The first chromosome-level Fallopia multiflora genome assembly provides insights into stilbene biosynthesis

Abstract

Fallopia multiflora (Thunb.) Harald, a vine belonging to the Polygonaceae family, is used in traditional medicine. The stilbenes contained in it have significant pharmacological activities in anti-oxidation and anti-aging. This study describes the assembly of the F. multiflora genome and presents its chromosome-level genome sequence containing 1.46 gigabases of data (with a contig N50 of 1.97 megabases), 1.44 gigabases of which was assigned to 11 pseudochromosomes. Comparative genomics confirmed that F. multiflora shared a whole-genome duplication event with Tartary buckwheat and then underwent different transposon evolution after separation. Combining genomics, transcriptomics, and metabolomics data to map a network of associated genes and metabolites, we identified two FmRS genes responsible for the catalysis of one molecule of p-coumaroyl-CoA and three molecules of malonyl-CoA to resveratrol in F. multiflora. These findings not only serve as the basis for revealing the stilbene biosynthetic pathway but will also contribute to the development of tools for increasing the production of bioactive stilbenes through molecular breeding in plants or metabolic engineering in microbes. Moreover, the reference genome of F. multiflora is a useful addition to the genomes of the Polygonaceae family.

Acknowledgements

This study was funded by the National Natural Science Foundation of China (No. 81973432), the Major Increase and Reduction Project at the Central Level (No. 2060302), Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine (ZYYCXTD-D-202005), and CAMS Innovation Fund for Medical Sciences (2019-I2M-5-065).

Author contributions

Y.Z., H.P. and L.H. conceived and supervised the study. Y.Z., Q.F., and Y.Q. collected the samples. Z.Z. carried out comparative genomics analysis and phylogenetic analysis. Z.Y., L.Z., and Z.T. contributed to molecular experiments and bioinformatics analysis. Y.Z. and M.Y. wrote the paper. S.C. prepared the supplementary figures and tables. Y.Y., L.H., and H.P. revised the paper. All authors read, edited, and approved the final paper.

Data availability

The data described in this work is available upon reasonable request to the corresponding author. The raw genome sequencing data, Hi-C data, RNA-seq data, and genome assembly of F. multiflora in this study have been submitted to the NCBI BioProject database under accession number PRJNA793351. Other data, such as the assembled genome sequence and gene structure annotation are available at the FigShare database (10.6084/m9.figshare.19720381).

Conflict of interests

The authors declare that they have no known conflicts of interest.

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