Gapless indica rice genome reveals synergistic contributions of active transposable elements and segmental duplications to rice genome evolution

查看全文 作　　者：Kui [1]Li;Wenkai [2]Jiang;Yuanyuan [1]Hui;Mengjuan [1]Kong;Li-Ying [3]Feng;Li-Zhi [3]Gao;Pengfu [1]Li;Shan [1,4]Lu

机构地区：[1]State Key Laboratory of Pharmaceutical Biotechnology,School of Life Sciences,Nanjing University,Nanjing 210023,China;[2]Novogene Bioinformatics Institute,Building 301,Zone A10 Jiuxianqiao North Road,Chaoyang District,Beijing 100083,China;[3]Institution of Genomics and Bioinformatics,South China Agricultural University,Guangzhou 510642,China;[4]Shenzhen Research Institute of Nanjing University,Shenzhen 518000,China

出　　处：《Molecular Plant》索引2021年第14卷第10期,共12页

基　　金：This study was supported by the National Natural Science Foundation of China(NSFC,nos.31770331 and 31970318);Guangdong Basic and Applied Basic Research Foundation(no.2020B1515120023). 摘　　要：The ultimate goal of genome assembly is a high-accuracy gapless genome.Here,we report a new assembly pipeline that is used to produce a gapless genome for the indica rice cultivar Minghui 63.The resulting 397.71-Mb final assembly is composed of 12 contigs with a contig N50 size of 31.93 Mb.Each chromosome is represented by a single contig and the genomic sequences of all chromosomes are gapless.Quality evaluation of this gapless genome assembly showed that gene regions in our assembly have the highest completeness compared with the other 15 reported high-quality rice genomes.Further comparison with the japonica rice genome revealed that the gapless indica genome assembly contains more transposable elements(TEs)and segmental duplications(SDs),the latter of which produce many duplicated genes that can affect agronomic traits through dose effect or sub-/neo-functionalization.The insertion of TEs can also affect the expression of duplicated genes,which may drive the evolution of these genes.Furthermore,we found the expansion of nucleotide-binding site with leucine-rich repeat disease-resistance genes and cis-zeatin-O-glucosyltransferase growth-related genes in SDs in the gapless indica genome assembly,suggesting that SDs contribute to the adaptive evolution of rice disease resistance and developmental processes.Collectively,our findings suggest that active TEs and SDs synergistically contribute to rice genome evolution. 关键词：EVOLUTION gapless GENOME rice segmental duplications transposable elements

相关文献

参考文献（85）
引证文献（16）
耦合文献（9）

参考文献(85)

引证文献(16)

耦合文献(9)

互联网出版许可证新出网证(渝)字10号全国400电话 - 免长途话费

Gapless indica rice genome reveals synergistic contributions of active transposable elements and segmental duplications to rice genome evolution

参考文献(85)

引证文献(16)

耦合文献(9)

用户提示