Horizontal Transfers And Activity Analysis Of LTR Retrotransposons In Seven Rosales Species

Horizontal transfer(HT)is a way of genetic material communicating between different species.HT plays important roles in the species evolution.Transposable elements(TEs)are mobile genomic units that can move freely in the host genome.In the genome era,TEs are extensively found in the genomes of eukaryotes and are important components of the genomes.LTR(long terminal repeat)retrotransposon belongs to the major type of RNA-mediated retrotransposons(Class I TE).Since the LTR retrotransposons transfer in the form of "copy-and-paste",they play important roles in the genome size and structure.Horizontal transposable elements transfer(HTT)also plays an important roles in all aspects of genome and evolution of species,which is regarded as major force in propelling genomic variation and biological innovation.The genome-wide sequencing of several Rosales species have been completed.Currently,methods of HTT identification and analysis are available.Studies on the horizontal transfer and transposable activity of LTR retrotransposons in Rosales species will reveal the effect of HTT on the genome size and composition,and give us a chance to interpret the evolutionary relationships among species of the Rosales.In the present study,seven species that have been sequenced in the Rosales,including Morus notabilis,Cannabis sativa,Ziziphus jujuba,Fragaria vesca,Prunus persica,Malus domestica and Pyrus bretschneideri were chosen.Horizontal transfers of LTR retrotransposons were identified among them using comprehensive bioinformatics methods and the active transposition of LTR retrotransposons was also analyzed.The main results of the study are as follows:Identification of horizontal transfers of LTR retrotransposons in seven Rosales speciesFirst of all,LTR retrotransposons in seven sequenced Rosales species genomes were identified.And then,71 of candidate LTR retrotransposon horizontal transfer families were identified by a series of bioinformatics methods including BLAST comparison,Si Li X clustering,and CD-hit identity statistics.The results indicated that the whole sequences of LTR retrotransposons and reverse transcriptase(RT)were high consistent,and the Ka/Ks value of RT were lower than 1 as well as conserved genes,suggesting that they were both under purifying constrains.Moreover,the phylogenetic relationship and divergence time of the LTR retrotransposon were not consistent in the Rosales species.All of data pointed out that the horizontal transfers of LTR retrotransposons(HTT)happened among seven Rosales species.Finally,we identified 7 HTTs of LTR retrotransposons among seven species of Rosales.Two HTTs occurred between M.notabilis and Z.jujuba,named as Mn.Zj.1 and Mn.Zj.2,and the remaining five HTTs occurred between M.domestica and P.bretschneideri,were named as Md.Pb.1-5.The dating of horizontal transfers of LTR retrotransposons between M.notabilis and Z.jujuba was about 900 Mya and that between M.domestica and P.bretschneideri was about 300 Mya.Activity analysis of LTR retrotransposons in 7 HTTs familiesThe intact functional structures of LTR retrotransposons in 7 HTTs have been proved at first.To order to know whether the LTR retrotransposon is still active in the host genome after HTT and estimate the direction of the horizontal transfers of the LTR retrotransposons,we estimated the amplification times of the LTR retrotransposon copies for 7 HTTs in seven Rosale species.The results indicated that in Mn.Zj.1 and Mn.Zj.2,the LTR retrotransposons were active in both host genomes after HT.In Mn.Zj.1,the insertion time of LTR retrotransposon copies of Z.jujuba were lower than that of M.notabilis,suggesting that the LTR retrotransposon was transferred from M.notabilis to Z.jujuba.In Md.Pb.1-5,the results showed that in Md.Pb.2 and Md.Pb.3,lots of LTR retrotransposon copies existed in each species,indicating that the LTR retrotransposons remain active in the host genome after HTT.Especially in Md.Pb.3,LTR retrotransposon amplified in the host genome.However,other families were silent without activities.The amplification of LTR retrotransposons in host genome after HT will have a profound impact on composition and evolution of the genome in these species.