The Buxus Austro-Yunnanesis(Buxales) Genome And Karyotype Evolution Of Early Eudicots

Eudicots represent the most diverse group of flower plants(angiosperms)and account for most of terrestrial plants.Eudicots provide abundant living goods for human,such as food,clothes and wood,having the closest relationships with human.According to APG IV,eudicots can be divided into five lineages,including the four basal eudicot orders(Ranunculales,Proteales,Trochodendrales and Buxales)and the core eudicot,which contains most of species of eudicots.However,phylogenetic relationships among these five lineages and chromosome evolution of eudicots remain unclear.Meanwhile,only Buxales remains the lack of high-quality genomes until now.Thus,it will help us greatly to resolve the relationships among eudicots as long as we obtained genomes of Buxales.Buxus austro-yunnanesis(2n=2x=28)belongs to Buxales,which is often discovered in Yunnan province.Here,we report a high-quality chromosome-level genome of Buxus austro-yunnanesis(Buxales)based on Nanopore sequencing and HiC technology,which enriches genome data sources of important eudicots.Phylogenomic analyses of the 25 eudicot orders verified that Buxales and Trochodendrales are sister clades and they are together clustered to core eudicots with Ranunculales diverging firstly.In our analyses,we found that the relationships of these five major lineages were stable,while the major discordance was mainly in the phylogeny of Caryophyllales,Vitales,Saxifragales and Myrtales.We also evaluated impacts of three factors found to affect phylogeny.Incomplete lineage sorting and hybridization were found to contribute most of the phylogenetic discordance(34.33%)among these lineages,and gene tree estimation error takes up only 8.13%.In whole-genome duplication(WGD)analyses,we found B.austro-yunnanesis experienced only one WGD event and there is no inter-chromosomes rearrangement occurred after this WGD.We also corrected several polyploidization histories after theγ event in some species,which differ from their genome research papers.Such polyploidization events include one extra whole genome triplication(WGT)occurred in Simmondsia chinensis(Caryophyllales)and Carthamus tinctorius(Asterales)independently,and there should be one WGD and one WGT occurred in Olea europaea(Lamiales)after γ event.Collinear gene phylogenetic analyses of the five major eudicot lineages showed separately independent polyploidizations among them.With representative genomes from five major eudicot lineages,we reconstructed the ancestry eudicot karyotype(AEK)and generated a nearly gapless karyotype projection for each eudicot species in this study,which shows better accuracy and integrity than the previous one.Within core eudicots,we recovered a chromosome fusion event in asterids and malvids respectively.In addition,we found that Aquilegia(Ranunculales)and Vitis(core eudicots)had experienced different polyploidization events and chromosome fusion histories.In conclusion,we reported a high-quality genome of Buxales,which can be used as important data source for phylogeny and evolution analyses of eudicots.After phylogenetic analysis,we evaluated phylogenetic discordance caused by different factors,which can be a reference to analysis the reason why there are difference among gene tree topologies.And we put forward a most possible relationships of eudicots by combining the construction of AEK.This study provides blueprints for phylogeny and karyotype evolution analyses of eudicots in the future.