Thirteen Dipterocarpoideae genomes provide insights into their evolution and borneol biosynthesis

Abstract

Dipterocarpoideae, the largest subfamily of the Dipterocarpaceae, is a dominant component of Southeast Asian rainforests and is widely used as a source of wood, damar resin, medicine, and essential oil. However, many Dipterocarpoideae species are currently on the IUCN Red List owing to severe degradation of their habitats under global climate change and human disturbance. Genetic information regarding these taxa has only recently been reported with the sequencing of four Dipterocarp genomes, providing clues to the function and evolution of these species. Here, we report on 13 high-quality Dipterocarpoideae genome assemblies, ranging in size from 302.6 to 494.8 Mb and representing the five most species-rich genera in Dipterocarpoideae. Molecular dating analyses support the Western Gondwanaland origin of Dipterocarpaceae. Based on evolutionary analysis, we propose a three-step chromosome evolution scenario to describe the karyotypic evolution from an ancestor with six chromosomes to present-day species with 11 and 7 chromosomes. We discovered an expansion of genes encoding cellulose synthase (CesA), which is essential for cellulose biosynthesis and secondary cell-wall formation. We functionally identified five bornyl diphosphate synthase (BPPS) genes, which specifically catalyze the biosynthesis of borneol, a natural medicinal compound extracted from damar resin and oils, thus providing a basis for large-scale production of natural borneol in vitro.

Keywords: Dipterocarpoideae; borneol; cellulose synthase; chromosome evolution; genome.

Figure 1

Characteristics of five chromosome-level genomes (D. gracilis, H. mollissima, P. chinensis, S. henryana, and V. rassak). (a) Chromosomes, (b) GC density, (c) gene density, (d) transposable element (TE) coverage, (e) Copia coverage, (f) Gypsy coverage, and (g) links between two adjacent genomes connecting syntenic gene blocks, as detected using MCScanX.

Figure 2

Comparative genomic analysis. (A) Phylogenetic tree of 18 species, including divergence times, based on 429 single-copy genes. Ovals indicate polyploidization events during angiosperm history. All nodes were supported with bootstrap values of 100. (B) Genome size, TE size, and different TE contents in 13 species. (C) Correlation between genome size and TE content.

Figure 3

Whole-genome duplication and chromosome evolutionary history in Dipterocarpoideae species. (A) Synonymous substitution rate distributions of syntenic block pairs in five Dipterocarpoideae species and between P. chinensis and T. cacao. (B) Collinearity analysis between Dipterocarpeae tribe (chr5, chr6, chr7) and T. cacao; black and yellow arrows represent positions of fission and fusion, respectively. (C) Collinearity analysis of five chromosome-level genomes. Black and yellow arrows represent positions of fission and fusion, respectively; dotted and solid arrows indicate positions supported by multiple and single species, respectively. (D) Three-step chromosome evolution scenario of Dipterocarpoideae species from six ancestral chromosomal Dipterocarpoideae karyotypes.

Figure 4

Overview of gene families and genes associated with SCW formation. (A and B) Maximum-likelihood phylogenetic trees of the CesA(A) and the CKX(B) gene families (CesA and CKX gene families were identified from 13 Dipterocarpoideae species, T. cacao, A. sinensis and A. thaliana). Different colored dots correspond to different species, different colored circles correspond to different CesA or CKX groups, and yellow stars indicate approximate positions of WGD events in the gene trees. (C) Plant hormone metabolic pathways in Dipterocarpoideae species. (D) Dipterocarpoideae-specific mutations located in the histidine-containing phototransfer (Hpt) domain of the AHP gene in Dipterocarpoideae species. (E) Gene Ontology (GO) terms enriched in expanded gene families from five Dipterocarpoideae lineages. Each lineage was represented by one species in each genus.

Figure 5

Biosynthetic pathway for borneol and functional identification of BPPS genes. (A) Primary pathway leading to the formation of borneol and other monoterpenoid products, according to a previous study (Ma et al., 2021). (B) Phylogenetic analysis of 14 candidate genes from the genus Dipterocarpus. Genes in colored fonts function in borneol production. (C) GC-MS analysis of five BPPS genes (DiTPS2, DiTPS3, DzTPS3, DaTPS3, and DgTPS1). Peak 1, α-pinene; peak 2, β-pinene; peak 3, α-phellandrene; peak 4, limonene; peak 5, borneol; peak 6, α-terpineol.