The chromosome-based lavender genome provides new insights into Lamiaceae evolution and terpenoid biosynthesis

Liang

Plant Biotechnology Journal

et al. 2021

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.

Section: Resultsmentioning

confidence: 99%

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

Liang

Plant Biotechnology Journal

et al. 2021

“…In citrus, a total of 55 CsTPS genes have been identified, and seven TPS genes are related to sesquiterpene biosynthesis, including one related to β-farnesene biosynthesis and two related to β-caryophyllene biosynthesis (Alquézar et al, 2017). More recently, 52 TPS family genes have been identified in wintersweet (Chimonanthus praecox), indicating a possible mechanism for the formation of flower aroma (Shang et al, 2020), while 100 TPS genes have been found in the lavender genome (Li et al, 2021). Here, the identification of 34 TPS genes in the red bayberry genome (Supplementary Table 7), much less than those in the genomes mentioned above, supports red bayberry not having had a whole genome duplication event (Jia et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

MrTPS3 and MrTPS20 Are Responsible for β-Caryophyllene and α-Pinene Production, Respectively, in Red Bayberry (Morella rubra)

et al. 2022

Red bayberry is a sweet, tart fruit native to China and grown widely in the south. The key organic compounds forming the distinctive aroma in red bayberry, are terpenoids, mainly β-caryophyllene and α-pinene. However, the key genes responsible for different terpenoids are still unknown. Here, transcriptome analysis on samples from four cultivars, during fruit development, with different terpenoid production, provided candidate genes for volatile organic compound (VOC) production. Terpene synthases (TPS) are key enzymes regulating terpenoid biosynthesis, and 34 TPS family members were identified in the red bayberry genome. MrTPS3 in chromosome 2 and MrTPS20 in chromosome 7 were identified as key genes regulating β-caryophyllene and α-pinene synthesis, respectively, by qRT-PCR. Subcellular localization and enzyme activity assay showed that MrTPS3 was responsible for β-caryophyllene (sesquiterpenes) production and MrTPS20 for α-pinene (monoterpenes). Notably, one amino acid substitution between dark color cultivars and light color cultivars resulted in the loss of function of MrTPS3, causing the different β-caryophyllene production. Our results lay the foundation to study volatile organic compounds (VOCs) in red bayberry and provide potential genes for molecular breeding.

“…In the D. carota and A. graveolens that belonged to Apiaceae, one shared WGD occurred in about 43 Mya, and one recent WGD only existed in A. graveolens in approximately 1.9 Mya, and this duplication contributed to the expansion of terpene synthase gene families ( Song X. et al, 2020 ). The second branch in the eudicots part includes six plants belonging to Lamiales, one shared WGD (almost 60.7 Mya) was identified in S. baicalensis , S. barbata , S. miltiorrhiza , and S. indicum , which might be responsible for chromosomal expansion and rearrangement ( Xu et al, 2020a ), and two rounds of WGD were found in S. splendens and L. angustifolia , which could result in the gene families expansion related to terpenoid biosynthesis ( Li et al, 2021 ). In P. cuspidatum , it experienced current lineage-specific WGD at 6.6 Mya after the divergence with F. tataricum from the ancestor, and it shared the ancient and common WGD with F. tataricum at 65 Mya ( Zhang Y. et al, 2019 ), after this WGD, the genome of F. tataricum experienced dramatic chromosomal rearrangements, resulting in very fragmented intra-genome collinear blocks ( Zhang L. et al, 2017 ).…”

Section: Application Of Medicinal Plant Genomesmentioning

confidence: 99%

Review on the Development and Applications of Medicinal Plant Genomes

et al. 2021

With the development of sequencing technology, the research on medicinal plants is no longer limited to the aspects of chemistry, pharmacology, and pharmacodynamics, but reveals them from the genetic level. As the price of next-generation sequencing technology becomes affordable, and the long-read sequencing technology is established, the medicinal plant genomes with large sizes have been sequenced and assembled more easily. Although the review of plant genomes has been reported several times, there is no review giving a systematic and comprehensive introduction about the development and application of medicinal plant genomes that have been reported until now. Here, we provide a historical perspective on the current situation of genomes in medicinal plant biology, highlight the use of the rapidly developing sequencing technologies, and conduct a comprehensive summary on how the genomes apply to solve the practical problems in medicinal plants, like genomics-assisted herb breeding, evolution history revelation, herbal synthetic biology study, and geoherbal research, which are important for effective utilization, rational use and sustainable protection of medicinal plants.