密码子第二位发生的替换数最多,第一位其次,第三位最少;SLA-2、SLA-3密码子第一位替换数最多,第二位其次,第三位最少。3个基因在密码子第二位的转换/颠换比值最高,第一、三位则相近。
4.从江香猪、大花白猪SLAⅠ类分子与HLAⅠ类分子中NK细胞受体的配体序列比较发现缺乏与NK细胞受体结合的关键氨基酸残基序列;与HLAⅠ类分子α1功能区相比较具有相同的与人CD8分子识别结合的关键氨基酸残基序列,其它在第119、121、123、126、127位存在变异。与HLAⅠ类分子α2功能区参与CD8分子识别结合的关键氨基酸残基序列相比有两个关键氨基酸残基发生变异:Ala-223-Val、Ala-235-Lys,在其余多个非关键氨基酸残基位置也都有变异。
5.在SLA-1和SLA-2的外显子2、3整体分别检测到极显著和显著的正选择,而SLA-3外显子2、3无正选择(P＞0.05)。SLA-1的外显子2和外显子3都有正选择(0.01＜P＜0.05)。SLA-2外显子2无正选择但外显子3有正选择(0.01＜P＜0.05)。分别对三个基因外显子2和外显子3的α螺旋区、β折叠区进行正选择检验,结果检测到有正选择的包括SLA-1外显子2(P＜0.01)和外显子3的α螺旋区(0.01＜P＜0.05),SLA-2外显子3的α螺旋区(0.01＜P＜0.05)以及SLA-3外显子2的α螺旋区(0.01＜P＜0.05)。三个基因外显子2、3中的β折叠区都未检测到显著的正选择(P＞0.05)。分别检验外显子2、3中抗原结合槽(Binding cleft)、T细胞受体结合区(TCR directed)、外侧氨基酸残基区以及非ARS区的正选择,结果只在按抗原结合槽检测到正选择(P＜0.01)。
6.综合SLA-1、SLA-2、SLA-3基因单个氨基酸位点正选择检验结果来看,SLA经典Ⅰ类分子中正选择位点有23个:24、54、62、66、67、73、75、77、79、95、97、114、116、124、138、147、151、152、155、156、163、167、169,除了54、79、124、138位点外其余19个位点在HLA经典Ⅰ类分子中都属于ARS位点。其中6个(66、73、75、147、155、169)在HLAⅠ类分子中未检测到正选择作用,很可能也是作为ARS位点存在。
Major histocompatibility complex(MHC) antigen was such gene cluster that linked with certain chromosome encoding a group of cell membrance glycoprotein that correlated with immune response. MHC classⅠgenes encode the MHC classⅠmolecule that take responsibility of the presentation of endogenous antigen,correlated with the organism immune response,and act in graft rejective reaction, which have been investgated much in Human and Mouse.In this article,these methods of RT-PCR, cloning,PCR-SSCP and DNA sequencing were used to study the polymorphism of the second exon and third exon of three SLA classⅠgenes in Congjiangxiang(CJ) pig and Dahuabai(DHB) pig,the phylogenetic and selective mechanisms were analysised.Further,some antigen reconized sites(ARSs) were proposed by detecting positive selection at single amino acid sites in SLA classⅠgenes,which provide the rationale bases for the studies of polymorphism,adaptive evolution,antigen presentation of SLA classⅠgenes.The results were as follows:
1.By aligning with alleles of SLA classⅠgenes from Genbank,53 new alleles of SLA-1,30 new alleles of SLA-2,31 new alleles of SLA-3 were found in the 222 sequences obtained by DNA sequencing and 12 alleles on Genbank were confirmed in this study,.Each of the new alleles was given a systematical naming following the principles of systematic nomenclature system for SLA classⅠalleles by the ISAG Nomenclature Committee,and the phylogenetic trees of alleles were constructed.
2.Exons 2 and 3 of the three SLA classic classⅠgenes are highly polymorphic.71 variable sites(57 parsim-information sites and 14 singleton sites),64 variable sites(50 parsim-information sites and 14 singleton sites) were respectively found in the amino acid sequences of 169 amino acid residues that encoded by the entire exon 2 and 5'part of exon 3 of SLA- 1,SLA-2 in CJ pig,while 75 variable sites(55 parsim-information sites and 20 singleton sites) were found in the sequences of 182 amino acid residues that encoded by the entire exon 2 and exon 3 of SLA-3.A insert of 9 nucleotides (AGTGGCAGG) was found between the 238 and 239 site in CDS of SLA-3*0702dh01 allele,while a insert of 3 nucleotides(TGT) was found between the 881 and 882 site in CDS of SLA-3~*05dh01 allele. Three nucleotides deletion just like SLA-3~*04sc 19(AY135586) were not detected.The sixth exon was found deleted in a certain SLA-1 allele of CJ pig,also in SLA-3 alleles of both CJ and DHB pig.
