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De novo genome assembly of a high-protein soybean variety HJ117

Authors :
Zhi Liu
Qing Yang
Bingqiang Liu
Chenhui Li
Xiaolei Shi
Yu Wei
Yuefeng Guan
Chunyan Yang
Mengchen Zhang
Long Yan
Source :
BMC Genomic Data, Vol 25, Iss 1, Pp 1-5 (2024)
Publication Year :
2024
Publisher :
BMC, 2024.

Abstract

Abstract Objectives Soybean is an important feed and oil crop in the world due to its high protein and oil content. China has a collection of more than 43,000 soybean germplasm resources, which provides a rich genetic diversity for soybean breeding. However, the rich genetic diversity poses great challenges to the genetic improvement of soybean. This study reports on the de novo genome assembly of HJ117, a soybean variety with high protein content of 52.99%. These data will prove to be valuable resources for further soybean quality improvement research, and will aid in the elucidation of regulatory mechanisms underlying soybean protein content. Data description We generated a contiguous reference genome of 1041.94 Mb for HJ117 using a combination of Illumina short reads (23.38 Gb) and PacBio long reads (25.58 Gb), with high-quality sequence coverage of approximately 22.44× and 24.55×, respectively. HJ117 was developed through backcross breeding, using Jidou 12 as the recurrent parent and Chamoshidou as the donor parent. The assembly was further assisted by 114.5 Gb Hi-C data (109.9×), resulting in a contig N50 of 19.32 Mb and scaffold N50 of 51.43 Mb. Notably, Core Eukaryotic Genes Mapping Approach (CEGMA) assessment and Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment results indicated that most core eukaryotic genes (97.18%) and genes in the BUSCO dataset (99.4%) were identified, and 96.44% of the genomic sequences were anchored onto twenty pseudochromosomes.

Details

Language :
English
ISSN :
27306844
Volume :
25
Issue :
1
Database :
Directory of Open Access Journals
Journal :
BMC Genomic Data
Publication Type :
Academic Journal
Accession number :
edsdoj.5dfc5a90b2284a5a8d91e43ed03af029
Document Type :
article
Full Text :
https://doi.org/10.1186/s12863-024-01213-1