Chromosome-level genome assembly and improved annotation of onion genome (Allium cepa L.)

Onion (Allium cepa L.) is an economically valuable crop, but its large, repeat-enriched genome makes genome assembly difficult and limits molecular breeding and biological studies. Herein, we present a chromosomal-level reference genome assembly of the double-haploid onion line DHW30006, constructed by combining PacBio, Illumina, and Hi-C sequencing approaches. The assembled genome totaled 12.77 Gb, with 65,730 gene models, and was anchored to eight pseudo-chromosomes covering 12.07 Gb (94.5%), with a scaffold N50 of 1.40 Gb. DHW30006 onion genome contained improved gene models covering approximately 580 Mb (4.54%) of the genic regions with an average gene length of 8,827 bp and 5.48 exons per gene. These gene models represented the most improved annotation among Allium genomes. This onion genome will serve as a valuable resource for breeding and biological research in Allium plants.