3.The nucleotide content in exons 2 and 3 of the three SLA classic classⅠgenes were as follows: G＞C＞A＞T.Nucleotide contents at the 1st,2nd,3rd codon between the three genes were similar,and the 3rd codon was abundant of GC with its G+C content(87.6%) much higher than that of A+T(12.4%). Overall,No.of transversions was more than that of transitions in the three genes.Frequency of the four kinds of transversion:T-A,T-G,A-C,C-G were close to each other,but frequency of C-T was obviously less than that of A-G.Nucleotide substitution at each codon in exons 2 and 3 of the three genes were different from each other.In SLA-1,substitutions at the 2nd codon was the most,the 1st codon next, and the 3rd least.In SLA-2 and SLA-3,the most substitutions was at the 1st codon,the 2nd less,and the 3rd least.The highest transition/transversion ratio was at the 2nd codon,while that of the 1 st and 3rd codon were similar to each other.
4.Comparing with the ligand sequence of NK cell receptor in HLA classⅠmolecules,the SLA classⅠmolecules of CJ and DHB pig were short of the critical amino acid residues that linking to human NK cell receptor.Theα2 domain of SLA classⅠmolecules had the same critical anmino acid redidues that recognizing and linking to human CD8 molecule compared with HLA classⅠmolecules,but variations were existed at sites of 119,121,123,126,127.And theα3 domain of SLA classⅠmolecules had variations at two critical amino acid residues:Ala-223-Val,Ala-235-Lys compared with that of HLA classⅠmolecules which recognizing and linking to CD8 molecule,also had many variations at other no-critical amino acid residues.
5.Extremely significant and significant positive selection were respectively detected at the whole exons 2 and 3 of SLA-1 and SLA-2 but not SLA-3.For SLA-1,positive selection was detected by P-distance but not Jukes-cantor-distance at its exon 2,also positive selection was detected at exon 3. While for SLA-2,positive selection was detected at exon 3(0.01＜P＜0.05) but not exon 2.To consider theα-helices andβ-strands in exon 2 and exon 3 of the three genes,positive selection was also detected at theα-helices in exon 2(P＜0.01) and exon 3(0.01＜P＜0.05) of SLA-1,exon 3(0.01＜P＜0.05) of SLA-2 and exon 2(0.01＜P＜0.05) of SLA-3.No positive selection was detected at theβ-strands in exon 2 and exon 3 of both three genes(P＞0.5).Finally,to the binding cleft,TCR directed region and out directed region in exons 2 and 3,positive selection was only detected at binding cleft(P＜0.01).
6.It was concluded that there was 23 positive selection sites(24,54,62,66,67,73,75,77,79,95, 97,114,116,124,138,147,151,152,155,156,163,167,169)along the SLAclassic class I molecules after combining the results of SLA-1,SLA-2,SLA-3 genes.Except 54,79,124,138 sites,the other 19 positive selection sites were as ARS sites in HLA classic classⅠmolecules.6(66,73,75,147,155,169) of the 20 sites could be as ARSs even though they were not detected to be positive selection sites in HLA classⅠmolecules,.
1.通过与网上已有的SLAⅠ类基因对比分析,在从江香猪及大花白猪测序得到的222条序列中共发现53个SLA-1新等位基因,30个SLA-2新等位基因,31个SLA-3新等位基因,GenBank上有12个等位基因在本试验得到验证。按照国际动物遗传学会(ISAG)2004年制定的SLAⅠ类基因系统命名法要求进行了系统命名,建立了等位基因间系统进化树。
2.三个SLA经典Ⅰ类基因的外显子2、3具有高度多态性,在氨基酸水平从江香猪SLA-1、SLA-2完整外显子2、大部分外显子3编码的169个氨基酸序列中变异位点分别有71个(57P+14S)、64个(50P+14S),SLA-3完整外显子2、3编码的182个氨基酸序列中变异位点有75个(55P+20S)。SLA-3~*0702dh01在CDS序列第238、239位间有9个碱基的插入(AGTGGCAGG);SLA-3~*05dh01在CDS序列第881、882位间有3个碱基的插入(TGT);未发现如等位基因SLA-3~*04sc19(AY135586)在CDS序列第507、511位间有3个碱基缺失的情况。大花白猪中发现有第6外显子缺失SLA-1等位基因;从江香猪和大花白猪都发现有第6外显子缺失的SLA-3等位基因。
