Buxus and Tetracentron genomes help resolve eudicot genome history

Abstract

Ancient whole-genome duplications (WGDs) characterize many large angiosperm lineages, including angiosperms themselves. Prominently, the core eudicot lineage accommodates 70% of all angiosperms and shares ancestral hexaploidy, termed gamma. Gamma arose via two WGDs that occurred early in eudicot history; however, the relative timing of these is unclear, largely due to the lack of high-quality genomes among early-diverging eudicots. Here, we provide complete genomes for Buxus sinica (Buxales) and Tetracentron sinense (Trochodendrales), representing the lineages most closely related to core eudicots. We show that Buxus and Tetracentron are both characterized by independent WGDs, resolve relationships among early-diverging eudicots and their respective genomes, and use the RACCROCHE pipeline to reconstruct ancestral genome structure at three key phylogenetic nodes of eudicot diversification. Our reconstructions indicate genome structure remained relatively stable during early eudicot diversification, and reject hypotheses of gamma arising via inter-lineage hybridization between ancestral eudicot lineages, involving, instead, only stem lineage core eudicot ancestors.

A high-quality Buxus austro-yunnanensis (Buxales) genome provides new insights into karyotype evolution in early eudicots

“…For the five eudicot lineages, our results based on nuclear genes support a sister relationship between Buxales and Trochodendrales and indicate that they are together sister to all core eudicots. This result is similar with the 1000 plant transcriptomes analyses [ 27 ] and the recently published B. sinica genome research [ 25 ]. However, plastome evidence indicated that Buxales and core eudicots are sister clades (Additional file 1 : Fig.…”

“…However, this genomic fusion could be an example of parallel homoplasy, since it may have occurred independently on different phylogenetic and evolutionary timescales by each individual lineage [ 24 ]. A recent study has reconstructed the most recent common ancestors at the three early-diverging eudicot nodes and found that such fusion events have not occurred in all ancestors [ 25 ]. Still, this study does not consider how phenotypes of karyotype evolved over time.…”

“…Here, we present a high-quality chromosome-level reference genome for Buxus austro-yunnanensis (2n = 28) [ 25 ] that was generated by combining Oxford Nanopore Technologies (ONT) long reads, Illumina short reads, and Hi-C sequencing technologies. Using this genome, we reconstructed the phylogenetic relationships between five eudicot lineages, including a total of 25 eudicot orders.…”

A genome for Cissus illustrates features underlying the evolutionary success in dry savannas

“…It is exciting to observe the evidence of the palaeo-hexaploidy event shared byCissus and grape. Moreover, the lack of any other WGDs suggestsCissus also might hold a relatively ancestral state of genome organization after divergence from their common ancestors (Chanderbali et al, 2022;Qin et al, 2021;Van de Peer et al, 2009). This would be reflected by ˜13.7 % of the total genes inCissus (˜17.7 % of grape) belonging to the 3:1 duplicated region to Amborella and considerable high collinearity of chromosomes to grape.…”

The evolution and function of the PSEUDO RESPONSE REGULATOR gene family in the plant circadian clock

“…While the appearance of the PRR7/3 and PRR9/5 clades precedes the Eudicot-Monocot split, their expansion probably happened independently in both groups. Analysis of the eudicot PRR7/3 and PRR9/5 gene expansions using chromosomal synteny suggests that it is the result of the γ (gamma) polyploidy event, a whole-genome duplication (WGD) event that occurred early in eudicot divergence ( Tang et al, 2008 ; Takata et al, 2010 ; Chanderbali et al, 2022 ). The same analysis suggests that the expansion of the PRR7/3 clade in monocots resulted from the ρ (rho) polyploidy event, but the PRR5/9 clade was duplicated before ( Takata et al , 2010 ).…”