The Chloranthus Sessilifolius Genome And The Early Evolution Of Mesangiospermae

The angiosperms represent one of the most widespread,diverse,and adaptable groups of terrestrial plants on the planet,and have greatly influenced the evolution of other organisms.However,due to the rapid rediation evolution of angiosperms in their early diversification,the internal evolutionary relationships has not been resolved for a long time.This problem was also referred by Darwin as an"abominable mystery".Through the continuous efforts of scientists,it is now generally accepted that angiosperms can be divided into basal angiosperms and Mesangiospermae.The basal angiosperms contain only three orders:Amborellales,Nymphaeales,and Austrobaileyales,which are also collectively referred as the ANA grade.The vast majority(～99.95%)of angiosperms form a strongly supported clade called Mesangiospermae,which comprises five major clades:eudicots,monocots,magnoliids,Chloranthales,and Ceratophyllales.The evolutionary relationships among these clades have been controversial.With the development of sequencing technology,the nuclear genome of representative species of each clade had been assembled in recent years.Their evolutionary history has been extensively studied,but the lack of a Chloranthales genome has greatly limited our understanding of phylogenetic relationships and early diversification of these angiosperm lineages.To this end,we present the high-quality chromosome-level reference genome of Chloranthus sessilifolius(2n=2×=30)using various sequencing tools and bioinformatics approach.Using phylogenomics and comparative genomics analyses,we revealed the early evolutionary history of angiosperms and the genetic mechanisms of specific traits in C.sessilifolius.The main results and conclusions are listed as follows:The high-quality reference genome of C.sessilifolius.Combining Nanopore,Hi-C and Illumina sequencing,a high-quality chromosome-level genome of C.sessilifolius was assembled with a size of 2,168.73 Mb and a contig N50 of 53.74 Mb.A total of34,065 protein-coding genes were annotated.Compared to other species,introns in C.sessilifolius genome were inserted by a large number of transposons,producing a significantly higher proportion of long genes.The C.sessilifolius genome had occurred only one whole genome duplication(WGD)event,which is independent of other species.In addition,explosive expansion of ancient transposons is the main reason for its genome size expansion.Evolutionary relationships among different clades of angiosperms.Through multiple phylogenomics analyses,including single copy genes,low copy genes and syntenic-based genes,coalescent-based and concatenated-based species trees were obtained,and yielded a highly plausible and consistent phylogeny topology that the magnoliids+Chloranthales clade was sister to the eudicots+Ceratophyllales clade,while the monocot lineage was sister to other Mesangiospermae lineages.Assessment of phylogenetic discordance.We evaluated the phylogenetic discordance bewteen gene trees or chloroplast trees and species trees using multiple approach,focusing on the contribution of incomplete lineage sorting and hybridization events.Three possible hybridization events were found by Phylo Networks analysis,which could explain part of the phylogenetic conflict.The short divergence intervals between five Mesangiospermae lineages(between 158 and 135 Mya)suggests that they diversified within a very short time,and ILS might had occurred.We estimated the theta parameter for each internal branch.Except for the magnoliids and Chloranthales,which had more stable sister relationship,all other clades had high theta values,especially the ancestral branches of Ceratophyllales and eudicots had high theta values.Evolutionary mechanism of special trait in C.sessilifolius.C.sessilifolius has no perianth,only stamens and pistils.To the end,we performed comparative transcriptome analysis,and found that the A genes in ABCE model have high expression levels in the stamen lobes,and the expression of all four types of genes lacks tissue specificity.Further comparative analysis across species revealed that the classical expression pattern of ABCE genes seems to occur only in core eudicots.In addition,we identified the terpenoid biosynthesis related gene families,in which the expansion of HMGR,DXS,TPS-a,and TPS-c gene families is the reasons for their enrichment in terpenoids.Gene tree simulations using Phyabse and Dendro Py showed that simulated trees with the ILS conditions and real trees had high agreement(R~2>0.99),while simulated trees without ILS and real trees had low correlation.These results suggest an important role of ILS in the evolution of internal branching of Mesangiosperms.In summary,through genome sequencing and phylogenetic analyses of the C.sessilifolius,we have clarified the evolutionary relationships among the major clades of Mesangiosperms and the causes of phylogenetic conflicts.These results provide scientific support and theoretical foundations for studies on the origin,radiative evolution,and adaptive evolution of Mesangiosperms.