Study Of LTR Retrotransposon In Algae Genome And Transcriptome Analysis Of Saccharina Japonica

Transposable elements (TE) are extremely wide distributed among plant and animal.In previous study, large amount of transposable elements have been isolated fromplant such as rice, maize etc. As a member of transposon, long term repeatretrotransposon (LTR retrotransposon) occupies an important portion within genome.LTR retrotransposons can affect gene expression and even lead to the formation ofnew gene. The rearrangement caused by transposable activity can change theorganizational structure of the genome. LTR retrotransposons are also the majorcomponents of eukaryotic chromosome heterochromatin and some reversetranscriptase show close relation to telomerease. LTR retrotransposons in advanceplant genome evolution is now being highly concerned in depth study. This is samealgae genomes, that the LTR retrotransposon research has considerable prospects.In this study, by the use of LTR_STRUC and LTR_FINDER into21alga species (6prokaryotic algae,15eukaryotic algae), we have conducted a series of work in LTRretrotransposon bioinformatics analysis. Total of1635LTR retrotransposon elementshave been annotated. There is no LTR retrotransposon annotated in prokaryotic algaein this research, while10of15eukaryotic algae have been annotated with potentialLTR retrotransposons. Exclude latest Guillardia theta and Chondrus cripus genome,structure analysis against rest predicted LTR retrotransposons suggests that LTRretrotransposon in algae are similar to higher plants. Statistic shows that in the restnine species of algae, LTR retrotransposons are all approximately lower than1%ofthe overall proportion of the genome while LTR elements make up of over10%ofC.cripus genome. Using the the LTR retrotransposon reverse transcriptase andribonuclease H into clustering process, presence of species diversity is shown amongalgae LTR retrotransposon, which may caused by different dynamics in early algaeevolutionary. Molecular phylogenetic analysis show that algae LTR retrotransposonswithin genome are generally under negative selection pressure. LTR Insertion analysisin brown alga Ectocarpus siliculosus genome and transcriptome finds that LTRtransposon distributes in various locations of thEChromosome, including intron regions within the region of the gene and non-gene region, and there is also thephenomenon of retrotransposon nested as well as the exonization phenomenon of LTRelements. The study provides for the presence of LTR retrotransposons in the algaegenome universality of the data. A series of conducted evolutionary analysis show thatthe the LTR retrotransposon in alga genome are under an interaction coevolution.Through the analysis of LTR retrotransposon in alga genome, we make contribution topaving the way for further exploration of the early process of biological evolution.Saccharina is one of the most important economical cold-water living marinebrown algal genuses. In this study, by using the high-throughput DNA sequencingtechnique, the Illumina HiSeq2000, we analyzed the transcriptome of Saccharinajaponica. About5.16GB of raw data were generated, and65,536scaffolds with anaverage length of454bases were assembled after SOAP de novo assembly method.Several higher analyses have been conducted:18,527unigenes were identified byBLAST,25,734scaffolds werEClustered into37Gene ontology functional groups,6,760scaffolds werEClassified into25COG categories,2,665scaffolds wereassigned to306KEGG pathways. Majority of the unigenes exhibited more similaritiesto alga including brown alga and diatom than other cyanobacteria, marine diatom, andplant. Saccharina japonica has the outstanding capability to accumulate halogen suchas Br-and I-via halogenations process from seawater. We acquired42differentvanadium-dependent haloperoxidases (vHPO) in S. japonica transcriptome data,which including5segments of vanadium-dependent iodoperoxidase (vIPO) and37segments of vanadium-dependent bromoperoxidase (vBPO). Complicated analysiscontaining identified full length S.japonica vBPO1and S.japonica vBPO2revealedthe high amino acid sequence identity of vBPO among brown alga species and theevolution relationship between marine algae and cyanobacterial vHPOs. The workwould enhance our understanding of biological characteristic and economic value ofspecies S.japonica.