Phylogenomics And Morphological Evolution Study Of Ulmus

Ulmus species have been widely distributed in the north temperate zone with several species in subtropical and tropical regions,which belonging to Ulmaceae within Rosales.Based on the field’s investigation and previous records,over 35 species have been accepted from Ulmus in the whole world,and there are more than 26 Ulmus species in China.Due to the limitation of sample collection,molecular markers and rapid radiation,the phylogenetic relationship of Ulmus is still not fully resolved now.In the current study,extensive samples of representative taxa from 5 sections and 5series within Ulmus were collected from all over the world,and further explored the phylogenetic relationships,origin and evolution patterns of Ulmus based on the chloroplast genomes and transcriptome sequencing technology.Firstly,clarified the structural evolution of chloroplast genomes and phylogeny;then the orthologs were identified from transcriptome data to study the reasons for gene tree conflicts caused by polyploidization,hybridization and incomplete lineage sorting of Ulmus;we finally integrated the core traits and geographical distribution of Ulmus species based on the above phylogenetic framework to estimate the divergence time and reconstruct the ancestral distribution area to discuss the key characters evolution and geographical distribution pattern.The specific results are as following:1)Comparative analyses of the chloroplast genomes from 31 Ulmus species found that all the Ulmus species exhibited a typical quadripartite structure,including a large single copy region(LSC)and a small single copy region(SSC),with two inverted repeat regions.The length of chloroplast genomes of Ulmus ranged from 158 kb to 159 kb and all cp genomes encoded the 113 unique genes,including 79 protein-coding genes,30 t RNA,and 4 r RNA.The chloroplast genomes showed a relatively conserved genome structure without gene loss and rearrangement.Furthermore,two gene of 79 proteincoding genes were identified under the positive selection(atp F and rps15),which may be relative to the adaptive evolution of Ulmus species.Phylogenetic construction based on different data sets of cp genomes firstly confirmed the systematic position of U.mianzhuensis based on molecular evidence and divided into Sect.Microptelea.The phylogenetic results divided all the species into two Clades(Clade Ⅰ: Sect.Ulmus+Sect.Microptelea,Clade Ⅱ: Sect.Chaetoptelea+Sect.Blepharocapa+Sect.Trichoptelea),which was inconsistent with traditional taxonomy;our results suggested that U.lanceifolia should be assigned to Sect.Lanceifolia,and merged U.crassifolia and U.rubra to Sect.Trichoptelea and Sect.Blepharocarpa,respectively.2)Based on the 25 newly sequenced transcriptome data of Ulmus combing with25 published genome and transcriptome data of close genera in NCBI,we obtained1,050 orthologs with a strict standard for following phylogenetic analysis.The coverage of orthologs among species was basically over 80 %,with the total length was1,200,978 bp.The phylogenetic results based on Maximum likelihood and coalescence methods of Ulmus was highly consistent with cp genomes.It was mainly composed of two clades,which is basically consistent with its geographical distribution in North America,Europe and East Asia However,substantial conflicts were found in Sect.Ulmus and the topological structure of single gene tree based on orthologs supported that species tree was sorely affected by the conflict of gene tree.Moreover,a strand of analyses including incomplete lineage sorting,hybridization and gene duplication have hardly found the obvious signal of gene replication.The incorporations between the result of molecular clock,quartet sampling,and incomplete lineage sorting indicated that the conflict of gene tree in Ulmus may be caused by recent radiation of incomplete lineage sorting and hybridization.3)Based on the above phylogenetic backbone,we further studied the geographical distribution pattern and historical evolution of Ulmus by integrating the six core characteristics(inflorescence type,pubescent samara,the position of seed,flowering and fruiting period,leaf serrations in leaf margin and bud type).Our results found that Ulmus species have originated from East Asia during late of Cretaceous to Paleocene supporting the Out-of-Asia hypothesis.The analyses from reconstructed ancestral traits of Ulmus showed that the ancestral states of flowering in spring,the ancestral state of inflorescence type are mainly fascicled cymes.Whereas,there are still uncertainties in the ancestral state of bud type,the position of seed,pubescent samara and leaf serrations in leaf margin,and presented a complex evolutional process.The result of ancestral state reconstruction verified that the process from East Asia to Northern America and Europe was though multiple dispersal and vicariance,while BLB and NALB played essential roles in the dispersal of Ulmus species.Our results provided theoretical evidence for a better understanding of origin and evolution in north temperate zone species.In summary,our current studies of phylogenetic genomics,origin and evolution of Ulmus based on the cp genomes and transcriptome data will provide an important theoretical basis for the conservation of germplasm resources and genetic diversity of Ulmus.