3.三个基因外显子2、3核苷酸含量高低都依次为G＞C＞A＞T,三个基因间第一、二、三位密码子的碱基含量相近,第三位密码子偏向富含GC,G+C的含量(87.6%)远远高于A+T的含量(12.4%)。三个基因总体上来看颠换大于转换,4种颠换T—A、T—G、A—C、C—G发生的次数相近,而C—T转换数明显小于A—G转换数。三个SLA经典Ⅰ类基因外显子2、3各位密码子碱基替换情况不同,SLA-1密码子第二位发生的替换数最多,第一位其次,第三位最少;SLA-2、SLA-3密码子第一位替换数最多,第二位其次,第三位最少。3个基因在密码子第二位的转换/颠换比值最高,第一、三位则相近。
4.从江香猪、大花白猪SLAⅠ类分子与HLAⅠ类分子中NK细胞受体的配体序列比较发现缺乏与NK细胞受体结合的关键氨基酸残基序列;与HLAⅠ类分子α1功能区相比较具有相同的与人CD8分子识别结合的关键氨基酸残基序列,其它在第119、121、123、126、127位存在变异。与HLAⅠ类分子α2功能区参与CD8分子识别结合的关键氨基酸残基序列相比有两个关键氨基酸残基发生变异:Ala-223-Val、Ala-235-Lys,在其余多个非关键氨基酸残基位置也都有变异。
5.在SLA-1和SLA-2的外显子2、3整体分别检测到极显著和显著的正选择,而SLA-3外显子2、3无正选择(P＞0.05)。SLA-1的外显子2和外显子3都有正选择(0.01＜P＜0.05)。SLA-2外显子2无正选择但外显子3有正选择(0.01＜P＜0.05)。分别对三个基因外显子2和外显子3的α螺旋区、β折叠区进行正选择检验,结果检测到有正选择的包括SLA-1外显子2(P＜0.01)和外显子3的α螺旋区(0.01＜P＜0.05),SLA-2外显子3的α螺旋区(0.01＜P＜0.05)以及SLA-3外显子2的α螺旋区(0.01＜P＜0.05)。三个基因外显子2、3中的β折叠区都未检测到显著的正选择(P＞0.05)。分别检验外显子2、3中抗原结合槽(Binding cleft)、T细胞受体结合区(TCR directed)、外侧氨基酸残基区以及非ARS区的正选择,结果只在按抗原结合槽检测到正选择(P＜0.01)。
6.综合SLA-1、SLA-2、SLA-3基因单个氨基酸位点正选择检验结果来看,SLA经典Ⅰ类分子中正选择位点有23个:24、54、62、66、67、73、75、77、79、95、97、114、116、124、138、147、151、152、155、156、163、167、169,除了54、79、124、138位点外其余19个位点在HLA经典Ⅰ类分子中都属于ARS位点。其中6个(66、73、75、147、155、169)在HLAⅠ类分子中未检测到正选择作用,很可能也是作为ARS位点存在。
Major histocompatibility complex(MHC) antigen was such gene cluster that linked with certain chromosome encoding a group of cell membrance glycoprotein that correlated with immune response. MHC classⅠgenes encode the MHC classⅠmolecule that take responsibility of the presentation of endogenous antigen,correlated with the organism immune response,and act in graft rejective reaction, which have been investgated much in Human and Mouse.In this article,these methods of RT-PCR, cloning,PCR-SSCP and DNA sequencing were used to study the polymorphism of the second exon and third exon of three SLA classⅠgenes in Congjiangxiang(CJ) pig and Dahuabai(DHB) pig,the phylogenetic and selective mechanisms were analysised.Further,some antigen reconized sites(ARSs) were proposed by detecting positive selection at single amino acid sites in SLA classⅠgenes,which provide the rationale bases for the studies of polymorphism,adaptive evolution,antigen presentation of SLA classⅠgenes.The results were as follows:
1.By aligning with alleles of SLA classⅠgenes from Genbank,53 new alleles of SLA-1,30 new alleles of SLA-2,31 new alleles of SLA-3 were found in the 222 sequences obtained by DNA sequencing and 12 alleles on Genbank were confirmed in this study,.Each of the new alleles was given a systematical naming following the principles of systematic nomenclature system for SLA classⅠalleles by the ISAG Nomenclature Committee,and the phylogenetic trees of alleles were constructed.
2.Exons 2 and 3 of the three SLA classic classⅠgenes are highly polymorphic.71 variable sites(57 parsim-information sites and 14 singleton sites),64 variable sites(50 parsim-information sites and 14 singleton sites) were respectively found in the amino acid sequences of 169 amino acid residues that encoded by the entire exon 2 and 5'part of exon 3 of SLA- 1,SLA-2 in CJ pig,while 75 variable sites(55 parsim-information sites and 20 singleton sites) were found in the sequences of 182 amino acid residues that encoded by the entire exon 2 and exon 3 of SLA-3.A insert of 9 nucleotides (AGTGGCAGG) was found between the 238 and 239 site in CDS of SLA-3*0702dh01 allele,while a insert of 3 nucleotides(TGT) was found between the 881 and 882 site in CDS of SLA-3~*05dh01 allele. Three nucleotides deletion just like SLA-3~*04sc 19(AY135586) were not detected.The sixth exon was found deleted in a certain SLA-1 allele of CJ pig,also in SLA-3 alleles of both CJ and DHB pig.
