牦牛几个功能基因的结构及其系统进化研究
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摘要
本研究通过PCR扩增、T-A克隆测序分析牦牛的功能基因，与GenBank中其它物种相应基因核苷酸序列、氨基酸序列进行了比对分析，构建分子系统进化树。取得了一系列有价值的研究成果：
(1)牦牛GH基因全序列长为2847bp，由5个外显子和4个内含子组成，cDNA序列全长为654bp，GH前体氨基酸数目为217个，信号肽和成熟肽由26和191个氨基酸组成。其中牦牛GH基因全序列与普通牛同源性为98％，与水牛、山羊、绵羊同源性分别为97％、94％、93％。UPGMA、NJ和MP法构建分子系统树显示，牦牛与普通牛的亲缘关系最近，其次为水牛、山羊和绵羊、红鹿；在所测序列中，物种间该基因核苷酸变异类型包括转换、颠换和插入，以转换最为常见。
(2)序列分析结果表明，牦牛H-FABP基因由4个外显子和3个内含子组成，cDNA序列全长为402bp，前体氨基酸数为133个。4个外显子大小分别为73bp、173bp、102bp和54bp；3个内含子大小分别为3460bp、1892bp、1495bp。不同物种间在核苷酸和氨基酸序列上均有较高的保守性。牦牛与普通牛、绵羊、山羊、猪、人、鸡、大鼠、小鼠、斑马鱼各物种在H-FABP基因编码区核苷酸序列间同源性大小分别为99．8％、97．8％、97．0％、92．8％、88．8％、83．3％、83．1％、76．4％、68．7％；相应的氨基酸序列间同源性大小为100％、96．9％、96．9％、92．4％、88．7％、85．7％、85．7％、77．4％、69．9％。用H-FABP基因编码区核苷酸序列构建物种间分子进化树，结果表明，牦牛与上述各物种的系统聚类结果不仅与动物学分类一致，也同樊宝良、欧江涛以及用HSL基因对牦牛与其它物种间的系统进化聚类结果基本吻合。
(3)在牦牛H-FABP基因序列中，重复序列所占比率为13．07％。在内含子Ⅰ含有5个重复元件，包括SINE／Artiodactyls元件、SINE／MIR3元件、SINE／Bov-tA1元件各1个以及2个SINE／MIR元件；内含子Ⅱ无重复元件；内含子Ⅲ有3个重复元件，其中SINE／MIR元件、LINE／L2元件、SINE／Artiodactyls元件各1个。SINEs短重复序列所占比率为11．85％，哺乳动物分散性重复序列MIRs比率为6．44％。LINEs所占比率小于SINEs元件，为1．22％。其中，LINE1、BovB／Art2、L3／CR1重复元件以及LTR类反转录元件和DNA转座子元件在牦牛该基因区域中不存在。
(4)牦牛与普通牛、瘤牛、水牛、人、猪、大鼠、小鼠7个物种HSL基因外显子Ⅰ部分核苷酸序列间保守性较高，同源性大小依次为99．8％、99．6％、97．4％、90．6％、88．4％、83．5％、82．3％。相应氨基酸序列间保守性更高，同源性分别为100％、100％、98．2％、94．0％、92．2％、89．8％、89．8％。牦牛与各物种该基因部分核苷酸序列间碱基变异类型主要表现为碱基转换和颠换，无碱基插入和缺失发生；序列间单碱基变异位点大多出现在同一位点，符合分子进化的中性学说。
(5)利用HSL基因外显子Ⅰ部分核苷酸序列进行比对分析并构建系统进化树，结果表明，普通牛和瘤牛首先聚为一类，再分别与牦牛、水牛、猪、人聚类，最后与大鼠、小鼠聚为一类。该聚类结果与动物学上的分类结果一致。研究表明，牦牛、普通牛和瘤牛三个物种间的遗传距离远小于它们各自与水牛这一物种的遗传距离，三者之间的亲缘关系也相对于它们与水牛间的亲缘关系较近，故将牦牛、普通牛和瘤牛划分在同一个属—牛属(Bos)，而将水牛划分在另一个属更为合理。
(6)牦牛HSP72基因序列全长为1926bp，无内含子，共编码641个氨基酸；牦牛HSP72基因和HSP72蛋白与普通牛、猪、人相比存在着一定差异。从HSP72基因到HSP72蛋白的不同层次上对牦牛、普通牛、猪、人等物种进行聚类分析的结果，同进化的理论和其他基因的分析结果一致。
(7)九龙牦牛、大通牦牛、巴州牦牛和三江黄牛的EPO基因均由5个外显子和4个内含子组成，但其大小和碱基组成差异较大。九龙牦牛、大通牦牛、巴州牦牛和三江黄牛的该基因大小分别为3284bp、3281bp、3260bp和3245bp。核苷酸序列比较结果来看，大通牦牛与巴州牦牛、九龙牦牛、三江黄牛的同源性依次为99．7％、99．6％、99．5％，巴州牦牛与九龙牦牛、三江黄牛的同源性依次为99．5％、99．4％，九龙牦牛与三江黄牛的同源性为99．4％，表明牦牛品种间及牦牛与三江黄牛种间在该基因核苷酸水平上均具有较高的保守性，但也具有一定的差异，这种差异是否与牦牛适应高海拔低氧生态环境有关，值得深入研究。
(8)大通牦牛、巴州牦牛、九龙牦牛及三江黄牛EPO氨基酸序列比较结果表明，大通牦牛与巴州牦牛、九龙牦牛、三江黄牛的同源性依次为100％、99．5％、99．5％，巴州牦牛与九龙牦牛、三江黄牛的同源性均为99．5％，九龙牦牛与三江黄牛的氨基酸序列同源性高达100％。说明牦牛品种间及与三江黄牛种间在EPO氨基酸序列上更为保守，但也存在差异，这种差异是否会影响不同物种EPO的结构和表达，进而对不同物种适应高海拔、低氧生态环境的能力产生影响，有待进一步深入研究。应用EPO基因构建大通牦牛、巴州牦牛、九龙牦牛、三江黄牛、普通牛、猪、人等物种的分子系统进化树，表明系统树能反映各物种间的亲缘及进化关系。
