Chromosome-scale genome assembly of Rhododendron molle provides insights into its evolution and terpenoid biosynthesis

Abstract

Background Rhododendron molle (Ericaceae) is a traditional Chinese medicine, which has been used to treat rheumatism and relieve pain since ancient times. The characteristic grayanoids of this plant have been demonstrated to be the chemical basis for the analgesic activity. Moreover, unlike morphine, these diterpenoids are non-addictive. Grayanoids mainly distribute in the leaves, flowers, roots, and fruits of R. molle, with low content. Currently the research on the biosynthesis of grayanoids is hindered, partially due to lack of the genomic information. Results In the present study, a total of 744 Mb sequences were generated and assembled into 13 chromosomes. An ancient whole-genome duplication event (Ad-β) was discovered that occurred around 70 million years ago. Tandem and segmental gene duplications led to specific gene expansions in the terpene synthase and cytochrome P450 (CYP450) gene families. Two diterpene synthases were demonstrated to be responsible for the biosynthesis of 16α-hydroxy-ent-kaurane, the key precursor for grayanoids. Phylogenetic analysis revealed a species-specific bloom of the CYP71AU subfamily, which may involve the candidate CYP450s responsible for the biosynthesis of grayanoids. Additionally, three putative terpene biosynthetic gene clusters were found. Conclusions We reported the first genome assembly of R. molle and investigated the molecular basis underpinning terpenoids biosynthesis. Our work provides a foundation for elucidating the complete biosynthetic pathway of grayanoids and studying the terpenoids diversity in R. molle.

Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color

“…The highly continuous gapless assembly was achieved with 34 contigs, with a contig N50 of 44.85 Mb, thus, with much longer sequence continuity than for all previously released genome assemblies in Rhododendron [ 3 – 6 , 8 ]. Our assembly presented significant improvement (64 folds in contig N50) in continuity over an assembly recently reported for the same species [ 10 ], which is with 3764 contigs and contig N50 value of 0.71 Mb ( Fig. S3 ; Table S1 , see online supplementary material).…”

“…We generated the first gapless genome assembly in azaleas with the combination of long-read sequencing and Hi-C scaffolding technologies. The contig N50 of our assembly is 44.9 Mb, which is significantly higher than that of any other genome assemblies available for azaleas [ 3 – 10 ]. The highest proportion (99.4%) of the genome has been anchored on 13 chromosomes with the least nine gaps in our genome assembly.…”

“…Among the diverse lineages of angiosperms, the genus is best-known for its great species diversity and magnificent flowers [ 1 , 2 ]. Several high-quality Rhododendron genomes were released recently, including one draft genome [ 3 ] and eight pseudochromosome-level genomes [ 4 – 10 ], but no gapless genome has been obtained up to now. Gap-free or gapless genome assemblies have been accomplished in banana [ 11 ], rice [ 12 ], and Arabidopsis [ 13 ] with the developments of third-generation sequencing technologies.…”

“…The complexity of the variance in flower colors appears to be comparable to the diversity of the genus’s numerous species, and the Rhododendron has the potential to serve as a model to probe the evolution of flower color. Rhododendron molle is a perennial shrub native to East Asia [ 10 ], and is the yellow-flowered parent of many cultivated hybrids. However, the biochemical and molecular basis for the petal color formation remains unclear, although the genome of a red-flowered parent species of widely cultivated azaleas was assembled and the entire metabolic pathways for flower pigmentation were reconstructed recently [ 5 ].…”

A haplotype‐resolved genome for Rhododendron × pulchrum and the expression analysis of heat shock genes

“…Currently, nine chromosome-scale genomes from different Rhododendron species have been reported (Zhang et al, 2017;Soza et al, 2019;Yang et al, 2020;Ma et al, 2021;Shirasawa et al, 2021;Wang et al, 2021;Zhou et al, 2022aZhou et al, , 2022cNie et al, 2023), which has greatly improved our knowledge of functional genomics in Rhododendron, for example, deducing the pathways by which flower traits, such as color, are derived (Zhou et al, 2022a). From these highly contiguous genomes, it is evident that such high-quality assemblies are instrumental in understanding the genetic basis of different traits.…”