Chromosome-level genome assembly and improved annotation of onion genome (Allium cepa L.)
Abstract 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, co...
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Nature Portfolio
2025-02-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-04635-3 |
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| author | Heejung Cho Myunghee Jung Seung Jae Lee Ji Yeon Park Yedomon Ange Bovys Zoclanclounon Cheol-Woo Kim JiWon Han Jung Sun Kim Do-Sun Kim Younhee Shin Yoon-Jung Hwang Tae-Ho Lee Si Myung Lee Sang-Ho Kang So Youn Won Jin-Hyun Kim Hye Yoon Jang Hye-Eun Lee Eun Su Lee Sang-Choon Lee Hyeonso Ji Seong-Han Sohn Byoung Ohg Ahn |
| author_facet | Heejung Cho Myunghee Jung Seung Jae Lee Ji Yeon Park Yedomon Ange Bovys Zoclanclounon Cheol-Woo Kim JiWon Han Jung Sun Kim Do-Sun Kim Younhee Shin Yoon-Jung Hwang Tae-Ho Lee Si Myung Lee Sang-Ho Kang So Youn Won Jin-Hyun Kim Hye Yoon Jang Hye-Eun Lee Eun Su Lee Sang-Choon Lee Hyeonso Ji Seong-Han Sohn Byoung Ohg Ahn |
| author_sort | Heejung Cho |
| collection | DOAJ |
| description | Abstract 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. |
| format | Article |
| id | doaj-art-57deb22d3f6448299c5b1fa797618905 |
| institution | DOAJ |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-57deb22d3f6448299c5b1fa7976189052025-08-20T02:59:35ZengNature PortfolioScientific Data2052-44632025-02-011211910.1038/s41597-025-04635-3Chromosome-level genome assembly and improved annotation of onion genome (Allium cepa L.)Heejung Cho0Myunghee Jung1Seung Jae Lee2Ji Yeon Park3Yedomon Ange Bovys Zoclanclounon4Cheol-Woo Kim5JiWon Han6Jung Sun Kim7Do-Sun Kim8Younhee Shin9Yoon-Jung Hwang10Tae-Ho Lee11Si Myung Lee12Sang-Ho Kang13So Youn Won14Jin-Hyun Kim15Hye Yoon Jang16Hye-Eun Lee17Eun Su Lee18Sang-Choon Lee19Hyeonso Ji20Seong-Han Sohn21Byoung Ohg Ahn22Genomics Division, National Institute of Agricultural Sciences, RDAResearch and Development Center, Insilicogen, Inc.DNA Link Inc.Genomics Division, National Institute of Agricultural Sciences, RDAGenomics Division, National Institute of Agricultural Sciences, RDAAllium Vegetable Research Center, National Institute of Horticultural and Herbal Science, RDAAllium Vegetable Research Center, National Institute of Horticultural and Herbal Science, RDAGenomics Division, National Institute of Agricultural Sciences, RDAVegetable Division, National Institute of Horticultural and Herbal Science, RDAResearch and Development Center, Insilicogen, Inc.Department of Chemistry Life Science, Sahmyook UniversityGenomics Division, National Institute of Agricultural Sciences, RDAGenomics Division, National Institute of Agricultural Sciences, RDAGenomics Division, National Institute of Agricultural Sciences, RDAGenomics Division, National Institute of Agricultural Sciences, RDAGenomics Division, National Institute of Agricultural Sciences, RDADNA Link Inc.Vegetable Division, National Institute of Horticultural and Herbal Science, RDAVegetable Division, National Institute of Horticultural and Herbal Science, RDAPhyzen Genomics InstituteGene Engineering Division, National Institute of Agricultural Sciences, RDAGenomics Division, National Institute of Agricultural Sciences, RDAGenomics Division, National Institute of Agricultural Sciences, RDAAbstract 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.https://doi.org/10.1038/s41597-025-04635-3 |
| spellingShingle | Heejung Cho Myunghee Jung Seung Jae Lee Ji Yeon Park Yedomon Ange Bovys Zoclanclounon Cheol-Woo Kim JiWon Han Jung Sun Kim Do-Sun Kim Younhee Shin Yoon-Jung Hwang Tae-Ho Lee Si Myung Lee Sang-Ho Kang So Youn Won Jin-Hyun Kim Hye Yoon Jang Hye-Eun Lee Eun Su Lee Sang-Choon Lee Hyeonso Ji Seong-Han Sohn Byoung Ohg Ahn Chromosome-level genome assembly and improved annotation of onion genome (Allium cepa L.) Scientific Data |
| title | Chromosome-level genome assembly and improved annotation of onion genome (Allium cepa L.) |
| title_full | Chromosome-level genome assembly and improved annotation of onion genome (Allium cepa L.) |
| title_fullStr | Chromosome-level genome assembly and improved annotation of onion genome (Allium cepa L.) |
| title_full_unstemmed | Chromosome-level genome assembly and improved annotation of onion genome (Allium cepa L.) |
| title_short | Chromosome-level genome assembly and improved annotation of onion genome (Allium cepa L.) |
| title_sort | chromosome level genome assembly and improved annotation of onion genome allium cepa l |
| url | https://doi.org/10.1038/s41597-025-04635-3 |
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