The functional genes on yak were cloned by T-A method,and was sequenced andanalyzed,and blastned with the other species in the GenBank at the nucleoside acid andamino acid levels,and the phylogenetic evolution trees about the yak and the otherspecies are constructed.The following results are achieved:
(1)The lenghth of the GH gene in yak was 2847bp which including 5 exons and 4introns.The cDNA of GH was a 654bp nucleotide encoding a putative protein of 217amino acid (AA) residules,with a signal peptide of 26 AAs and the mature peptide of191 AAs.The comparison of these fragment sequences with those of other animalsthrough blastn of GeneBank,the results indicated that the homologies of nucleotidesequence of the GH gene of yak with Bos taurus are 98%,and with Bubalus bubalis,Capra hircus,Ovis aries are 97%,94%,93%,respectively.Molecular phylogenetic treeon these ruminant constructed by UPGMA,NJ and MP method,which showed that themolecular tree with relationship among species is unanimously.
(2)The analysis and the comparison of arrays indicate that the numbers of exons andintrons of H-FABP gene are the same between the yak and cattle,sheep,goat,pig,human,chick,rat,mouse,they all have 4 exons and 3 introns.The data suggest that thegene from the yak was highly conserved with other species at the nucleic acid and AAlevel.The homology rate ofnucleoside acid arrays of the coding region ofH-FABP geneamong species of cattle,sheep,goat,pig,human,chick,rat,mouse and zebrafish are99.8%,97.8%,97.0%,92.8%,88.8%,83.3%,83.1%,76.4%,68.7% respectively;whilethe homology rate of AA arrays are 100%,96.9%,96.9%,92.4%,88.7%,85.7%,85.7%,77.4%,69.9% respectively.The molecular phylogenetic tree between breeds isconstructed from the nucleotide arrays of the H-FABP gene.The result indicates that theresult of phylogenetic clustering is consistent with the zoological classification,but alsosame to the conarrays of phylogenetic clustering between yak and other speciesconstructed by Fan Baoliang and Ou Jiangtao,indicating that H-FABP gene is also fit toconstruct molecular phylogenetic tree between different species.
