A telomere-to-telomere gap-free genome assembly of the indica rice (Oryza sativa L.) cytoplasmic male sterile line Funong A.

Rice ( Oryza sativa L.) is a staple crop crucial for global food security, yet its productivity is limited by climate change, diseases, and genetic erosion. The indica cytoplasmic male sterile (CMS) line Funong A (FNA) is an elite breeding resource, exhibiting strong blast resistance, favorable floral traits, and enhanced stem strength through high silica and hemicellulose deposition. Its hybrids demonstrate >10% yield advantages with medium blast resistance, positioning FNA as a pivotal parent for subtropical hybrid breeding. breeding. Here, we present a fully gap-free, telomere-to-telomere (T2T) chromosome-scale genome assembly of FNA. By integrating PacBio HiFi, Oxford Nanopore long reads, and Hi-C sequencing, we produced a 394.7 Mb gap-free assembly with a contig N50 of 32 Mb, capturing all 24 telomeric regions. The assembly demonstrates exceptional accuracy and completeness, including fully resolved centromeres across all 12 chromosomes. We annotated 39,453 protein-coding genes and 1,376 lncRNAs, with the majority of genes functionally characterized. Repetitive elements comprise 51.1% of the genome, reflecting lineage-specific bursts of long terminal repeat retrotransposons. This high-quality T2T genome provides a valuable foundation for dissecting CMS mechanisms, centromere biology, and structural evolution, while offering critical resources for hybrid rice improvement.