利用棉纤维发育相关基因研究不同棉种分子进化
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摘要
棉花是世界性重要的经济作物。棉属植物的分类研究已有近百年的历史。最有权威的棉属分类结果是美国植物学家Fryxell在1992年提出的。他将棉属分为4个亚属,8个组,9个亚组,50个种。共包括45个二倍体种和5个异源四倍体种。异源四倍体种是由二倍体A染色体组棉种和二倍体D染色体组棉种种间杂交而成的。其中A染色体组棉种可产生可纺织的纤维,而D基因组棉种不能。本研究选择1个二倍体A基因组棉种(G.herbaceum),13个二倍体D基因组棉种和2个四倍体栽培代表种,共16个棉种,比较已克隆的棉纤维发育相关基因在这些棉种中的序列及结构异同,研究棉属D染色体组棉种之间的关系及异源四倍体D染色体亚组的可能供体种。
选择15个NCBI上已登录的棉纤维发育相关基因及本实验室新克隆的一个蔗糖合酶基因(SusA1),在16个棉种中获得基因全长序列。通过基因的结构分析发现,16个基因中有13个基因的结构在各棉种之间比较保守,其余3个基因(ManA2.CelA3和CIPK1)的结构在不同棉种间变异比较大。基因的进化速率分析显示,同一基因在不同棉种中的进化速率比较恒定,而同一棉种不同基因间的进化速率差异比较大,暗示无论供试棉种的纤维有无,其大部分纤维发育相关基因结构变异不大。相对于A基因组棉种,D基因组祖先种分化时不同的纤维发育相关基因分化程度差异较大；在漫长的进化过程中,TM-1的进化速率大于海7124。对各基因在16个棉种中的18条序列进行聚类分析,发现11个基因的亚类聚类情况与Fryxell(1992)的亚类分类相同,而其余的5个基因(ACT1、CelA3、LTP3、Sus1和Pel)的亚类聚类结果稍有变化。同时,除Exp1和SusAl外,其余14个基因的A染色体亚组和D染色体亚组在聚类时明显分开。12个基因的聚类结果显示均为雷蒙德氏棉与异源四倍体的D染色体亚组聚在一起,而ACT1、Exp、POD2和Pel的系统进化树显示,异源四倍体的D染色体亚组分别与其它的二倍体D染色体组棉种聚在一起。进一步将所有基因的序列按染色体组拼接,获得了18条序列,对其进行聚类分析发现,在亚组水平上,13个D染色体组棉种与Fryxell(1992)的亚组分类相同；异源四倍体形成后,A、D亚组是独立进化的,且雷蒙德氏棉与陆地棉和海岛棉D染色体亚组的亲缘关系最近。
Cotton from the genus Gossypium is the world's most important fiber crop plant. For nearly 100 years, a wide variety of data, including morphologic, meiotic, karyotypic, genetic and molecular, were generated to address the relationships among members of the genus. Now, the most authoritative classification for Gossypium follows Fryxell (1992), who divided Gossypium into four subgenera, eight sections, nine subsections and approximately 50 species. Forty-five cotton species are diploid and five are tetraploid. The five tetraploid species are of allopolyploid origins, originated from interspecific hybridization between diploid A- and D-genome species, the best extant model of the A-subgenome donor is G. herbaceum, while the D-subgenome donor remained unclear. So, in this study, based on the sequence and the structures of 16 fiber development genes in 16 cotton species, we revealed the relationship of 13 diploid D-genome species and the D-genome donor of tetraploid species.
16 fiber development genes, including 15 accessioned to NCBI and a new sucrose synthase gene(SusA1) cloned by our lab, were chose to study. First, we cloned these genes in the genome DNA of 16 cotton species, including one diploid A-genome species,13 diploid D-genome species and two tetraploid species. In the orthologues and homoelogous loci of 16 studied genes, the sequence and structure of 13 genes were conservative and 3 genes(ManA2, CelA3 and CIPK1) were diverse. The evolution rates between A and D-genome and between A (D)-genome and A (D)-subgenome revealed that the same gene may have same rates among different species and evolution rates were divergence among genes; D-subgenome of allotetraploid had higher evolution rate than A-subgenome, and Hai7124 may be more conserved than TM-1. Further, the phylogenetic trees of each gene were constructed. The results of 11 genes showed that 13 D-genome species were congruent with Fryxell's subsection taxonomy, while 5 genes, ACT1, CelA3, LTP3, Susl and Pel, were different. And except Expl and SusAl, the other 14 genes were independent evolution between A- and D-subgenome in the allopolyploid after polyploid formation. For 12 genes, the D-subgenomes of TM-1 and Hai7124 had closer relationship with G. raimondii, while D-subgenomes of ACT1, Exp, POD2 and Pel were in the same cluster with other diploid D-genome species. Further, the phylogenetic tree was constructed based on the combined sequence data. The results showed that 13 D-genome species were congruent with Fryxell's subsection taxonomy, the A- and D-subgenome in the allopolyploid were independent evolution after polyploid formation and G. raimondii has the closest gnetic relationship with the D-genome donor of G. hirsutum and G. barbadense.