(3)The rate of the repetitive arrays is 13.07% in the nucleoside acid arrays ofH-FABP gene of the yak.Five repetitive elements are found in the intronⅠ,including aSINE/Artiodactyls element,a SINE/MIR3 element,a SINE/Bov-tA1 element and twoSINE/MIR elements.No repetitive element is found in intronⅡ.Three repetitiveelements are found in intron3,including a SINE/MIR element,a LINE/L2 element anda SINE/Artiodactyls element.The rate is 11.85% for SINEs,6.44% for MIRs and 1.22% for LINEs respectively.In addition,LINE1,BovB/Art2,L3/CR1 repetitive elements,LTR anti-transcription element and DNA transposon element are not found in the arraysof this gene.
(4)Homology rate of nucleoside acid arrays of part exonⅠof HSL gene between yakand cattle,zebu,buffalo,human (Homo sapiens),pig (Sus scrofa),rat (Rattus) andmouse (Mus musculus) is higher,which is 99.8%,99.6%,97.4%,90.6%,88.4%,83.5%,82.3% respectively.Homology of the corresponding AA arrays is also higher,that is100%,100%,98.2%,94.0%,92.2%,89.8%,89.8% respectively.Base variation betweenthe yak and the other species is mainly base transition and transversion,no baseinsertion and deletion and invertion is discovered in the nucleoside arrays comparison.Most of the single-base-variations occurs at the same nucleoside acid array site which isaccordance with the neutralism hypothesis on the molecular evaluation.
(5)Molecular phylogenetic tree is constructed through multi-arrays comparison onpart nucleoside acid arrays of exonⅠof HSL gene.The result shows that firstly,zebu ismost closely related to cattle;secondly,closely related to yak,buffalo,pig,human,lastly,related to rat and mouse.The results of the phylogenetic trees reflect the molecularevolution relationship among these species,consistent with the zoological classification.The genetic distances among yak,cattle and zebu were relatively small,but geneticdistances between these three species and buffalo were relatively large.Therefore,itwas more reasonable to consider yak,cattle and zebu as independent species of thegenus Bos,while buffalo belongs to another category (Bubalus).
(6)The results indicate that the yak HSP72 gene was an intron-free 1926bpnucleotide,encoding a protein of 641 AAs.The difference of HSP72 gene and HSP72protein does exist in yak and cow,swine,human,which is main cause of differentadaption of these species to temperature,the clustering analysis results of HSP72 geneand HSP72 protein in yak,cow,swine and human on different levels are consistent withthose of evolutional theory and other genes.
(7) The EPO genes of Bazhou yak,Datong yak,Jiulong yak and Sanjiang cattle arecomprised by 5 exons and 4 introns,but the variance of the base coposition and size isdistinct.The lenghth of this gene was,respectively,3284bp,3281bp,3260bp and3245bp in Jiulong yak,Datong yak,Bazhou yak and Sanjiang cattle.The nucleotidesequences of EPO genes were compared,as a result,the homology was,respectively,99.7%,99.6%,99.5% between Datong yak and Bazhou yak,Jiulong yak,Sanjiangcattle,was 99.5%,99.4% between Bazhou yak and Jiulong yak,Sanjiang cattlerespectively,and was 99.4% between Jiulong yak and Sanjiang cattle,which indicatedthat there is high conservation among yaks,and the same between yaks and Sanjiangcattle.The difference at the nucleotide level of EPO gene may be related with high-altitude and oxygen-poor ecological environment,which is deserved to expore.
(8)The comparation of the EPO AA sequence among Bazhou yak,Datong yak,Jiulong yak and Sanjiang cattle showed that Datong yak has the homology with Bazhouyak,Jiulong yak and Sanjiang cattle,was 100%,99.5%,99.5% respectively;andBazhou yak with Jiulong yak and Sanjiang cattle are all 99.5%;Jiulong yak withSanjiang cattle is 100%.That is to say,it is more conservative among yaks,and equallybetween yaks and Sanjiang cattle.However,there is some difference in AA level.So,itis further required to research whether the change effect the adaptive capability to theharsh natural condition.Molecular phylogenetic tree is constructed about Bazhou yak,Datong yak,Jiulong yak,Sanjiang cattle,bovine,pig and human on nucleoside acidarrays of EPO gene.The result indicates that the molecular phylogenetic tree reflectsthe evolution and genetic relationship in every researched species.
