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Article|25 Feb 2022|OPEN
Chromosomal-level genome and multi-omics dataset of Pueraria lobata var. thomsonii provide new insights into legume family and the isoflavone and puerarin biosynthesis pathways
Xiaohong Shang1 ,† , Xinxin Yi2 ,† , Liang Xiao1 , Yansheng Zhang3 , Ding Huang4 , Zhengbao Xia2 , Kunpeng Ou1 , Ruhong Ming4 , Wendan Zeng1 , Dongqing Wu2 , Sheng Cao1 , Liuyin Lu1 and Huabing Yan,1 ,
1Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China
2Wuhan Frasergen Bioinformatics Co., Ltd, Wuhan, Hubei, 430075, China
3Shanghai Key Laboratory of Bio-Energy Crops, Research Center for Natural Products, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China
4College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, Guangxi, 530200, China
*Corresponding author. E-mail: h.b.yan@hotmail.com
Both authors contributed equally to the study.

Horticulture Research 9,
Article number: uhab035 (2022)
doi: https://doi.org/10.1093/hr/uhab035
Views: 442

Received: 16 Jun 2021
Revised: 08 Mar 2022
Accepted: 23 Oct 2021
Published online: 25 Feb 2022

Abstract

Pueraria lobata var. thomsonii (hereinafter abbreviated as Podalirius thomsonii), a member of the legume family, is one of the important traditional Chinese herbal medicines, and its puerarin extract is widely used in the health and pharmaceutical industry. Here, we assembled a high-quality genome of P. thomsonii using long-read single-molecule sequencing and Hi-C technologies. The genome assembly is ~1.37 Gb in size and consists of 5145 contigs with a contig N50 of 593.70 kb, further clustered into 11 pseudochromosomes. Genome structural annotation resulted in ~869.33 Mb (~62.70% of the genome) repeat regions and 45 270 protein-coding genes. Genome evolution analysis revealed that P. thomsonii is most closely related to soybean and underwent two ancient whole-genome duplication events; one was in the common ancestor shared by legume species and the other occurred independently at around 7.2 million years ago, after its speciation. A total of 2373 gene families were found to be unique in P. thomsonii compared with five other legume species. Genes and metabolites related to puerarin content in tuberous tissues were characterized. A total of 572 genes that were upregulated in the puerarin biosynthesis pathway were identified, and 235 candidate genes were further enriched by omics data. Furthermore, we identified six 8-C-glucosyltransferase (8-C-GT) candidate genes significantly involved in puerarin metabolism. Our study filled a key genomic gap in the legume family, and provided valuable multi-omic resources for the genetic improvement of P. thomsonii.