Chloranthus genome provides insights into the early diversification of angiosperms

Abstract

Chloranthales remain the last major mesangiosperm lineage without a nuclear genome assembly. We therefore assemble a high-quality chromosome-level genome of Chloranthus spicatus to resolve enigmatic evolutionary relationships, as well as explore patterns of genome evolution among the major lineages of mesangiosperms (eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales). We find that synteny is highly conserved between genomic regions of Amborella, Vitis, and Chloranthus. We identify an ancient single whole-genome duplication (WGD) (κ) prior to the divergence of extant Chloranthales. Phylogenetic inference shows Chloranthales as sister to magnoliids. Furthermore, our analyses indicate that ancient hybridization may account for the incongruent phylogenetic placement of Chloranthales + magnoliids relative to monocots and eudicots in nuclear and chloroplast trees. Long genes and long introns are found to be prevalent in both Chloranthales and magnoliids compared to other angiosperms. Overall, our findings provide an improved context for understanding mesangiosperm relationships and evolution and contribute a valuable genomic resource for future investigations.

Fig. 1. Phylogenetic summary of the flowering plants and placement of Chloranthaceae.

a Chloranthus spicatus in Guilin Botanical Garden, China, and b at the inflorescence stage (Photo credit: Qiang Zhang). c. A summary of phylogenetic placement of Chloranthaceae based on 2,329 low-copy nuclear (LCN) genes. In all, 61% of the gene trees placed Chloranthales as the sister lineage to magnoliids (bootstrap >70%). d Simplified backbone of the phylogenetic tree constructed in IQTREE using the 218 species data set, displaying the topology, polyploidy, and divergence times at the ordinal level. Whole-genome duplication/triplication events are positioned based on a previous report. Source data underlying Fig. 1d are provided as a Source Data file.

Fig. 2. The prevalence of longer genes and introns, and confirmation of a whole-genome duplication event in C. spicatus based on genomic collinearity.

a Comparison of gene and genome characteristics (i.e., genome size, gene size, exon, and intron sizes) of C. spicatus and 17 other flowering plants. b Comparison of the lengths of the coding regions among nine representative plant genomes. c Collinearity patterns between genomic regions of Amborella, Vitis, and Chloranthus. The colored (red/grey) wedges highlight the major syntenic blocks shared among these species. d The number of synonymous substitutions per synonymous site (Ks) distributions confirming the occurrence of a whole-genome duplication (WGD) event in C. spicatus. Source data underlying Fig. 2a are provided as a Source Data file.

Fig. 3. Gene tree discordances among the five major groups of Mesangiospermae.

a A summary of the conflicts among gene trees in the 2,329-LCN data set with regard to the proportions of trees supporting three different branching patterns for Chloranthales-magnoliids, monocots, and eudicots. b Gene tree incongruence between nuclear (2,329 LCN genes) and plastid (80 plastid genes) trees in a consensus DensiTree plot. c A consensus scenario showing ancient gene flow between monocots and eudicots, inferred by QuIBL, PhyloNet, and ABBA-BABA D-statistics. Source data underlying Fig. 3b are provided as a Source Data file.

Fig. 4. Evolution and expansion of terpene synthase genes and contraction of R genes in Chloranthales.

a A total of 44 genes related to the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway and the mevalonate (MVA) pathway were identified in C. spicatus (left panel). HMGR and DXS exhibited the highest copy numbers in the MEP and MVA pathways, respectively. Differentially expressed genes among seven representative tissues of C. spicatus involved in MEP and MVA pathways are shown in the right panel. b Identification of candidate terpene synthases (TPSs) in C. spicatus and subfamily classification revealed six major clades (TPS-a, b, c, e, f, and g). The gene family tree indicates that TPS-a and TPS-b gene clades are significantly expanded in magnoliids and Chloranthales. c Contraction of R genes in Chloranthales. The nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes were divided into three classes: TIR-NBS-LRR (TNL), CC-NBS-LRR (CNL), and RPW8-NBS-LRR (RNL). In all, 3,518 NBS genes were identified in 28 angiosperm species. ‘*’ indicates the data were obtained from a previous study.