(1)牦牛GH基因全序列长为2847bp，由5个外显子和4个内含子组成，cDNA序列全长为654bp，GH前体氨基酸数目为217个，信号肽和成熟肽由26和191个氨基酸组成。其中牦牛GH基因全序列与普通牛同源性为98％，与水牛、山羊、绵羊同源性分别为97％、94％、93％。UPGMA、NJ和MP法构建分子系统树显示，牦牛与普通牛的亲缘关系最近，其次为水牛、山羊和绵羊、红鹿；在所测序列中，物种间该基因核苷酸变异类型包括转换、颠换和插入，以转换最为常见。
(2)序列分析结果表明，牦牛H-FABP基因由4个外显子和3个内含子组成，cDNA序列全长为402bp，前体氨基酸数为133个。4个外显子大小分别为73bp、173bp、102bp和54bp；3个内含子大小分别为3460bp、1892bp、1495bp。不同物种间在核苷酸和氨基酸序列上均有较高的保守性。牦牛与普通牛、绵羊、山羊、猪、人、鸡、大鼠、小鼠、斑马鱼各物种在H-FABP基因编码区核苷酸序列间同源性大小分别为99．8％、97．8％、97．0％、92．8％、88．8％、83．3％、83．1％、76．4％、68．7％；相应的氨基酸序列间同源性大小为100％、96．9％、96．9％、92．4％、88．7％、85．7％、85．7％、77．4％、69．9％。用H-FABP基因编码区核苷酸序列构建物种间分子进化树，结果表明，牦牛与上述各物种的系统聚类结果不仅与动物学分类一致，也同樊宝良、欧江涛以及用HSL基因对牦牛与其它物种间的系统进化聚类结果基本吻合。
(3)在牦牛H-FABP基因序列中，重复序列所占比率为13．07％。在内含子Ⅰ含有5个重复元件，包括SINE／Artiodactyls元件、SINE／MIR3元件、SINE／Bov-tA1元件各1个以及2个SINE／MIR元件；内含子Ⅱ无重复元件；内含子Ⅲ有3个重复元件，其中SINE／MIR元件、LINE／L2元件、SINE／Artiodactyls元件各1个。SINEs短重复序列所占比率为11．85％，哺乳动物分散性重复序列MIRs比率为6．44％。LINEs所占比率小于SINEs元件，为1．22％。其中，LINE1、BovB／Art2、L3／CR1重复元件以及LTR类反转录元件和DNA转座子元件在牦牛该基因区域中不存在。
(4)牦牛与普通牛、瘤牛、水牛、人、猪、大鼠、小鼠7个物种HSL基因外显子Ⅰ部分核苷酸序列间保守性较高，同源性大小依次为99．8％、99．6％、97．4％、90．6％、88．4％、83．5％、82．3％。相应氨基酸序列间保守性更高，同源性分别为100％、100％、98．2％、94．0％、92．2％、89．8％、89．8％。牦牛与各物种该基因部分核苷酸序列间碱基变异类型主要表现为碱基转换和颠换，无碱基插入和缺失发生；序列间单碱基变异位点大多出现在同一位点，符合分子进化的中性学说。
(5)利用HSL基因外显子Ⅰ部分核苷酸序列进行比对分析并构建系统进化树，结果表明，普通牛和瘤牛首先聚为一类，再分别与牦牛、水牛、猪、人聚类，最后与大鼠、小鼠聚为一类。该聚类结果与动物学上的分类结果一致。研究表明，牦牛、普通牛和瘤牛三个物种间的遗传距离远小于它们各自与水牛这一物种的遗传距离，三者之间的亲缘关系也相对于它们与水牛间的亲缘关系较近，故将牦牛、普通牛和瘤牛划分在同一个属—牛属(Bos)，而将水牛划分在另一个属更为合理。
(6)牦牛HSP72基因序列全长为1926bp，无内含子，共编码641个氨基酸；牦牛HSP72基因和HSP72蛋白与普通牛、猪、人相比存在着一定差异。从HSP72基因到HSP72蛋白的不同层次上对牦牛、普通牛、猪、人等物种进行聚类分析的结果，同进化的理论和其他基因的分析结果一致。
(7)九龙牦牛、大通牦牛、巴州牦牛和三江黄牛的EPO基因均由5个外显子和4个内含子组成，但其大小和碱基组成差异较大。九龙牦牛、大通牦牛、巴州牦牛和三江黄牛的该基因大小分别为3284bp、3281bp、3260bp和3245bp。核苷酸序列比较结果来看，大通牦牛与巴州牦牛、九龙牦牛、三江黄牛的同源性依次为99．7％、99．6％、99．5％，巴州牦牛与九龙牦牛、三江黄牛的同源性依次为99．5％、99．4％，九龙牦牛与三江黄牛的同源性为99．4％，表明牦牛品种间及牦牛与三江黄牛种间在该基因核苷酸水平上均具有较高的保守性，但也具有一定的差异，这种差异是否与牦牛适应高海拔低氧生态环境有关，值得深入研究。
(8)大通牦牛、巴州牦牛、九龙牦牛及三江黄牛EPO氨基酸序列比较结果表明，大通牦牛与巴州牦牛、九龙牦牛、三江黄牛的同源性依次为100％、99．5％、99．5％，巴州牦牛与九龙牦牛、三江黄牛的同源性均为99．5％，九龙牦牛与三江黄牛的氨基酸序列同源性高达100％。说明牦牛品种间及与三江黄牛种间在EPO氨基酸序列上更为保守，但也存在差异，这种差异是否会影响不同物种EPO的结构和表达，进而对不同物种适应高海拔、低氧生态环境的能力产生影响，有待进一步深入研究。应用EPO基因构建大通牦牛、巴州牦牛、九龙牦牛、三江黄牛、普通牛、猪、人等物种的分子系统进化树，表明系统树能反映各物种间的亲缘及进化关系。
