Whole Genome Duplication of Intra- and Inter-chromosomes in the Tomato Genome  

作　　者：Chi Song Juan Guo Wei Sun Ying Wang 

机构地区：[1]Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture,Wuhan Botanical Garden,Chinese Academy of Sciences,Wuhan,Hubei 430074,China [2]Graduate University of Chinese Academy of Sciences,Beijing 100049,China [3]South China Botanical Garden,Chinese Academy of Sciences,Guangzhou,Guangdong 510650,China

出　　处：《Journal of Genetics and Genomics》2012年第7期361-368,共8页遗传学报（英文版）

基　　金：supported by the Major State Basic Research Development Program of China(973 Program) (Grant No.2010CB126603);the National Natural Science Foundation of China(No.30570172);the CAS/SAFEA International Partnership Program for Creative Research Teams

摘　　要：Whole genome duplication （WGD） events have been proven to occur in the evolutionary history of most angiosperms. Tomato is considered a model species of the Solanaceae family. In this study, we describe the details of the evolutionary process of the tomato genome by detecting collinearity blocks and dating the WGD events on the tree of life by combining two different methods： synonymous substitution rates （Ks） and phylogenetic trees. In total, 593 collinearity blocks were discovered out of 12 pseudo-chromosomes con- structed. It was evident that chromosome 2 had experienced an intra-chromosomat duplication event. Major inter-chromosomal dupli- cation occurred among all the pseudo-chromosome. We calculated the Ks value of these collinearity blocks. Two peaks of Ks distribution were found, corresponding to two WGD events occurring approximately 36-82 million years ago （MYA） and 148--205 MYA. Additionally, the results of phylogenetic trees suggested that the more recent WGD event may have occurred after the divergence of the rosidasterid clade, but before the major diversification in Solanaceae. The older WGD event was shown to have occurred before the divergence of the rosid-asterid clade and after the divergence of rice-Arabidopsis （monocot-dicot）.Whole genome duplication （WGD） events have been proven to occur in the evolutionary history of most angiosperms. Tomato is considered a model species of the Solanaceae family. In this study, we describe the details of the evolutionary process of the tomato genome by detecting collinearity blocks and dating the WGD events on the tree of life by combining two different methods： synonymous substitution rates （Ks） and phylogenetic trees. In total, 593 collinearity blocks were discovered out of 12 pseudo-chromosomes con- structed. It was evident that chromosome 2 had experienced an intra-chromosomat duplication event. Major inter-chromosomal dupli- cation occurred among all the pseudo-chromosome. We calculated the Ks value of these collinearity blocks. Two peaks of Ks distribution were found, corresponding to two WGD events occurring approximately 36-82 million years ago （MYA） and 148--205 MYA. Additionally, the results of phylogenetic trees suggested that the more recent WGD event may have occurred after the divergence of the rosidasterid clade, but before the major diversification in Solanaceae. The older WGD event was shown to have occurred before the divergence of the rosid-asterid clade and after the divergence of rice-Arabidopsis （monocot-dicot）.

关 键 词：Whole genome duplication Collinearity block Phylogenetic tree 

分 类 号：Q78[生物学—分子生物学] S828.2[农业科学—畜牧学]