3.The nucleotide content in exons 2 and 3 of the three SLA classic classⅠgenes were as follows: G＞C＞A＞T.Nucleotide contents at the 1st,2nd,3rd codon between the three genes were similar,and the 3rd codon was abundant of GC with its G+C content(87.6%) much higher than that of A+T(12.4%). Overall,No.of transversions was more than that of transitions in the three genes.Frequency of the four kinds of transversion:T-A,T-G,A-C,C-G were close to each other,but frequency of C-T was obviously less than that of A-G.Nucleotide substitution at each codon in exons 2 and 3 of the three genes were different from each other.In SLA-1,substitutions at the 2nd codon was the most,the 1st codon next, and the 3rd least.In SLA-2 and SLA-3,the most substitutions was at the 1st codon,the 2nd less,and the 3rd least.The highest transition/transversion ratio was at the 2nd codon,while that of the 1 st and 3rd codon were similar to each other.
4.Comparing with the ligand sequence of NK cell receptor in HLA classⅠmolecules,the SLA classⅠmolecules of CJ and DHB pig were short of the critical amino acid residues that linking to human NK cell receptor.Theα2 domain of SLA classⅠmolecules had the same critical anmino acid redidues that recognizing and linking to human CD8 molecule compared with HLA classⅠmolecules,but variations were existed at sites of 119,121,123,126,127.And theα3 domain of SLA classⅠmolecules had variations at two critical amino acid residues:Ala-223-Val,Ala-235-Lys compared with that of HLA classⅠmolecules which recognizing and linking to CD8 molecule,also had many variations at other no-critical amino acid residues.
5.Extremely significant and significant positive selection were respectively detected at the whole exons 2 and 3 of SLA-1 and SLA-2 but not SLA-3.For SLA-1,positive selection was detected by P-distance but not Jukes-cantor-distance at its exon 2,also positive selection was detected at exon 3. While for SLA-2,positive selection was detected at exon 3(0.01＜P＜0.05) but not exon 2.To consider theα-helices andβ-strands in exon 2 and exon 3 of the three genes,positive selection was also detected at theα-helices in exon 2(P＜0.01) and exon 3(0.01＜P＜0.05) of SLA-1,exon 3(0.01＜P＜0.05) of SLA-2 and exon 2(0.01＜P＜0.05) of SLA-3.No positive selection was detected at theβ-strands in exon 2 and exon 3 of both three genes(P＞0.5).Finally,to the binding cleft,TCR directed region and out directed region in exons 2 and 3,positive selection was only detected at binding cleft(P＜0.01).
6.It was concluded that there was 23 positive selection sites(24,54,62,66,67,73,75,77,79,95, 97,114,116,124,138,147,151,152,155,156,163,167,169)along the SLAclassic class I molecules after combining the results of SLA-1,SLA-2,SLA-3 genes.Except 54,79,124,138 sites,the other 19 positive selection sites were as ARS sites in HLA classic classⅠmolecules.6(66,73,75,147,155,169) of the 20 sites could be as ARSs even though they were not detected to be positive selection sites in HLA classⅠmolecules,.
引文
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唐军,陈福祥,李宁丽,等.中国版纳猪MHC Ⅰ类P1分子全长的原核表达与纯化.中国免疫学杂志,2002,18(4):264-267.
[19]Oleksiewicz MB,Kristensen B,Ladekj(?)r-Mikkelsen AS,et.al.Development of a rapid in vitro protein refolding assay which discriminates between peptide-bound and peptide-free forms of recombinant porcine major histocompatibility class Ⅰ complex(SLA-Ⅰ).Veterinary Immunology and Immunopathology,2002,86(1-2):55-77.
[20]GAO Feng-Shan,FANG Qin-Mei,LI Yun-Gang et.al.Reconstruction of a swine SLA-Ⅰ protein complex and determination of binding nonameric peptides derived from the foot-and-mouth disease virus.Veterinary Immunology and Immunopathology,2006,113(3-4):328-338.
[21]WEI Xi-Hui,WANG Lin-Yun,XU Yin-Xue,et.al.Preliminary serological study on swine lymphocyte antigen(SLA) of the Wuzhishan pig.Acta Veterinaria et Zootechnica Sinica,1996,27(3):199-206.
