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

Abstract

The ultimate goal of genome assembly is a high-accuracy gapless genome. Here we report a new assembly pipeline to produce a gapless genome for the indica rice cultivar Minghui 63. The 397.71 Mb final assembly is composed of 12 contigs with a contig N50 size of 31.93 Mb. All chromosomes are now gapless, with each chromosome represented by a single contig. BUSCO evaluation showed that gene regions of our assembly have the highest completeness among the 16 high-quality rice genomes. Compared with the japonica rice, the indica genome has more transposable elements (TEs) and segmental duplications (SDs), the latter of which produce many duplicated genes that can affect plant 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. We also found the expansion of NBS-LRR disease resistance genes and cZOGT growth-related genes in SDs, suggesting that SDs contribute to the adaptive evolution of rice disease resistance and developmental processes. Our findings suggest that active TEs and SDs together provide synergistic contributions to rice genome evolution.