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

Abstract

Pueraria lobata var. montana (P. montana) belongs to the genus Pueraria and originated in Asia. Compared with its sister P. thomsonii, P. montana has stronger growth vigor and cold-adaption, but contains less bioactive metabolites such as puerarin. To promote the investigation of metabolic regulation and genetic improvement of Pueraria, the present study reports a chromosome-level genome of P. montana with length of 978.59 Mb and scaffold N50 of 80.18 Mb. Comparative genomics analysis showed that P. montana possesses smaller genome size than that of P. thomsonii owing to less repeat sequences and duplicated genes. A total of 6,548 and 4,675 variety-specific gene families were identified in P. montana and P. thomsonii, respectively. The identified variety-specific and expanded/contracted gene families related to biosynthesis of bioactive metabolites and microtubules are likely the causes for the different characteristics of metabolism and cold-adaption of P. montana and P. thomsonii. Moreover, a graphic genome was constructed based on 11 P. montana accessions. Total 92 structural variants were identified and most of which are related to stimulus-response. In conclusion, the chromosome-level and graphic genomes of P. montana will not only facilitate the studies of evolution and metabolic regulation, but also promote the breeding of Pueraria.

Chromosome-Level Genome Assembly and Multi-Omics Dataset Provide Insights into Isoflavone and Puerarin Biosynthesis in Pueraria lobata (Wild.) Ohwi

“…As another wild species of Pueraria, the genome size of P. montana was ~978.59 Mb, with contig N50 of 80.18 Mb. A comparative genomics analysis showed that the genome size of P. montana was smaller than that of P. thomsonii because of fewer repetitive sequences and duplicated genes [ 14 ]. Compared with the previous two species of pueraria, the genome of P. lobata was smaller and had fewer repetitive sequences and duplicated genes: the genome size of P. lobata was only ~939 Mb.…”

“…At present, many research reports are available on the transcriptome and related isoflavone synthesis genes of P. lobata or P. thomsonii . Additionally, there are two reports on the genome of P. thomsonii and P. montana [ 13 , 14 ], but the data on the genome of P. lobata have not been reported [ 10 ]. The lack of reference genome information on P. lobata hinders further investigation of potential genes in important biological processes related to isoflavone biosynthesis [ 10 , 15 ].…”

The International Weed Genomics Consortium: Community Resources for Weed Genomics Research

“…Panicum miliaceum wild proso millet 9 18 0.85 [187] Poa annua annual bluegrass 7 14 1.78 [143] 1.89 [188] Poa infirma early meadowgrass 7 7 1.17 [189] 1.13 [189] Poa supina supine bluegrass 7 7 0.66 [189] 0.64 [189] Pueraria montana var. lobata kudzu 11 11 0.98 [190] Setaria viridis green foxtail 9 9 0.40 [191] 0.40 [191] Striga asiatica red witchweed 12 12 0.6 [192] 0.47 [192] 5 3…”

Genome-wide identification and expression pattern analysis of R2R3-MYB transcription factor gene family involved in puerarin biosynthesis and response to hormone in Puararia lobata var. thomsonii

“…The genus Pueraria belonging to the Leguminosae family was originated in Asia and comprises of more than 20 species (Mo et al, 2022). Puararia lobata is a well-known traditional Chinese medicinal herb and widely grown in China for a long time.…”