韦习会,王林云,徐银学,等.五指山猪白细胞抗原血清学研究.畜牧兽医学报,1996,27(3):199-206.
[22]LI Hua,LUO Huai-Rong,ZHANG Ya-Ping,et.al.Detection and typing for swine leukocyte antigen.Hereditas(Beijing),2004,26(2):211-214.
李华,罗怀容,张亚平,等.SLA的分型与检测.遗传,2004,26(2):211-214.
[23]Chardon P,Renard C,Vaiman M.The major histocompatibility complex in swine.Immunological Reviews,1999,167:179-192.
[24]Jung YC,Rothschild MF,Flanagan MP,et.al.Genetic variability between two breeds based on restriction fragment length polymorphisms(RFLPs) of major histocompatibility complex class Ⅰ genes in the pig.Theoretical and Applied Genetics,1989,77(2):1432-1442.
[25]Jung YC,Rothschild MF,Flanagan MP,et.al.Association of restriction fragment length polymorphisms of swine leucocyte antigen class Ⅰ genes with production traits of Duroc and Hampshire boars.Animal Genetics,1989,20(1):79-91.
[26]DUAN Yu-You,WANG Lin-Yun,CUI Zhi-Zhong.Primary RFLP analysis of MHC class Ⅰ gene in Chinese breeds of Meishan and Erhuanlian pigs.Journal of Jiangsu Agricultural college,1993,14(4):39-42.
段玉友,王林云,崔治中.猪MHC Ⅰ类基因区基因组DNA的RFLP初步分析.江苏农学院学报,1993,14(4):39-42.
[27]Lee JH,Simond D,Hawthorne WJ,et.al.Characterization of the swine major histocompatibility complex alleles at eight loci in Westran pigs.Xenotransplantation,2005,12(4):303-307.
[28]Martens GW,Lunney JK,Baker JE,et.al.Rapid assignment of swine leukocyte antigen haplotypes in pedigreed herds using a polymerase chain reaction-based assay.Immunogenetics,2003,55(6):395-401.
[29]Smith DM,Martens GW,Ho CS,et.al.DNA sequence based typing of swine leukocyte antigens in Yucatan miniature pigs.Xenotransplantation,2005,12(6):481-488.
[30]Ando A,Ota M,Sada M,et.al.Rapid assignment of the swine major histocompatibility complex(SLA)class Ⅰ and Ⅱ genotypes in Clawn miniature swine using PCR-SSP and PCR-RFLP methods.Xenotransplantation,2005,12(2):121-126.
[31]Ho CS,Rochelle ES,Martens GW,et.al.Characterization of swine leukocyte antigen polymerphism by sequence-based and PCR-SSP methods in Meishan pigs.Immunogenetics,2006,58(11):873-882.
[32]Nunez Y,Ponz F,Gallego FJ.Microsatellite-based genotyping of the swine lymphocyte alloantigens (SLA) in miniature pigs.Research in Veterinary Science,2004,77(1):59-62.
[33]Tanaka M,Ando A,Renard C,et.al.Development of dense microsatellite markers in the entire SLA region and evaluation of their polymorphisms in porcine breeds.Immunogenetics,2005,57(9):690-696.
[34]Singer DS,Erlich R,Satz L,et.al.Structure and expression of class Ⅰ MHC genes in the miniature swine.Veterinary Immunology and Immunopathology,1987,17(1-4):211-221.
[35]Ando A,Kawata H,Shigenari A,et.al.Genetic polymorphism of the swine major histocompatibility complex(SLA) class Ⅰ genes,SLA-1,-2 and -3.Immunogenetics,2003,55(9):583-593.
[36]CHEN Fu-Xiang,TANG Jun,LI Ning-Li,et.al.Novel SLA class Ⅰ alleles of Chinese pig strains and their significance in xenotransplantation.Cell Research,2003,13(4):285-294.
[37]WU Qun,XIONG Ping,CHEN Shi,et.al.Sequence Analysis of classical swine leukocyte antigens (SLA) class Ⅰ and class Ⅱ molecules in inbred strain of Chinese Wuzhishan pigs.Current Immunology,2004,24(1):23-26.
吴群,熊平,陈实,等.近交系海南五指山猪SLA经典Ⅰ类和Ⅱ类分子序列分析.现代免疫学,2004,24(1):23-26.
[38]Renard C,Hart E,Sehra H,et.al.The genomic sequence and analysis of the swine major histocompatibility complex.Genomics,2006,88(1):96-110.
[39]Gunther E,Walter L.The major histocompatibility complex of the rat(Rattus norvegicus).Immunogenetics,2001,53(7):520-542.
