Comparative Analysis Of Transposable Elements Mined From Reduced-representation Genome Sequences In Genus Rehmannia

Transposable elements(TEs)as potent broad-spectrum mutagens generating variation in the host genome,have a role as key players in the ecology of the genome and the evolution of the host species.Until now,almost TE analysis have generally been carried out on a species-by-species basis,and comparative studies of TEs between taxa in plant have been rare,which should shed light on the structural,epigenetic and functional modification driven by TEs,provide detailed information about the evolutionary dynamics of TEs,and somehow underline the phylogenetic relationship of their host species.As a small genus of Orobanchaceae,Rehmannia Libosch.ex Fisch.et Mey consists of six species,all Rehmannia species are endemic plants in China except Rehmannia glutinosa,which is commonly used as traditional Chinese medicine,expand its distribution into east Asia-Japan.The significant differences of ploidy and phenotype among Rehmannia species ultimately stem from genetic difference,and transposable elements might play a key role during the divergence of these species.Here,we compared the content of TEs of five Rehmannia species(R.chingii,R.piasezkii,R.elata,R.henryi and R.solanifolia)from reduced-representation genome sequences,uncovered the difference of TEs between tetraploid species and diploid species in genus Rehmannia and further surmised the cause and effect of these differences.In addition,frontal support and complementary evidence were provided to reconstruct the phylogenetic relationship of Rehmannia species.Finally,the role TEs play in the mutation differences between CDs and non-CDs and the niche TEs occupy in the ecology of host genome was discussed.The main conclusions are as follows:(1)Transposable elements were identified and annotated for five Rehmannia species include R.chingii,R.piasezkii,R.elata,R.henryi and R.solanifolia.Those sequences annotated as TEs were classified into 28 superfamilies.Repetitive sequence accounts for over 60%of the partial genome of the Rehmannia species,among them,TEs that classified clearly have a content of 33%or so.The content of each class of TEs remained similar except for some TEs superfamilies(L1?hAT etc.)have a significant difference between R.solanifolia and others.(2)The unrooted trees constructed based on different data and different methods supported the close relationships of R.elata and R.chingii,R.henryi and R.solanifolia.Moreover,the cluster analysis based on copy number of TEs obtained a clustering relation that is the same to the topological structure of phylogenetic tree,successfully evidenced the evolutionary relationships of Rehmannia species.(3)Much of the difference of mutation number between coding regions and non-coding regions in the genome of Rehmannia species has arisen from the highly variable TEs,that is,the location of TE insertion has determined the regions where mutation hotspots occurred.And it's not hard to imagine the great efforts TEs made to acclimatize themselves to and interact with the evolution of their host sequences.