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

Abstract

Pueraria lobata var. thomsonii (hereinafter abbreviated as Podalirius thomsonii), a member of legumes, is one of the important traditional Chinese herbal medicines, and its puerarin extraction is widely used in 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 approximately 1.37 Gb in size and consists of 5145 contigs with a contig N50 of 593.70 Kb, further clustered into 11 pseudochromosomes. The genome structural annotation resulted in about 869.33 Mb (about 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, the other occurred independently at around 7.2 million years ago after its specification. A total of 2373 gene families were found unique in P. thomsonii comparing to five other legume species. Genes and metabolites related to puerarin content in tuberous tissues were characterized. A total of 572 genes upregulated in the puerarin biosynthesis pathway were identified, and 235 candidate genes were further enriched by omics data. Furthermore, we identified 6 8-C-glucosyltransferase (8-C-GT) candidate genes significantly involved in puerarin metabolism. Our study filled in a key genomic gap in legume family, and provided valuable multi-omic resources for the genetic improvement of P. thomsonii.

Chromosome-level and graphic genomes provide insights into metabolism of bioactive metabolites and cold-adaption of Pueraria lobata var. montana

“…Compared with the P. thomsonii genome (1,381.61 Mb), 11 the P. montana genome has smaller genome size and more compact gene distribution ( Fig. 1a ).…”

“…The genome of P. thomsonii was recently published, which provided valuable resource for clarifying the metabolic pathways of medicinal compounds. 11 However, the unavailability of P. montana genome greatly hinder the identification and utilization of excellent gene resources in this variety.…”

Genome-wide Analysis of the bHLH Transcription Factor Family and Functional Identification of bHLH Genes Related to Puerarin Biosynthesis in Pueraria lobata var. thomsonii (Benth.)

“…In view of this, MeJA treatment analysis was performed to narrow down the candidate structural genes. The RNA-seq result of Shang et al (2022) and results of the qRT-PCR detection indicated PlCHS1 (Pmon008G00376), PlCHR3 (Pmon003G00389), PlIFS1 (Pmon003G02838), PlIFS2 (Pmon003G02830) and PlUGT155 (Pmon006G01850) were up-regulated expressed after treatment with MeJA within 24 h (Fig. 6).…”

“…Expression pattern of each PlbHLH gene was analyzed from our previously reported RNA-seq data (Shang et al 2022). The data included three tissues, including root, stem and leave.…”

“…However, it remains largely unknown whether the bHLH gene family members are involved in the regulation of puerarin biosynthesis in P. thomsonii. Currently, we nished the genome sequencing of P. thomsonii, which provides an excellent opportunity for further genome-wide analysis of P. thomsonii genes (Shang et al 2022). In this study, we performed a genome-wide analysis of bHLH genes in P. thomsonii and 219 PlbHLH genes were identi ed.…”