基于ISSR、AFLP分子标记和Cyclins基因克隆的四倍体鱼进化分析
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摘要
多倍化不仅仅是植物进化的特征之一,在包括从原生动物到人类的所有动物的进化历程中都可能发生过多倍化事件。特别是在鱼类,多倍化更是一个非常普遍的现象。多倍化导致的基因组复制和基因拷贝的增加,为生物的进化跃迁提供了必须的物质基础,在脊椎动物的进化历程中起着非常重要的作用。
异源四倍体鲫鲤是通过远缘杂交的方式首次在脊椎动物中人工培育的两性可育、遗传性状稳定的多倍体鱼,其体细胞包含2套红鲫和2套鲤鱼染色体。为了了解异源四倍体鲫鲤形成后基因组的进化情况,本研究以异源四倍体鲫鲤及其原始亲本为材料,从基因组和单个基因的变化两个角度探讨了异源四倍体鲫鲤的基因组变化及其与原始父母本的分子进化关系。研究结果对进一步了解鱼类乃至脊椎动物多倍体的形成与进化机制具有重要的意义。主要研究内容如下:
采用ISSR和AFLP分子标记,对异源四倍体鲫鲤及其原始亲本群体的遗传结构及基因组的变化进行分析。研究结果表明,异源四倍体鲫鲤经过连续15代的培育,仍然保持了原始亲本遗传性状的稳定性。但遗传相似率表明,异源四倍体鲫鲤与其原始母本红鲫的亲缘关系更近,表现出偏母性遗传的特性;DNA带纹分析发现,在异源四倍体鲫鲤基因组中发生了原始亲本条带的丢失,两种分子标记统计的原始母本红鲫基因组带纹消失比例分别为19%和26.5%,原始父本鲤鱼基因组带纹消失的比例分别为46.8%和28.4%,父本基因组比母本基因组的带纹消失比例大。同时,在异源四倍体鲫鲤群体中发现一些原始父母本没有的DNA条带。
Cyclin A1和B1基因是细胞周期调控关键基因。首次分离和克隆出异源四倍体鲫鲤及其原始亲本Cyclin A1和B1基因cDNA全长序列,在此基础上,对异源四倍体鲫鲤及其原始亲本进行了序列同源性比较及碱基差异位点分析。结果表明,异源四倍体鲫鲤与原始父母本编码区序列同源性都在90%以上,特别是在周期蛋白框区的序列同源性更高(94%以上)。而四倍体鲫鲤与原始母本红鲫的同源性高于与原始父本的同源性。系统进化树也显示异源四倍体鲫鲤总是首先与其原始母本红鲫聚合,也表现出与偏母性遗传的特性。在Cyclin A1基因编码区,异源四倍体鲫鲤相对于原始母本红鲫的碱基变异水平为1.8%、相对于原始父本鲤鱼的碱基变异水平为4.7%;在Cyclin B_l基因编码区,相对于原始母本的碱基变异水平为O.9%,相对于原始父本的碱基变异水平为5.7%,说明在四倍体鲫鲤中原始父本比原始母本的Cyclin A1和B1基因碱基变异程度更高。Cyclin A1和B1氨基酸序列比对发现,异源四倍体鲫鲤分别存在4个和2个与其原始父母本不同的位点,新的氨基酸位点的产生是由密码子单个碱基位点的非同义突变所致。
根据斑马鱼Cyclin B1基因的剪切方式,设计4对兼并引物,首次扩增出异源四倍体鲫鲤及其原始亲本红鲫和鲤鱼Cyclin B基因8个内含子,内含子剪切位点符合GT-AG规则。将异源四倍体鲫鲤Cyclin B基因内含子合并序列与原始母本红鲫和原始父本鲤鱼进行比较,它们之间的同源性分别为96.8%和66.4%。通过第2对引物(P3/P4)PCR扩增,获得三倍体鲫鲂、四倍体鲫鲂、五倍体鲫鲂和团头鲂、草鱼、鲢鱼、鳙鱼等鲤科鱼Cyclin B基因部分DNA序列。结合异源四倍体鲫鲤及其原始亲本红鲫和鲤鱼Cyclin B基因对应DNA序列,对不同倍性鲤科鱼类Cyclin B基因DNA片段序列进行比较分析。结果表明:由相同引物扩增的染色体数为48的鲂、草、鲢、鳙鱼,只扩增出1条DNA片段,片段长度分别为750 bp、950 bp、720 bp和720 bp,而染色体数目加倍的红鲫、鲤鱼、异源四倍体鲫鲤、异源四倍体鲫鲂,扩增出2条DNA片段(1200 bp和900 bp),三倍体和五倍体鲫鲂扩增出3条DNA片段(1200 bp、900 bp和750 bp),每个DNA片段均含Cyclin B基因第2、3内含子和第2、3、4外显子。序列分析表明,四倍体鲫鲤、三倍体鲫鲂、四倍体鲫鲂和五倍体鲫鲂与其母本1200 bp片段同源性分别为99.5%、98.9%、99.5%和88.7%,与母本900 bp片段同源性分别为97.5%、94.6%、94.2%和89.9%,说明四倍体鲫鲤与多倍体鲫鲂1200 bp和900 bp Cyclin B基因片段与母本红鲫同源性高,在进化上具有偏母性遗传特性。而三倍体和五倍体鲫鲂的750 bp CyclinB基因片段与父本同源性分别高达98.6%和98.2%,说明其来自父本团头鲂。在两性可育的异源四倍体鲫鲤和异源四倍体鲫鲂中存在各自父本Cyclin B基因片段序列消除现象。此外,用Cyclin B基因内含子3序列构建不同倍性鲤科鱼的系统进化树,‘结果表明,由Cyclin B基因内含子序列构建的系统进化树可以正确反映亲缘关系较近的鲤亚科属间鱼类系统进化关系,而不适合亲缘关系较远的亚科间杂交鱼类系统进化分析。
采用荧光定量PCR方法,比较了雌核发育二倍体鲫鲤与普通红鲫和鲤鱼早期卵巢Cyclin A1和B1基因的表达,结果表明两个基因在雌核发育二倍体鲫鲤早期卵巢的表达量明显低于红鲫和鲤鱼早期卵巢的表达量,同时也低于二倍体鲫鲤成熟期卵巢表达量。雌核发育二倍体鲫鲤早期卵巢Cyclin A1和B1基因的低量表达,推测与早期卵巢生殖细胞核内复制有关。