[40]Renard C,Chardon P,Vaiman M.The phylogenetic history of the MHC class Ⅰ gene families in Pig,including a fossil gene predating mammalian radiation.Journal of Molecular Evolution,2003,57(4):420-434.
[41]Doherty PC,Zinkernagel RM.Enhanced immunological surveillance in mice heterozygous at the H-2gene complex.Nature,1975,256(5512):50-52.
[42]Hughes AL,Nei M.Pattern of nucleotide substitution at major histocompatibility complex class Ⅰ loci reveals overdominant selection.Nature,1988,335:167-170.
[43]Hughes AL,Ota T,Nei M.Positive darwinian selection promotes charge profile diversity in the antigen-binding cleft of class Ⅰ major-histocompatibility-complex molecules.Molecular Biology and Evolution,1990,7(6):515-524.
[44]LI Bo,LI Hua,LI Xue-Wei,et.al.Latest advances on the nomenclature for factors of the SLA class-Ⅰsystem.Hereditas(Beijing),2006,28(5):606-610.
李波,李华,李学伟,等.SLA Ⅰ类基因最新命名进展.遗传,2006,28(5):606-610.
[45]Nei M.Kumar S.Molecular evolution and phylogenetics.Oxford University Press;Oxford,New York,2000.
[46]Nielsen R,Yang Z.Likelihood models for detecting positively selected amino-acid sites and applications to the HIV-1 envelope gene.Genetics,1998,148:929-936.
[47]Yang Z,Nielsen R,Goldman N,et.al.Codon-substitution models for heterogeneous selection pressure at amino acid sites.Genetics,2000,155:431-449.
[48]Gu X.Statistical methods for testing functional divergence after gene duplication.Mol.Biol.Evol 1999,16:1664-1674.
[49]Gu X.Maximum likelihood approach for gene family evolution under functional divergence Mol.Biol.Evol,2001,18:453-464.
[50]Suzuki Y,Gojobori T.A method for detecting positive selection at single amino acid sites.Mol.Biol.Evol,1999,16:1315-1328.
[51]Yang Z.Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution.Mol.Biol.Evol,1998,15:568-573.
[52]Yang Z,Nielsen R.Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages.Mol.Biol.Evol,2002,19:908-917.
[53]Zhang J,Nielsen R,Yang Z.Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level.Mol.Biol.Evol,2005,22(12):2472-2479.
[54]Zhang J,Rosenberg HF,Nei M.Positive Darwinian selection after gene duplication in primate ribonuclease genes.Proc.Natl.Acad.Sci.USA,1998,95:3708-3713.
[55]Zhang J.Evolution by gene duplication:an update.TRENDS in Ecology and Evolution,2003,18(6):292-298.
[56]Anisimova M,Bielawski JP,Yang Z,Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution.Mol.Biol.Evol.2001,18(8):1585-1592.
[57]Anisimova M,Bielawski JP,Yang Z,Accuracy and power of Bayes prediction of amino acid sites under positive selection.Mol.Biol.Evol.2002,19(6):950-958.
[58]Anisimova M,Nielsen R,Yang Z.Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites.Genetics,2003,164(3):1229-1236.
[59]Suzuki Y,Nei M.Reliabilities of parsimony-based and likelihood-based methods for detecting positive selection at single amino acid sites.Mol.Biol.Evol,2001,18:2179-2185.
[60]Suzuki Y,Nei M.Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites.Mol.Biol.Evol 2002,19:1865-1869.
[61]Yang Z,Swanson WJ.Codeon-substitution models to detect adaptive evolution that accout for heterogeneous selective pressures among site classes.Mol.Biol.Evol,2002,19:49-57.
[62]Wong WSW,Yang Z,Goldman N,et.al.Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites.Genetics,2004,168:1041-1051.
[63]ZHANG Guo-Wei,SONG Huai-Dong,CHEN Zhu.Molecular mechanism of mRNA alternative splicing.Acta Genetica Sinica,2004,31(1):102-107.
章国卫,宋怀东,陈竺.mRNA选择性剪接的分子机制.遗传学报,2004,31(1):102-107
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[18]TANG Jun,CHEN Fu-Xiang,Li Ning-Li,et.al.Expressionin E.coli of Chinese Banna pig SLA class Ⅰ P1 protein and its purification.Chinese Journal of Immunology,2002,18:264-267.
唐军,陈福祥,李宁丽,等.中国版纳猪MHC Ⅰ类P1分子全长的原核表达与纯化.中国免疫学杂志,2002,18(4):264-267.
[19]Oleksiewicz MB,Kristensen B,Ladekj(?)r-Mikkelsen AS,et.al.Development of a rapid in vitro protein refolding assay which discriminates between peptide-bound and peptide-free forms of recombinant porcine major histocompatibility class Ⅰ complex(SLA-Ⅰ).Veterinary Immunology and Immunopathology,2002,86(1-2):55-77.
