Cho Heejung, Jung Myunghee, Lee Seung Jae, Park Ji Yeon, Zoclanclounon Yedomon Ange Bovys, Kim Cheol-Woo, Han JiWon, Kim Jung Sun, Kim Do-Sun, Shin Younhee, Hwang Yoon-Jung, Lee Tae-Ho, Lee Si Myung, Kang Sang-Ho, Won So Youn, Kim Jin-Hyun, Jang Hye Yoon, Lee Hye-Eun, Lee Eun Su, Lee Sang-Choon, Ji Hyeonso, Sohn Seong-Han, Ahn Byoung Ohg
Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea.
Research and Development Center, Insilicogen, Inc., Yongin, 16954, Republic of Korea.
Sci Data. 2025 Feb 26;12(1):336. doi: 10.1038/s41597-025-04635-3.
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.
洋葱（Allium cepa L.）是一种具有经济价值的作物，但其庞大且富含重复序列的基因组使得基因组组装困难，限制了分子育种和生物学研究。在此，我们展示了通过结合PacBio、Illumina和Hi-C测序方法构建的双单倍体洋葱品系DHW30006的染色体水平参考基因组组装。组装后的基因组总计127.7亿碱基对，有65730个基因模型，并被锚定到8条假染色体上，覆盖120.7亿碱基对（94.5%），支架N50为14.0亿碱基对。DHW30006洋葱基因组包含改进的基因模型，覆盖约5.8亿碱基对（4.54%）的基因区域，平均基因长度为8827碱基对，每个基因有5.48个外显子。这些基因模型代表了葱属基因组中最完善的注释。这个洋葱基因组将为葱属植物的育种和生物学研究提供宝贵资源。