Polyploidy is not only a typical characteristic of plant species,but can also be found in almost all organisms from protists to humans,which is especially a more common phenomenon in fishes.Duplication of the genome,and extra-copies of genes resulting from polyploidy,provide the necessary genetic materials for biological evolution and play an important role in the evolutionary process of the vertebrate.
The allotetraploid produced by distant hybridization(red crucian carp♀X common carp♂),is the first case artificial polyploid fish with the bisexual fertile and stable inheritance in vertebrate in the wold.It has been proved to have two chromosome sets of red crucian carp and two chromosome sets of common carp.In order to understand how allotetraploid genomes evolve after their formation,in this study,we investigated the genomic change and molecular evolution relationships of the allotetraploid and their original parents.The research results will have great significance of further understanding the formation and evolution mechanisms of the polyploid in the fish and even vertebrate.The major results in this paper were presented as follows:
Population genetic structure and genomic change of the allotetraploid and their Original parents were revealed by ISSR-PCR and AFLP-PCR markers.The abundant genetic polymorphism were detected among the three populations.The genetic distances and cluster analysis indicated that the allotetraploids inherited the greater part of genetic materials from their original parents after 15 successive generations,and kept the stable genetic characteristics.But the allotetraploids had a higher sister relationships with their original maternal red crucian carp and were inclined to inherite more genetic information from the female parents;The analysis of DNA fingerprintings showed that the allotetraploids,derived from crossing of two original parents genomes,had undergone DNA sequence eliminations, the percentages of sequence elimination statisted from two sets of markers were 19%and 26.5%,respectively,comparing to the female parents,and 48.6%and 28.4%,respectively,comparing to the male parents.The ratio of sequence eliminatiuon from the male parents was larger than the from the female parents.At the same time,some non-parentage bands were founded in the allotetraploid hygbrids.
