Chromosome-scale reference genome assembly of an Aokubi Raphanus sativus doubled haploid line

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Abstract
Radish ( Raphanus sativus L.) exhibits substantial morphological and agronomic diversity, with Aokubi cultivars representing a major lineage in Japanese breeding programs. Although several radish genomes have been published so far, no chromosome-scale reference for the Aokubi lineage exists. Here we present a chromosome-scale genome assembly of an Aokubi doubled haploid line generated using Oxford Nanopore long-read sequencing and Bionano optical genome mapping. PromethION sequencing produced 71.0 Gb of long-read data (N50 = 41.2 kb; 123 × coverage). Hybrid scaffolding with Bionano optical maps, complemented by ntLink long-read scaffolding, anchored the assembly into nine pseudochromosomes, yielding a total size of 476.1 Mb with a scaffold N50 of 52.2 Mb. BUSCO analysis using brassicales_odb12 indicated 99.2% completeness. Telomeric repeats were identified at 17 of 18 chromosome termini, and centromeric regions were identified on all nine pseudochromosomes. Repeat annotation showed 61.5% repetitive content, and BRAKER3 gene prediction produced 40,973 protein-coding genes. This assembly provides a foundational resource for structural variation analysis, functional genomics, and molecular breeding in radish.
Funding Information
  • NODAI Genome Research Center, Tokyo University of Agriculture, the Cooperative Research Grant of the Genome Research for BioResource (no grant number applicable)