The chromosome‐scale genomes of Dipterocarpus turbinatus and Hopea hainanensis (Dipterocarpaceae) provide insights into fragrant oleoresin biosynthesis and hardwood formation

Abstract

Summary Dipterocarpaceae are typical tropical plants (dipterocarp forests) that are famous for their high economic value because of their production of fragrant oleoresins, top‐quality timber and usage in traditional Chinese medicine. Currently, the lack of Dipterocarpaceae genomes has been a limiting factor to decipher the fragrant oleoresin biosynthesis and gain evolutionary insights into high‐quality wood formation in Dipterocarpaceae. We generated chromosome‐level genome assemblies for two representative Dipterocarpaceae species viz. Dipterocarpus turbinatus Gaertn. f. and Hopea hainanensis Merr. et Chun. Our whole‐genome duplication (WGD) analysis revealed that Dipterocarpaceae underwent a shared WGD event, which showed significant impacts on increased copy numbers of genes related to the biosynthesis of terpene, BAHD acyltransferases, fatty acid and benzenoid/phenylpropanoid, which probably confer to the formation of their characteristic fragrant oleoresin. Additionally, compared with common soft wood plants, the expansion of gene families was also found to be associated with wood formation, such as in CESA (cellulose synthase), CSLE (cellulose synthase‐like protein E), laccase and peroxidase in Dipterocarpaceae genomes, which might also contribute to the formation of harder, stronger and high‐density timbers. Finally, an integrative analysis on a combination of genomic, transcriptomic and metabolic data from different tissues provided further insights into the molecular basis of fragrant oleoresins biosynthesis and high‐quality wood formation of Dipterocarpaceae. Our study contributes the first two representative genomes for Dipterocarpaceae, which are valuable genetic resources for further researches on the fragrant oleoresins and superior‐quality timber, genome‐assisted breeding and improvement, and conservation biology of this family.

A chromosome-scale genome and transcriptomic analysis of the endangered tropical treeVatica mangachapoi(Dipterocarpaceae)

“…3A ). The comparison of collinearity within the cotton genome and between the V. mangachapoi and cotton genomes both identified a large number of collinear blocks, consistent with the finding that cotton has undergone a WGD event 54 ( Supplementary Figs S3 and S4 ). The distribution of Ks within a genome can be used to detect WGD and estimate the time of such an event.…”

“…A shared WGD event between D. turbinatus and H. hainanensis Chun was reported, and WGD in the common ancestor of Dipterocarpaceae was suggested. 54 The WGD detected in V. mangachapoi is likely the indication of WGD in the common ancestor of the three species. However, the timing of the WGD based on Ks plot analyses of V. mangachapoi genome is much younger than the time estimated in Wang et al 54 and deserve further investigation.…”

“… 54 The WGD detected in V. mangachapoi is likely the indication of WGD in the common ancestor of the three species. However, the timing of the WGD based on Ks plot analyses of V. mangachapoi genome is much younger than the time estimated in Wang et al 54 and deserve further investigation. In summary, WGD might contribute not only to the expansion of gene families in V. mangachapoi but also to the massive growth of its population size ( Fig.…”

“…et Chun: 434.3 Mb). 54 The resulting genome is a milestone for the study of dipterocarp forests as it is the first genome of this quality in Vatica as well as for the entire Dipterocarpaceae family.…”

Genome sequence and population genomics provide insights into chromosomal evolution and phytochemical innovation of Hippophae rhamnoides

“…Polyploidization has long been regarded as an important driving force for plant evolution, and it may endow genes with potential sub‐functionalization and neo‐functionalization (Wang et al ., 2021). By performing KEGG enrichment on the α‐event‐related genes (duplicated by the α event and retained) obtained based on the median Ks value, we found that genes related to ascorbate and aldarate metabolism, lipid biosynthesis, and fatty acid elongation were significantly enriched, which coincided with the fact that seabuckthorn fruits were rich in AsA and fatty acids (Table S35).…”