A Telomere-to-Telomere Genome Assembly of a Japonica Variety ‘BD8’ Provides Insights into Rice Salt Tolerance

Background: Accurate genomic information in specific rice varieties is essential for functional gene mining and advancing molecular breeding. Bindao8 (BD8) is an elite Japonica rice variety, exhibiting salt tolerance in especial. Results: This study presented a telomere-to-telomere (T2T) gap-free genome assembly of ‘BD8’, with 384.2 Mb in size and contig N50 of 31.69 Mb. This assembly featured evident improvements in continuity and quality, which was approximate to Nip-T2T reference genome. In total, 58,685 genes were identified and 95.93% (56297) of them were functionally annotated. A phylogenetic analysis showed that this cultivar had the closest genetic relationship with ‘ZH11’, ‘Kosh’ ‘02428’, and ‘Nip-T2T’ . Although BD8 and reference genome Nip-T2T exhibit high similarity, there are still abundant structure variations causing mutations in gene function. Enrichment analysis was performed with present and absentgenes by comparing BD8 and Nip-T2T , and four KEGG pathways were enriched and issued. Subsequently, BD8’s feature of salt tolerance was addressed by utilizing this genome along with time-course continuous transcriptomic profile analysis. Two salt-specific clusterscontaining 347 (Profile12) and 607 (Profile19) genes were obtained and five salt-specific KEGG pathways were significantly enriched. Notably, the pathway of amino sugar and nucleotide sugar metabolism (ko00520) was commonly enriched from BD8’s special present genes and salt-specific gene clusters. Conclusion: The high quality BD8 genome assembly will serve as a genome resource for rice functional genomics as well as genomics-driven and/or molecular breeding.