Newswise — A research team has achieved a groundbreaking improvement in the haplotype-resolved genome sequence of the japonica rice cultivar Nipponbare. This enhancement reveals the identification and annotation of over 3,000 new genes, potentially offering significant advancements in crop improvement and breeding strategies. The japonica rice cultivar Nipponbare has been pivotal as a reference in rice genomics since its first sequencing over two decades ago, marking a significant breakthrough in plant genomics.
Despite continuous improvements in sequencing technology, the Nipponbare genome assembly still contains unresolved gaps, primarily due to repetitive DNA sequence. Ongoing efforts and technological advances have enhanced genome assembly in other rice species and extended to telomere sequencing. However, achieving a fully haplotype-resolved assembly remains an unaddressed problem in rice genomic research, presenting a critical area for future study.
A study (DOI: 10.48130/tp-0024-0007) published in Tropical Plants on 03 April 2024, generates an improved haplotype resolved rice genome for a comprehensive telomere-to-telomere (T2T) improvement. In this study, PacBio HiFi reads and Hi-C reads were utilized to generate a contig assembly with Hifiasm, resulting in a haplotype phased assembly.
This assembly process yielded distinct contigs for nine of the chromosomes. In contrast, the assembly for the remaining three chromosomes involved two separate contigs for each. The a.
