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

被引:57
|
作者
Li, Kui [1 ]
Jiang, Wenkai [2 ]
Hui, Yuanyuan [1 ]
Kong, Mengjuan [1 ]
Feng, Li-Ying [3 ]
Gao, Li-Zhi [3 ]
Li, Pengfu [1 ]
Lu, Shan [1 ,4 ]
机构
[1] Nanjing Univ, Sch Life Sci, State Key Lab Pharmaceut Biotechnol, Nanjing 210023, Peoples R China
[2] Novogene Bioinformat Inst, Bldg 301,Zone A10 Jiuxianqiao North Rd, Beijing 100083, Peoples R China
[3] South China Agr Univ, Inst Genom & Bioinformat, Guangzhou 510642, Peoples R China
[4] Nanjing Univ, Shenzhen Res Inst, Shenzhen 518000, Peoples R China
基金
中国国家自然科学基金;
关键词
evolution; gapless; genome; rice; segmental duplications; transposable elements; MULTIPLE SEQUENCE ALIGNMENT; ADAPTIVE EVOLUTION; BLAST RESISTANCE; WEB SERVER; GENES; ANNOTATION; PREDICTION; REPEAT; IDENTIFICATION; GENERATION;
D O I
10.1016/j.molp.2021.06.017
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
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 ciszeatin-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.
引用
收藏
页码:1745 / 1756
页数:12
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