The cyclin A and B gene are the key regulators ofcell cycle,which can regulate the cell from G_2/M to an M phase.The cDNA encoding cyclin A and B were derived from the ovaries of the allotetraploid and their original parents,using RT-PCR and RACE.Based on the cDNA and amino acids sequences of cyclin Al and Bl genes,the sequence homology and nucleotide divergence loci were analyzed between the allotetraploid and its original parents,the results indicated the the homology of encoding cDNA sequences of allotetraploid and its original parents were more than 90%, especially,the homology of cyclin boxes sequences were more than 94%, and all the sequence homology between the allotetraploid and its female parent was higher than that between the allotetraploid and its male parent.The well-resolved phylogenetic trees showed that the allotetraploid had more close relative relationship with the original maternal red crucian carp in the evolution process.On the encoding regions of cyclin Al and Bl, the nucleotides mutation levels of allotetraploid were 1.8%and 0.9%, respectively,comparing with the original maternal red crucian carp,and which were 4.7%and 5.7%,respectively,in contrasting to the original paternal common carp,which suggesting that the mutation degrees of cyclin Al and Bl,in the genome of allotetraploid,the original paternal common carp was higher than that of the original maternal red crucian carp. The amino acids sequence alignments of cyclin Al and Bl revealed that there were 4 and 2 amino acids mutation loci between allotetraploids and their original parents,respectively,and the non-parentage loci were resulted from the nonsynonymous substitutions of single nucleotide of codon.
According to the splicing ways of the zebrafish cyclin Bl gene,four pairs degenerate primers were designed to be specific for the exon regions of cyclin B in allotetraploid and its original parents,we amplified 8 introns of cycline B gene from allotetraploid and its original parents by PCR,and all the introns obeyed "GT-AG" rule.The combined intron sequence of allotetraploid shared 96.8%and 66.4%homology respectively,with those of the original maternal red crucian carp and original paternal common carp. Partial fragments of the cyclin B gene from triploid,tetraploid,and pentaploid hybrids of red crucian carpx blunt snout bream,blunt snout bream,grass carp,silver carp,and bighead carp were amplified by the primer pairs P3/P4.One DNA fragment was amplified from the blunt snout bream,grass carp,silver carp,and bighead carp(750,900,720,and 720 bp, respectively).Two fragments(1200 and 900 bp) were amplified from the red crucian carp,common carp,and allotetraploids.The triploid and pentaploid hybrids yielded three DNA fragments(1200,900,and 750 bp). The 1200 bp fragments of the allotetraploid crucian carp,triploid, tetraploid,pentaploid hybrids of red crucian carp~x blunt snout bream shared 99.5,98.9,99.5,and 88.7%homology,respectively,with the maternal DNA.The 900 bp fragment shared 97.5,94.6,94.2 and 89.9% homology,respectively.Our results suggest that inheritance is maternally dominated.Furthermore,we observed preferential elimination of the paternal sequences in the allotetraploid hybrids.Based on these sequences analyses we constructed a phylogenetic tree to explain the relationships among the different ploidy levels.
Real-time Quantitative RT-PCR was used to analyze the cyclin Al and Bl gene expression in ovary of the diploid gynogenetic progeny of allotetraploid hybrid,red crucian carp and common carp at the early stage. The results showed that the expression level of cyclin Al and Bl gene in
the diploid gynogenesis hybrid was significantly lower than that in red crucian carp and common carp,at the same time,which was also lower of the diploid gynogenetic progeny of allotetraploid hybrid at the early stage than that at the mature stage.The low expression level of cyclin Al and Bl gene in ovary of the diploid gynogenesis may be correlative to the endoreduplication of oogonia at the early stage.
