Oryza sativa genome sequencing. Oryza sativa cultivar:93-11

Assembly a high-quality rice reference genome is essential for basic and applied research, which benefit downstream yield and related industries. The current rice reference genome contain considerable number of gaps, and many contigs are arbitrarily ordered and oriented. Here using single-molecule real-time (SMRT) sequencing, we largely improved assembly of two rice japonica group cultivar Nipponbare (Nip) and indica Group cultivar 93-11 genomes, which have 2.2-fold and 460-fold higher contiguity than the previous published Nip MSU7 and 93-11 BGI genomes, respectively. Notably, the gap number was greatly reduced from 905 of MSU7 to 18 for Nip, and 54,600 of BGI to 65 for 93-11. The annotation of gene and intergenic regions was further improved. Moreover, we reported genome-wide N6-methyldeoxyadenine (6mA) DNA methylation at single-nucleotide resolution in Nip and 93-11, which was validated by 6mA immunoprecipitation followed by sequencing (6mA-IP-seq). We found that 6mA 6mA was associated with actively expressed genes in rice. Finally, we show that 6mA levels are positively correlated with expression of the stress related key genes, which may contribute to the different stress tolerance between Nip and 93-11.