Comparative effect of allopolyploidy on transposable element composition and gene expression between Gossypium hirsutum and its two diploid progenitors  

作　　者：Hua Cheng Gaofei Sun Shoupu He Wenfang Gong Zhen Peng Ruiping Wang Zhongxu Lin Xiongming Du 

机构地区：[1]Research Base,Anyang Institute of Technology,State Key Laboratory of Cotton Biology,Institute of Cotton Research,the Chinese Academy of Agricultural Science [2]College of Plant Science & Technology of Huazhong Agricultural University [3]Department of Computer Science and Information Engineering,Anyang Institute of Technology

出　　处：《Journal of Integrative Plant Biology》2019年第1期45-59,共15页植物学报（英文版）

基　　金：supported by the International Cooperation Program of Henan Provincial Bureau of Foreign Experts Affairs Authority(2016GH18);the National Key R&D Program of China(2017YFD0101600,2016YFD0100203);the Foundation and Frontier Research Grant of Henan Provincial Science and Technology Bureau(162300410171);the Research Fund Project of Anyang Institute of Technology(YJJ2015013)

摘　　要：An allopolyploidization event formed allotetraploid Gossypium species from an A-genome diploid species and a D-genome diploid species. To explore the responses of transposable elements(TEs) to allopolyploidy, we assembled parallel TE datasets from G. hirsutum, G. arboreum and G. raimondii and analyzed the TE types and the effects of TEs on orthologous gene expression in the three Gossypium genomes.Gypsy was the most abundant TE type and most TEs were located $500 bp from genes in all three genomes. In G. hirsutum, 35.6% of genes harbored TE insertions, whereas insertions were more frequent in G. arboreum and G. raimondii. G. hirsutum had the highest proportion of uniquely matching 24-nt small interfering RNAs(siRNAs) that targeted TEs. TEs,particularly those targeted by 24-nt siRNAs, were associated with reduced gene expression, but the effect of TEs on orthologous gene expression varied substantially among species. Orthologous gene expression levels in G. hirsutum were intermediate between those of G. arboreum and G. raimondii, which did not experience TE expansion or reduction resulting from allopolyploidization. This study underscores the diversity of TEs co-opted by host genes and provides insights into the roles of TEs in regulating gene expression in Gossypium.An allopolyploidization event formed allotetraploid Gossypium species from an A-genome diploid species and a D-genome diploid species. To explore the responses of transposable elements(TEs) to allopolyploidy, we assembled parallel TE datasets from G. hirsutum, G. arboreum and G. raimondii and analyzed the TE types and the effects of TEs on orthologous gene expression in the three Gossypium genomes.Gypsy was the most abundant TE type and most TEs were located $500 bp from genes in all three genomes. In G. hirsutum, 35.6% of genes harbored TE insertions, whereas insertions were more frequent in G. arboreum and G. raimondii. G. hirsutum had the highest proportion of uniquely matching 24-nt small interfering RNAs(siRNAs) that targeted TEs. TEs,particularly those targeted by 24-nt siRNAs, were associated with reduced gene expression, but the effect of TEs on orthologous gene expression varied substantially among species. Orthologous gene expression levels in G. hirsutum were intermediate between those of G. arboreum and G. raimondii, which did not experience TE expansion or reduction resulting from allopolyploidization. This study underscores the diversity of TEs co-opted by host genes and provides insights into the roles of TEs in regulating gene expression in Gossypium.

关 键 词：progenitors ALLOPOLYPLOIDIZATION 

分 类 号：Q[生物学]