选择15个NCBI上已登录的棉纤维发育相关基因及本实验室新克隆的一个蔗糖合酶基因(SusA1),在16个棉种中获得基因全长序列。通过基因的结构分析发现,16个基因中有13个基因的结构在各棉种之间比较保守,其余3个基因(ManA2.CelA3和CIPK1)的结构在不同棉种间变异比较大。基因的进化速率分析显示,同一基因在不同棉种中的进化速率比较恒定,而同一棉种不同基因间的进化速率差异比较大,暗示无论供试棉种的纤维有无,其大部分纤维发育相关基因结构变异不大。相对于A基因组棉种,D基因组祖先种分化时不同的纤维发育相关基因分化程度差异较大；在漫长的进化过程中,TM-1的进化速率大于海7124。对各基因在16个棉种中的18条序列进行聚类分析,发现11个基因的亚类聚类情况与Fryxell(1992)的亚类分类相同,而其余的5个基因(ACT1、CelA3、LTP3、Sus1和Pel)的亚类聚类结果稍有变化。同时,除Exp1和SusAl外,其余14个基因的A染色体亚组和D染色体亚组在聚类时明显分开。12个基因的聚类结果显示均为雷蒙德氏棉与异源四倍体的D染色体亚组聚在一起,而ACT1、Exp、POD2和Pel的系统进化树显示,异源四倍体的D染色体亚组分别与其它的二倍体D染色体组棉种聚在一起。进一步将所有基因的序列按染色体组拼接,获得了18条序列,对其进行聚类分析发现,在亚组水平上,13个D染色体组棉种与Fryxell(1992)的亚组分类相同；异源四倍体形成后,A、D亚组是独立进化的,且雷蒙德氏棉与陆地棉和海岛棉D染色体亚组的亲缘关系最近。
Cotton from the genus Gossypium is the world's most important fiber crop plant. For nearly 100 years, a wide variety of data, including morphologic, meiotic, karyotypic, genetic and molecular, were generated to address the relationships among members of the genus. Now, the most authoritative classification for Gossypium follows Fryxell (1992), who divided Gossypium into four subgenera, eight sections, nine subsections and approximately 50 species. Forty-five cotton species are diploid and five are tetraploid. The five tetraploid species are of allopolyploid origins, originated from interspecific hybridization between diploid A- and D-genome species, the best extant model of the A-subgenome donor is G. herbaceum, while the D-subgenome donor remained unclear. So, in this study, based on the sequence and the structures of 16 fiber development genes in 16 cotton species, we revealed the relationship of 13 diploid D-genome species and the D-genome donor of tetraploid species.
16 fiber development genes, including 15 accessioned to NCBI and a new sucrose synthase gene(SusA1) cloned by our lab, were chose to study. First, we cloned these genes in the genome DNA of 16 cotton species, including one diploid A-genome species,13 diploid D-genome species and two tetraploid species. In the orthologues and homoelogous loci of 16 studied genes, the sequence and structure of 13 genes were conservative and 3 genes(ManA2, CelA3 and CIPK1) were diverse. The evolution rates between A and D-genome and between A (D)-genome and A (D)-subgenome revealed that the same gene may have same rates among different species and evolution rates were divergence among genes; D-subgenome of allotetraploid had higher evolution rate than A-subgenome, and Hai7124 may be more conserved than TM-1. Further, the phylogenetic trees of each gene were constructed. The results of 11 genes showed that 13 D-genome species were congruent with Fryxell's subsection taxonomy, while 5 genes, ACT1, CelA3, LTP3, Susl and Pel, were different. And except Expl and SusAl, the other 14 genes were independent evolution between A- and D-subgenome in the allopolyploid after polyploid formation. For 12 genes, the D-subgenomes of TM-1 and Hai7124 had closer relationship with G. raimondii, while D-subgenomes of ACT1, Exp, POD2 and Pel were in the same cluster with other diploid D-genome species. Further, the phylogenetic tree was constructed based on the combined sequence data. The results showed that 13 D-genome species were congruent with Fryxell's subsection taxonomy, the A- and D-subgenome in the allopolyploid were independent evolution after polyploid formation and G. raimondii has the closest gnetic relationship with the D-genome donor of G. hirsutum and G. barbadense.
引文
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