A Chromosome-Level Genome of the Camphor Tree and the Underlying Genetic and Climatic Factors for Its Top-Geoherbalism

Abstract

Camphor tree [Cinnamomum camphora (L.) J. Presl], a species in the magnoliid family Lauraceae, is known for its rich volatile oils and is used as a medical cardiotonic and as a scent in many perfumed hygiene products. Here, we present a high-quality chromosome-scale genome of C. camphora with a scaffold N50 of 64.34 Mb and an assembled genome size of 755.41 Mb. Phylogenetic inference revealed that the magnoliids are a sister group to the clade of eudicots and monocots. Comparative genomic analyses identified two rounds of ancient whole-genome duplication (WGD). Tandem duplicated genes exhibited a higher evolutionary rate, a more recent evolutionary history and a more clustered distribution on chromosomes, contributing to the production of secondary metabolites, especially monoterpenes and sesquiterpenes, which are the principal essential oil components. Three-dimensional analyses of the volatile metabolites, gene expression and climate data of samples with the same genotype grown in different locations showed that low temperature and low precipitation during the cold season modulate the expression of genes in the terpenoid biosynthesis pathways, especially TPS genes, which facilitates the accumulation of volatile compounds. Our study lays a theoretical foundation for policy-making regarding the agroforestry applications of camphor tree.

The chromosome‐level genome of female ginseng (Angelica sinensis) provides insights into molecular mechanisms and evolution of coumarin biosynthesis

“…Higher Ka/Ks ratios and smaller Ks values were found for TD and PD gene pairs (Figure 3a,b), suggesting TD and PD genes formed recently (limited level of synonymous mutation) and might undergo selection for neo‐ or sub‐functionalization (higher level of non‐synonymous mutation). The same results were also found in Rhododendron simsii (Yang et al., 2020) and Cinnamomum camphora (Jiang et al., 2022).…”

“…We compared the Ks and Ka/Ks values among groups of and might undergo selection for neo-or subfunctionalization (higher level of non-synonymous mutation). The same results were also found in Rhododendron simsii (Yang et al, 2020) and Cinnamomum camphora (Jiang et al, 2022).…”

Phylogenetic studies of magnoliids: Advances and perspectives

“…Consistently, the results of nuclear genome sequencing analysis of M. officinalis , M. biondii , C. camphora , etc. support that magnoliids form a sister clade to monocots and eudicots ( Dong et al., 2021 ; Yin et al., 2021 ; Jiang et al., 2022 ).…”

“…The reported species of magnoliids with sequenced nuclear genomes include Magnoliales, Laurales, and Piperales (17 species, 23 references in total). Examples include Laurales: Cinnamomum kanehirae ( Chaw et al., 2019 ), avocado ( Persea americana ) ( Rendón-Anaya et al., 2019 ; Nath et al., 2022 ), Litsea cubeba ( Chen Y. C. et al., 2020 ), Phoebe bournei ( Chen S. P. et al., 2020 ; Han et al., 2022 ), Cinnamomum camphora ( Jiang et al., 2022 ; Shen et al., 2022 ; Sun et al., 2022 ; Wang et al., 2022 ), C. burmannii ( Li et al., 2022 ), Litsea coreana ( Zhang et al., 2022 ) of Lauraceae, Chimonanthus praecox ( Shang et al., 2020 ; Shen et al., 2021 ) and C. salicifolius ( Lv et al., 2020 ) of Calycanthaceae; Magnoliales: L. chinense ( Chen et al., 2019 ), Magnolia biondii ( Dong et al., 2021 ), M. officinalis ( Yin et al., 2021 ); Annona muricata ( Strijk et al., 2021 ), A. glabra ( He et al., 2022 ); Pepperales: Piper nigrum ( Hu et al., 2019 ), Aristolochia fimbriata ( Qin et al., 2021 ) and A. contorta ( Cui et al., 2022 ). Twenty of the 23 references in the genome analysis magnoliids discussed the evolutionary status of magnoliids, providing new insights into the early evolution of angiosperms, but the results of the analysis are inconsistent.…”

Multi-omics Comparison among Populations of Three Plant Sources of Amomi Fructus

“…Top-geoherbalism, similar to "Daodi" in China and "Provenance" or "Terroir" in Europe, refers to traditional herbs grown in certain native ranges with better quality and efficacy than those grown elsewhere 1,2 , which reflects the difference of the component and abundance of secondary metabolites among populations, resulting from multiple factors, such as genetic elements, environmental factors, cultural processing etc [3][4][5] . The varied efficacy of traditional medicine with multiple sources results in the mixture of the inferior and the superior in the market, which inhibits the standardization and internalization of traditional medicine.…”