Oryza sativa isolate:KP | cultivar:Karuppunel Genome sequencing and assembly
Karuppanel, recognized as a promising donor for high zinc accumulation in the rice endosperm, has been identified under the ICAR CRP Biofortification project for its potential in developing biofortified rice varieties with enhanced grain zinc content. To elucidate the genetic mechanisms governing zinc uptake, transport, and accumulation, whole genome sequencing was performed using the Oxford Nanopore long-reads and Illumina short reads. The sequencing emanated in high-quality long reads that were pre-processed, aligned to the rice reference genomes, de novo genome assembled and structurally annotated. Comprehensive repeat analysis was performed to identify transposable elements, tandem repeats, and other repetitive sequences contributing to genome architecture. Functional annotation focused on zinc-related genes, including those involved in metal ion transporters, and regulatory pathways influencing grain micronutrient loading. Furthermore, the chromosome-level assembled genome underwent comparative genomic analysis with other well-characterized rice genomes to assess phylogenetic relationships and identify unique genomic signatures associated with high zinc content. This genomic resource provides critical insights into the molecular mechanisms of zinc biofortification and supports marker-assisted breeding and genome editing strategies for development of nutritionally superior rice varieties.