Gapless indica rice genome reveals synergistic effects of active transposable elements and segmental duplications that promote rice genome evolution

Abstract The ultimate goal of genome assembly is a high-accuracy gapless genome. Here we report a new assembly pipeline which we have used to produce a gapless genome for the indica rice cultivar Minghui 63. The 395.82 Mb final assembly is composed of 12 contigs with a contig N50 size of 31.82 Mb. All chromosomes are now gapless, with each chromosome represented by a single contig. This is the first gapless genome assembly achieved for higher plants or animals. BUSCO evaluation showed that gene regions of our assembly have higher completeness than the current rice reference genome (IRGSP-1.0). Compared with japonica rice, indica 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 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 adaptative evolution of rice disease resistance and developmental processes. Our findings suggest that active TEs and SDs together provide synergistic effects to promote rice genome evolution.