异源四倍体鲫鲤是通过远缘杂交的方式首次在脊椎动物中人工培育的两性可育、遗传性状稳定的多倍体鱼,其体细胞包含2套红鲫和2套鲤鱼染色体。为了了解异源四倍体鲫鲤形成后基因组的进化情况,本研究以异源四倍体鲫鲤及其原始亲本为材料,从基因组和单个基因的变化两个角度探讨了异源四倍体鲫鲤的基因组变化及其与原始父母本的分子进化关系。研究结果对进一步了解鱼类乃至脊椎动物多倍体的形成与进化机制具有重要的意义。主要研究内容如下:
采用ISSR和AFLP分子标记,对异源四倍体鲫鲤及其原始亲本群体的遗传结构及基因组的变化进行分析。研究结果表明,异源四倍体鲫鲤经过连续15代的培育,仍然保持了原始亲本遗传性状的稳定性。但遗传相似率表明,异源四倍体鲫鲤与其原始母本红鲫的亲缘关系更近,表现出偏母性遗传的特性;DNA带纹分析发现,在异源四倍体鲫鲤基因组中发生了原始亲本条带的丢失,两种分子标记统计的原始母本红鲫基因组带纹消失比例分别为19%和26.5%,原始父本鲤鱼基因组带纹消失的比例分别为46.8%和28.4%,父本基因组比母本基因组的带纹消失比例大。同时,在异源四倍体鲫鲤群体中发现一些原始父母本没有的DNA条带。
Cyclin A1和B1基因是细胞周期调控关键基因。首次分离和克隆出异源四倍体鲫鲤及其原始亲本Cyclin A1和B1基因cDNA全长序列,在此基础上,对异源四倍体鲫鲤及其原始亲本进行了序列同源性比较及碱基差异位点分析。结果表明,异源四倍体鲫鲤与原始父母本编码区序列同源性都在90%以上,特别是在周期蛋白框区的序列同源性更高(94%以上)。而四倍体鲫鲤与原始母本红鲫的同源性高于与原始父本的同源性。系统进化树也显示异源四倍体鲫鲤总是首先与其原始母本红鲫聚合,也表现出与偏母性遗传的特性。在Cyclin A1基因编码区,异源四倍体鲫鲤相对于原始母本红鲫的碱基变异水平为1.8%、相对于原始父本鲤鱼的碱基变异水平为4.7%;在Cyclin B_l基因编码区,相对于原始母本的碱基变异水平为O.9%,相对于原始父本的碱基变异水平为5.7%,说明在四倍体鲫鲤中原始父本比原始母本的Cyclin A1和B1基因碱基变异程度更高。Cyclin A1和B1氨基酸序列比对发现,异源四倍体鲫鲤分别存在4个和2个与其原始父母本不同的位点,新的氨基酸位点的产生是由密码子单个碱基位点的非同义突变所致。
根据斑马鱼Cyclin B1基因的剪切方式,设计4对兼并引物,首次扩增出异源四倍体鲫鲤及其原始亲本红鲫和鲤鱼Cyclin B基因8个内含子,内含子剪切位点符合GT-AG规则。将异源四倍体鲫鲤Cyclin B基因内含子合并序列与原始母本红鲫和原始父本鲤鱼进行比较,它们之间的同源性分别为96.8%和66.4%。通过第2对引物(P3/P4)PCR扩增,获得三倍体鲫鲂、四倍体鲫鲂、五倍体鲫鲂和团头鲂、草鱼、鲢鱼、鳙鱼等鲤科鱼Cyclin B基因部分DNA序列。结合异源四倍体鲫鲤及其原始亲本红鲫和鲤鱼Cyclin B基因对应DNA序列,对不同倍性鲤科鱼类Cyclin B基因DNA片段序列进行比较分析。结果表明:由相同引物扩增的染色体数为48的鲂、草、鲢、鳙鱼,只扩增出1条DNA片段,片段长度分别为750 bp、950 bp、720 bp和720 bp,而染色体数目加倍的红鲫、鲤鱼、异源四倍体鲫鲤、异源四倍体鲫鲂,扩增出2条DNA片段(1200 bp和900 bp),三倍体和五倍体鲫鲂扩增出3条DNA片段(1200 bp、900 bp和750 bp),每个DNA片段均含Cyclin B基因第2、3内含子和第2、3、4外显子。序列分析表明,四倍体鲫鲤、三倍体鲫鲂、四倍体鲫鲂和五倍体鲫鲂与其母本1200 bp片段同源性分别为99.5%、98.9%、99.5%和88.7%,与母本900 bp片段同源性分别为97.5%、94.6%、94.2%和89.9%,说明四倍体鲫鲤与多倍体鲫鲂1200 bp和900 bp Cyclin B基因片段与母本红鲫同源性高,在进化上具有偏母性遗传特性。而三倍体和五倍体鲫鲂的750 bp CyclinB基因片段与父本同源性分别高达98.6%和98.2%,说明其来自父本团头鲂。在两性可育的异源四倍体鲫鲤和异源四倍体鲫鲂中存在各自父本Cyclin B基因片段序列消除现象。此外,用Cyclin B基因内含子3序列构建不同倍性鲤科鱼的系统进化树,‘结果表明,由Cyclin B基因内含子序列构建的系统进化树可以正确反映亲缘关系较近的鲤亚科属间鱼类系统进化关系,而不适合亲缘关系较远的亚科间杂交鱼类系统进化分析。
采用荧光定量PCR方法,比较了雌核发育二倍体鲫鲤与普通红鲫和鲤鱼早期卵巢Cyclin A1和B1基因的表达,结果表明两个基因在雌核发育二倍体鲫鲤早期卵巢的表达量明显低于红鲫和鲤鱼早期卵巢的表达量,同时也低于二倍体鲫鲤成熟期卵巢表达量。雌核发育二倍体鲫鲤早期卵巢Cyclin A1和B1基因的低量表达,推测与早期卵巢生殖细胞核内复制有关。
