The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements

Abstract

Background Tetracentron sinense is an endemic and endangered deciduous tree. It belongs to the Trochodendrales, one of four early diverging lineages of eudicots known for having vesselless secondary wood. Sequencing and resequencing of the T. sinense genome will help us understand eudicot evolution, the genetic basis of tracheary element development, and the genetic diversity of this relict species. Results Here, we report a chromosome-scale assembly of the T. sinense genome. We assemble the 1.07 Gb genome sequence into 24 chromosomes and annotate 32,690 protein-coding genes. Phylogenomic analyses verify that the Trochodendrales and core eudicots are sister lineages and showed that two whole-genome duplications occurred in the Trochodendrales approximately 82 and 59 million years ago. Synteny analyses suggest that the γ event, resulting in paleohexaploidy, may have only happened in core eudicots. Interestingly, we find that vessel elements are present in T. sinense, which has two orthologs of AtVND7, the master regulator of vessel formation. T. sinense also has several key genes regulated by or regulating TsVND7.2 and their regulatory relationship resembles that in Arabidopsis thaliana. Resequencing and population genomics reveals high levels of genetic diversity of T. sinense and identifies four refugia in China. Conclusions The T. sinense genome provides a unique reference for inferring the early evolution of eudicots and the mechanisms underlying vessel element formation. Population genomics analysis of T. sinense reveals its genetic diversity and geographic structure with implications for conservation.

The Chloranthus sessilifolius genome provides insight into early diversification of angiosperms

“…All SCW genes are found in C. sessilifolius. The formation of primary vessel elements in this species may follow a more complex process that depends on fine regulations of these genes and others 75,76 .…”

Buxus and Tetracentron genomes help resolve eudicot genome history

“…Annotation of the repeat-masked assemblies yielded 27,027 and 30,704 protein-coding gene models, including 86.9% and 80.5% of the BUSCO genes, in Buxus and Tetracentron , respectively (Supplementary Data 2 ). Our Tetracentron assembly is similar to one produced for another individual of this species 33 in terms of BUSCO statistics and annotation metrics, but differs in size (908 vs 1170 Mb) and the number of chromosome-size scaffolds (19 vs 24). We are unable to account for these differences, but our assembly closely matches the genome size measured by flow cytometry, and the only reported chromosome count of n = 24 41 for Tetracentron has been discredited 37 .…”

“…We here provide genome assemblies for Buxus sinica (Buxales) and Tetracentron sinense (Trochodendrales), which represent, either individually or collectively, the sister lineage of core eudicots 15 . These two genome assemblies complement those available for other early-diverging eudicot lineages 22 , 31 – 33 and permit evaluations of eudicot phylogeny and gamma origins based on phylogenomics, molecular evolution, and synteny. In addition, we employ the RACCROCHE 34 pipeline of algorithms to infer the ancestral genomes at three sequential nodes of the eudicot radiation.…”

The genome of the endangered Macadamia jansenii displays little diversity but represents an important genetic resource for plant breeding

“…Nelumbo nucifera (Proteales) (Ming et al, 2013), Trochodendron aralioides (Trochodendrales) (Strijk et al, 2019), and Tetracentron sinense (Trochodendrales) (Liu et al, 2020). The M. jansenii genome…”