[20]GAO Feng-Shan,FANG Qin-Mei,LI Yun-Gang et.al.Reconstruction of a swine SLA-Ⅰ protein complex and determination of binding nonameric peptides derived from the foot-and-mouth disease virus.Veterinary Immunology and Immunopathology,2006,113(3-4):328-338.
[21]WEI Xi-Hui,WANG Lin-Yun,XU Yin-Xue,et.al.Preliminary serological study on swine lymphocyte antigen(SLA) of the Wuzhishan pig.Acta Veterinaria et Zootechnica Sinica,1996,27(3):199-206.
韦习会,王林云,徐银学,等.五指山猪白细胞抗原血清学研究.畜牧兽医学报,1996,27(3):199-206.
[22]LI Hua,LUO Huai-Rong,ZHANG Ya-Ping,et.al.Detection and typing for swine leukocyte antigen.Hereditas(Beijing),2004,26(2):211-214.
李华,罗怀容,张亚平,等.SLA的分型与检测.遗传,2004,26(2):211-214.
[23]Chardon P,Renard C,Vaiman M.The major histocompatibility complex in swine.Immunological Reviews,1999,167:179-192.
[24]Jung YC,Rothschild MF,Flanagan MP,et.al.Genetic variability between two breeds based on restriction fragment length polymorphisms(RFLPs) of major histocompatibility complex class Ⅰ genes in the pig.Theoretical and Applied Genetics,1989,77(2):1432-1442.
[25]Jung YC,Rothschild MF,Flanagan MP,et.al.Association of restriction fragment length polymorphisms of swine leucocyte antigen class Ⅰ genes with production traits of Duroc and Hampshire boars.Animal Genetics,1989,20(1):79-91.
[26]DUAN Yu-You,WANG Lin-Yun,CUI Zhi-Zhong.Primary RFLP analysis of MHC class Ⅰ gene in Chinese breeds of Meishan and Erhuanlian pigs.Journal of Jiangsu Agricultural college,1993,14(4):39-42.
段玉友,王林云,崔治中.猪MHC Ⅰ类基因区基因组DNA的RFLP初步分析.江苏农学院学报,1993,14(4):39-42.
[27]Lee JH,Simond D,Hawthorne WJ,et.al.Characterization of the swine major histocompatibility complex alleles at eight loci in Westran pigs.Xenotransplantation,2005,12(4):303-307.
[28]Martens GW,Lunney JK,Baker JE,et.al.Rapid assignment of swine leukocyte antigen haplotypes in pedigreed herds using a polymerase chain reaction-based assay.Immunogenetics,2003,55(6):395-401.
[29]Smith DM,Martens GW,Ho CS,et.al.DNA sequence based typing of swine leukocyte antigens in Yucatan miniature pigs.Xenotransplantation,2005,12(6):481-488.
[30]Ando A,Ota M,Sada M,et.al.Rapid assignment of the swine major histocompatibility complex(SLA)class Ⅰ and Ⅱ genotypes in Clawn miniature swine using PCR-SSP and PCR-RFLP methods.Xenotransplantation,2005,12(2):121-126.
[31]Ho CS,Rochelle ES,Martens GW,et.al.Characterization of swine leukocyte antigen polymerphism by sequence-based and PCR-SSP methods in Meishan pigs.Immunogenetics,2006,58(11):873-882.
[32]Nunez Y,Ponz F,Gallego FJ.Microsatellite-based genotyping of the swine lymphocyte alloantigens (SLA) in miniature pigs.Research in Veterinary Science,2004,77(1):59-62.
[33]Tanaka M,Ando A,Renard C,et.al.Development of dense microsatellite markers in the entire SLA region and evaluation of their polymorphisms in porcine breeds.Immunogenetics,2005,57(9):690-696.
[34]Singer DS,Erlich R,Satz L,et.al.Structure and expression of class Ⅰ MHC genes in the miniature swine.Veterinary Immunology and Immunopathology,1987,17(1-4):211-221.
[35]Ando A,Kawata H,Shigenari A,et.al.Genetic polymorphism of the swine major histocompatibility complex(SLA) class Ⅰ genes,SLA-1,-2 and -3.Immunogenetics,2003,55(9):583-593.
[36]CHEN Fu-Xiang,TANG Jun,LI Ning-Li,et.al.Novel SLA class Ⅰ alleles of Chinese pig strains and their significance in xenotransplantation.Cell Research,2003,13(4):285-294.
[37]WU Qun,XIONG Ping,CHEN Shi,et.al.Sequence Analysis of classical swine leukocyte antigens (SLA) class Ⅰ and class Ⅱ molecules in inbred strain of Chinese Wuzhishan pigs.Current Immunology,2004,24(1):23-26.