The functional genes on yak were cloned by T-A method,and was sequenced andanalyzed,and blastned with the other species in the GenBank at the nucleoside acid andamino acid levels,and the phylogenetic evolution trees about the yak and the otherspecies are constructed.The following results are achieved:
(1)The lenghth of the GH gene in yak was 2847bp which including 5 exons and 4introns.The cDNA of GH was a 654bp nucleotide encoding a putative protein of 217amino acid (AA) residules,with a signal peptide of 26 AAs and the mature peptide of191 AAs.The comparison of these fragment sequences with those of other animalsthrough blastn of GeneBank,the results indicated that the homologies of nucleotidesequence of the GH gene of yak with Bos taurus are 98%,and with Bubalus bubalis,Capra hircus,Ovis aries are 97%,94%,93%,respectively.Molecular phylogenetic treeon these ruminant constructed by UPGMA,NJ and MP method,which showed that themolecular tree with relationship among species is unanimously.
(2)The analysis and the comparison of arrays indicate that the numbers of exons andintrons of H-FABP gene are the same between the yak and cattle,sheep,goat,pig,human,chick,rat,mouse,they all have 4 exons and 3 introns.The data suggest that thegene from the yak was highly conserved with other species at the nucleic acid and AAlevel.The homology rate ofnucleoside acid arrays of the coding region ofH-FABP geneamong species of cattle,sheep,goat,pig,human,chick,rat,mouse and zebrafish are99.8%,97.8%,97.0%,92.8%,88.8%,83.3%,83.1%,76.4%,68.7% respectively;whilethe homology rate of AA arrays are 100%,96.9%,96.9%,92.4%,88.7%,85.7%,85.7%,77.4%,69.9% respectively.The molecular phylogenetic tree between breeds isconstructed from the nucleotide arrays of the H-FABP gene.The result indicates that theresult of phylogenetic clustering is consistent with the zoological classification,but alsosame to the conarrays of phylogenetic clustering between yak and other speciesconstructed by Fan Baoliang and Ou Jiangtao,indicating that H-FABP gene is also fit toconstruct molecular phylogenetic tree between different species.