Polyploidy is not only a typical characteristic of plant species,but can also be found in almost all organisms from protists to humans,which is especially a more common phenomenon in fishes.Duplication of the genome,and extra-copies of genes resulting from polyploidy,provide the necessary genetic materials for biological evolution and play an important role in the evolutionary process of the vertebrate.
The allotetraploid produced by distant hybridization(red crucian carp♀X common carp♂),is the first case artificial polyploid fish with the bisexual fertile and stable inheritance in vertebrate in the wold.It has been proved to have two chromosome sets of red crucian carp and two chromosome sets of common carp.In order to understand how allotetraploid genomes evolve after their formation,in this study,we investigated the genomic change and molecular evolution relationships of the allotetraploid and their original parents.The research results will have great significance of further understanding the formation and evolution mechanisms of the polyploid in the fish and even vertebrate.The major results in this paper were presented as follows:
Population genetic structure and genomic change of the allotetraploid and their Original parents were revealed by ISSR-PCR and AFLP-PCR markers.The abundant genetic polymorphism were detected among the three populations.The genetic distances and cluster analysis indicated that the allotetraploids inherited the greater part of genetic materials from their original parents after 15 successive generations,and kept the stable genetic characteristics.But the allotetraploids had a higher sister relationships with their original maternal red crucian carp and were inclined to inherite more genetic information from the female parents;The analysis of DNA fingerprintings showed that the allotetraploids,derived from crossing of two original parents genomes,had undergone DNA sequence eliminations, the percentages of sequence elimination statisted from two sets of markers were 19%and 26.5%,respectively,comparing to the female parents,and 48.6%and 28.4%,respectively,comparing to the male parents.The ratio of sequence eliminatiuon from the male parents was larger than the from the female parents.At the same time,some non-parentage bands were founded in the allotetraploid hygbrids.