吴群,熊平,陈实,等.近交系海南五指山猪SLA经典Ⅰ类和Ⅱ类分子序列分析.现代免疫学,2004,24(1):23-26.
[38]Renard C,Hart E,Sehra H,et.al.The genomic sequence and analysis of the swine major histocompatibility complex.Genomics,2006,88(1):96-110.
[39]Gunther E,Walter L.The major histocompatibility complex of the rat(Rattus norvegicus).Immunogenetics,2001,53(7):520-542.
[40]Renard C,Chardon P,Vaiman M.The phylogenetic history of the MHC class Ⅰ gene families in Pig,including a fossil gene predating mammalian radiation.Journal of Molecular Evolution,2003,57(4):420-434.
[41]Doherty PC,Zinkernagel RM.Enhanced immunological surveillance in mice heterozygous at the H-2gene complex.Nature,1975,256(5512):50-52.
[42]Hughes AL,Nei M.Pattern of nucleotide substitution at major histocompatibility complex class Ⅰ loci reveals overdominant selection.Nature,1988,335:167-170.
[43]Hughes AL,Ota T,Nei M.Positive darwinian selection promotes charge profile diversity in the antigen-binding cleft of class Ⅰ major-histocompatibility-complex molecules.Molecular Biology and Evolution,1990,7(6):515-524.
[44]LI Bo,LI Hua,LI Xue-Wei,et.al.Latest advances on the nomenclature for factors of the SLA class-Ⅰsystem.Hereditas(Beijing),2006,28(5):606-610.
李波,李华,李学伟,等.SLA Ⅰ类基因最新命名进展.遗传,2006,28(5):606-610.
[45]Nei M.Kumar S.Molecular evolution and phylogenetics.Oxford University Press;Oxford,New York,2000.
[46]Nielsen R,Yang Z.Likelihood models for detecting positively selected amino-acid sites and applications to the HIV-1 envelope gene.Genetics,1998,148:929-936.
[47]Yang Z,Nielsen R,Goldman N,et.al.Codon-substitution models for heterogeneous selection pressure at amino acid sites.Genetics,2000,155:431-449.
[48]Gu X.Statistical methods for testing functional divergence after gene duplication.Mol.Biol.Evol 1999,16:1664-1674.
[49]Gu X.Maximum likelihood approach for gene family evolution under functional divergence Mol.Biol.Evol,2001,18:453-464.
[50]Suzuki Y,Gojobori T.A method for detecting positive selection at single amino acid sites.Mol.Biol.Evol,1999,16:1315-1328.
[51]Yang Z.Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution.Mol.Biol.Evol,1998,15:568-573.
[52]Yang Z,Nielsen R.Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages.Mol.Biol.Evol,2002,19:908-917.
[53]Zhang J,Nielsen R,Yang Z.Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level.Mol.Biol.Evol,2005,22(12):2472-2479.
[54]Zhang J,Rosenberg HF,Nei M.Positive Darwinian selection after gene duplication in primate ribonuclease genes.Proc.Natl.Acad.Sci.USA,1998,95:3708-3713.
[55]Zhang J.Evolution by gene duplication:an update.TRENDS in Ecology and Evolution,2003,18(6):292-298.
[56]Anisimova M,Bielawski JP,Yang Z,Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution.Mol.Biol.Evol.2001,18(8):1585-1592.
[57]Anisimova M,Bielawski JP,Yang Z,Accuracy and power of Bayes prediction of amino acid sites under positive selection.Mol.Biol.Evol.2002,19(6):950-958.
[58]Anisimova M,Nielsen R,Yang Z.Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites.Genetics,2003,164(3):1229-1236.
[59]Suzuki Y,Nei M.Reliabilities of parsimony-based and likelihood-based methods for detecting positive selection at single amino acid sites.Mol.Biol.Evol,2001,18:2179-2185.
[60]Suzuki Y,Nei M.Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites.Mol.Biol.Evol 2002,19:1865-1869.
[61]Yang Z,Swanson WJ.Codeon-substitution models to detect adaptive evolution that accout for heterogeneous selective pressures among site classes.Mol.Biol.Evol,2002,19:49-57.
[62]Wong WSW,Yang Z,Goldman N,et.al.Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites.Genetics,2004,168:1041-1051.
[63]ZHANG Guo-Wei,SONG Huai-Dong,CHEN Zhu.Molecular mechanism of mRNA alternative splicing.Acta Genetica Sinica,2004,31(1):102-107.
章国卫,宋怀东,陈竺.mRNA选择性剪接的分子机制.遗传学报,2004,31(1):102-107