(3)The rate of the repetitive arrays is 13.07% in the nucleoside acid arrays ofH-FABP gene of the yak.Five repetitive elements are found in the intronⅠ,including aSINE/Artiodactyls element,a SINE/MIR3 element,a SINE/Bov-tA1 element and twoSINE/MIR elements.No repetitive element is found in intronⅡ.Three repetitiveelements are found in intron3,including a SINE/MIR element,a LINE/L2 element anda SINE/Artiodactyls element.The rate is 11.85% for SINEs,6.44% for MIRs and 1.22% for LINEs respectively.In addition,LINE1,BovB/Art2,L3/CR1 repetitive elements,LTR anti-transcription element and DNA transposon element are not found in the arraysof this gene.
(4)Homology rate of nucleoside acid arrays of part exonⅠof HSL gene between yakand cattle,zebu,buffalo,human (Homo sapiens),pig (Sus scrofa),rat (Rattus) andmouse (Mus musculus) is higher,which is 99.8%,99.6%,97.4%,90.6%,88.4%,83.5%,82.3% respectively.Homology of the corresponding AA arrays is also higher,that is100%,100%,98.2%,94.0%,92.2%,89.8%,89.8% respectively.Base variation betweenthe yak and the other species is mainly base transition and transversion,no baseinsertion and deletion and invertion is discovered in the nucleoside arrays comparison.Most of the single-base-variations occurs at the same nucleoside acid array site which isaccordance with the neutralism hypothesis on the molecular evaluation.
(5)Molecular phylogenetic tree is constructed through multi-arrays comparison onpart nucleoside acid arrays of exonⅠof HSL gene.The result shows that firstly,zebu ismost closely related to cattle;secondly,closely related to yak,buffalo,pig,human,lastly,related to rat and mouse.The results of the phylogenetic trees reflect the molecularevolution relationship among these species,consistent with the zoological classification.The genetic distances among yak,cattle and zebu were relatively small,but geneticdistances between these three species and buffalo were relatively large.Therefore,itwas more reasonable to consider yak,cattle and zebu as independent species of thegenus Bos,while buffalo belongs to another category (Bubalus).
(6)The results indicate that the yak HSP72 gene was an intron-free 1926bpnucleotide,encoding a protein of 641 AAs.The difference of HSP72 gene and HSP72protein does exist in yak and cow,swine,human,which is main cause of differentadaption of these species to temperature,the clustering analysis results of HSP72 geneand HSP72 protein in yak,cow,swine and human on different levels are consistent withthose of evolutional theory and other genes.
(7) The EPO genes of Bazhou yak,Datong yak,Jiulong yak and Sanjiang cattle arecomprised by 5 exons and 4 introns,but the variance of the base coposition and size isdistinct.The lenghth of this gene was,respectively,3284bp,3281bp,3260bp and3245bp in Jiulong yak,Datong yak,Bazhou yak and Sanjiang cattle.The nucleotidesequences of EPO genes were compared,as a result,the homology was,respectively,99.7%,99.6%,99.5% between Datong yak and Bazhou yak,Jiulong yak,Sanjiangcattle,was 99.5%,99.4% between Bazhou yak and Jiulong yak,Sanjiang cattlerespectively,and was 99.4% between Jiulong yak and Sanjiang cattle,which indicatedthat there is high conservation among yaks,and the same between yaks and Sanjiangcattle.The difference at the nucleotide level of EPO gene may be related with high-altitude and oxygen-poor ecological environment,which is deserved to expore.
(8)The comparation of the EPO AA sequence among Bazhou yak,Datong yak,Jiulong yak and Sanjiang cattle showed that Datong yak has the homology with Bazhouyak,Jiulong yak and Sanjiang cattle,was 100%,99.5%,99.5% respectively;andBazhou yak with Jiulong yak and Sanjiang cattle are all 99.5%;Jiulong yak withSanjiang cattle is 100%.That is to say,it is more conservative among yaks,and equallybetween yaks and Sanjiang cattle.However,there is some difference in AA level.So,itis further required to research whether the change effect the adaptive capability to theharsh natural condition.Molecular phylogenetic tree is constructed about Bazhou yak,Datong yak,Jiulong yak,Sanjiang cattle,bovine,pig and human on nucleoside acidarrays of EPO gene.The result indicates that the molecular phylogenetic tree reflectsthe evolution and genetic relationship in every researched species.
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