The cyclin A and B gene are the key regulators ofcell cycle,which can regulate the cell from G_2/M to an M phase.The cDNA encoding cyclin A and B were derived from the ovaries of the allotetraploid and their original parents,using RT-PCR and RACE.Based on the cDNA and amino acids sequences of cyclin Al and Bl genes,the sequence homology and nucleotide divergence loci were analyzed between the allotetraploid and its original parents,the results indicated the the homology of encoding cDNA sequences of allotetraploid and its original parents were more than 90%, especially,the homology of cyclin boxes sequences were more than 94%, and all the sequence homology between the allotetraploid and its female parent was higher than that between the allotetraploid and its male parent.The well-resolved phylogenetic trees showed that the allotetraploid had more close relative relationship with the original maternal red crucian carp in the evolution process.On the encoding regions of cyclin Al and Bl, the nucleotides mutation levels of allotetraploid were 1.8%and 0.9%, respectively,comparing with the original maternal red crucian carp,and which were 4.7%and 5.7%,respectively,in contrasting to the original paternal common carp,which suggesting that the mutation degrees of cyclin Al and Bl,in the genome of allotetraploid,the original paternal common carp was higher than that of the original maternal red crucian carp. The amino acids sequence alignments of cyclin Al and Bl revealed that there were 4 and 2 amino acids mutation loci between allotetraploids and their original parents,respectively,and the non-parentage loci were resulted from the nonsynonymous substitutions of single nucleotide of codon.
According to the splicing ways of the zebrafish cyclin Bl gene,four pairs degenerate primers were designed to be specific for the exon regions of cyclin B in allotetraploid and its original parents,we amplified 8 introns of cycline B gene from allotetraploid and its original parents by PCR,and all the introns obeyed "GT-AG" rule.The combined intron sequence of allotetraploid shared 96.8%and 66.4%homology respectively,with those of the original maternal red crucian carp and original paternal common carp. Partial fragments of the cyclin B gene from triploid,tetraploid,and pentaploid hybrids of red crucian carpx blunt snout bream,blunt snout bream,grass carp,silver carp,and bighead carp were amplified by the primer pairs P3/P4.One DNA fragment was amplified from the blunt snout bream,grass carp,silver carp,and bighead carp(750,900,720,and 720 bp, respectively).Two fragments(1200 and 900 bp) were amplified from the red crucian carp,common carp,and allotetraploids.The triploid and pentaploid hybrids yielded three DNA fragments(1200,900,and 750 bp). The 1200 bp fragments of the allotetraploid crucian carp,triploid, tetraploid,pentaploid hybrids of red crucian carp~x blunt snout bream shared 99.5,98.9,99.5,and 88.7%homology,respectively,with the maternal DNA.The 900 bp fragment shared 97.5,94.6,94.2 and 89.9% homology,respectively.Our results suggest that inheritance is maternally dominated.Furthermore,we observed preferential elimination of the paternal sequences in the allotetraploid hybrids.Based on these sequences analyses we constructed a phylogenetic tree to explain the relationships among the different ploidy levels.
Real-time Quantitative RT-PCR was used to analyze the cyclin Al and Bl gene expression in ovary of the diploid gynogenetic progeny of allotetraploid hybrid,red crucian carp and common carp at the early stage. The results showed that the expression level of cyclin Al and Bl gene in
the diploid gynogenesis hybrid was significantly lower than that in red crucian carp and common carp,at the same time,which was also lower of the diploid gynogenetic progeny of allotetraploid hybrid at the early stage than that at the mature stage.The low expression level of cyclin Al and Bl gene in ovary of the diploid gynogenesis may be correlative to the endoreduplication of oogonia at the early stage.
引文
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