Diversity Of Fish Transposons And Their Role In Evolution

Transposable elements(TEs)are essentially repetitive DNA fragments scattered throughout the genome and can ‘jump' in the genome by ‘cut-and-paste' or ‘copy-and-paste',so they are also called ‘jumping gene'.Although the function of TEs is controversial for a long time after they were discovered,researchers have realized the importance of TEs in biological evolution as more and more species' genomes have been sequenced and TEs have been studied step by step.Recent researches show that TEs possibly participate in a variety of biological processes,such as new gene formation,gene regulation,generation of novel regulatory elements,evolution of genome size,species differentiation,environmental adaptation and so on.As a result,TEs are becoming new clues to functional genomics and genome evolution studies in addition to functional genes.Fish is relatively early vertebrate,and they have a long history of evolution.There are numerous species of fish,showing great diversity in morphology and a variety of life history strategies.Through more round of whole genome duplication events and hundred millions years of the fish genomes evolution,which result in a high degree of variation in karyotype,size and component of existing fish genomes.Fish play a crucial role in modern biological research,they can be used as models for biological research,such as Danio rerio and Oryzias latipe.In addition,fish not only help us to trace the origin of vertebrates,but also provide data on several major events in the evolution of vertebrates,such as the emergence of the upper and lower jaws,the generation of hard bones,and the evolution of aquatic to terrestrial life,and so on.As a crucial genome component,TEs is an extremely important research object in these studies.However,the research foundation of fish transposons is relatively weak.Up to now,most studies on fish transposons are limited to the repeated sequence annotation of specific genomes,and most of the annotations have the defects of single method and fuzzy classification,the specific landscape and evolutionary characteristics of TEs in the fish genomes are still blank.Therefore,accurate annotation of fish transposons,comparative genomics analysis and further exploration of their role in the evolution of fish will be of great importance to the study of fish and even vertebrates.Development of high-throughput sequencing technology and the rapid decline in sequencing costs have promoted the prosperity of genomics research,being an opportunity for the research of TEs.Built on de novo,structure-based,and homology-based approaches,this study identified the selected fish TEs from the whole genome level and constructed an open source fish TEs database;the role of transposons in the evolution of fish and the evolution process of transposons themselves were discussed by systematically studying the inter-species diversity,active law,and activation time of fish transposons;finally,the role of transposons in vertebrate evolution is further explored through the clues obtained from comparative analysis.The main results were as follows:1.Identification of fish TEs and database construction(1)To accurately identify transposon sequences in genomes,considering the advantages and disadvantages of different methods and different tools,we finally chose the multi-method combination strategy to predict the TEs in 29 fish genomes and lancelet genome.De novo,structure-based and homology-based approaches were utilized to construct TEs identification pipeline.Through a series of filtering false positives and redundancy,and finally classified using REPCLASS and TEclass.In the end,we obtained a total of 33,260 consensus sequences,which were subdivided into nearly 50 superfamilies.Among them,Gypsy,L1,L2,R2,RTE,Rex,Tc-mariner,and hAT have a large proportion in the results of known classifications.(2)In order to make the obtained TEs data more widely utilized,we used LNMP(Linux,Nginx,MySQL,PHP)technique to build an user-friendly Web database,FishTEDB(http://www.fishtedb.org/).FishTEDB enables users to browse,search,and download all TEs data.In addition,three kinds of widely used online tools,BLAST,GetORF,and HMMER,were set on the database to achieve a simple and rapid analysis by users.FishTEDB construction will help drive research on TEs in fish and even vertebrates.Not only that,it will also provide some assistance to the genetic annotation of the fish genomes.2.Comparative analysis of TEs in fish genomes(1)Through the construction of fish TEs database,30 species of TE sequences were achieved.In order to make a more systematic comparative genomics analysis,we used the same TEs annotation process to predict TEs for the genomes of eight newly added species(We directly used the zebrafish TE library in Repbase).RepeatMasker was used to annotate the TEs in the genomes of 39 species,each of which was built on its own TEs library.The annotated results of each species were counted in different classification hierarchies,including a total amount,class,type,and superfamily.The results showed that there were significant differences in the total content of TEs in the fish genomes(from 5% of puffer fish to 57% of zebrafish),of which Class I TEs were generally larger.In different types,the alternation of DNA transposons and LINEs dominate the fish genomes,while LINEs in the genomes of ancient fish(early divergent fish)have a distinct advantage,especially in the elephant shark genome.In different superfamilies,Tc-mariner,hAT,L1,L2 and Gypsy are widely distributed in fish genomes and have a relatively high content.R2,RTE and Rex1 are also common in the fish genomes,but are lower in content than Tc-mariner,hAT,L1,L2 and Gypsy.Some TEs superfamilies have specific enrichment in some species,such as Gypsy in Boleophthalmus pectinirostris,L2 and RTE in Nothobranchius furzeri,Tc-mariner in Astyanax mexicanus,hAT in D.rerio,CR1,L1 and L2 in Latimeria chalumnae,and CR1 and L2 in Callorhinchus milii.(2)Pearson correlation coefficient analysis was used to assess the correlation between the content of TEs and genomes size in different classification hierarchies.On the overall level,TEs content in fish genomes is significant positively correlated with genomes size of fish(Pearson correlation coefficient r = 0.47,p-value = 0.002).In different classes,the content of Class I is positively correlated with the size of fish genomes(Pearson correlation coefficient r = 0.39,p-value = 0.013).In different types,the content of LTR is positively correlated with the size of fish genomes(Pearson correlation coefficient r = 0.43,p-value= 0.006).At the superfamily level,Helitron,Maverick,Kolobok,CMC,P,DIRS,I,L1,L2 and 5S are significantly positively correlated with the size of the fish genomes.(3)Diversity of TEs is different between the ancient fish and the latter differentiated fish.In early divergent fish(C.milii,L.chalumnae,Lepisosteus oculatus and Petromyzon marinus)and lancelet(Branchiostoma belcheri),the content of CR1 is very rich,while in the fish that differentiated after spotted gar(L.oculatus),the richness of CR1 is significantly reduced,replaced by ‘amplification' of Tc-Mariner and hAT.(4)The results of the prediction of the historical dynamics show that TEs ‘burst' occurred during the evolution of fish.Fish usually contain a small number of ancient TE copies(TE copies with a K value greater than 25),but most ancient fishes retain more ancient TEs copies than later differentiated fishes.LINEs in the fish genome dominated in the early period(K value approaching 50),and LINEs in the C.milii and L.chalumnae genomes dominated in the entire evolutionary history.Therefore,LINEs may be the transposons of fish in the very initial period and may play an important role in the evolution process of the fish transposon itself.3.TEs ‘burst' and fish species differentiation(1)The results of the observation of the historical dynamic prediction of the TEs in fish show that the ‘burst' event is common in the evolution of fish.In view of this phenomenon and the hypothesis that TEs interact with ‘host' genomes,we proposed the hypothesis that TEs ‘burst' is related to species differentiation,and whether the time of TEs ‘burst' is consistent with the differentiated time as a standard to verify the hypothesis.Eels(Anguilla anguilla,A.japonica),fugu(Takifugu rubripes,T.flavidus),African cichlids(Neolamprologus brichardi,Haplochromis burtoni,Pundamilia nyererei,Oreochromis niloticus,Maylandia zebra),mudskipper(Periophthalmodon schlosseri and Periophthalmus magnuspinnatus,Scartelaos histophorus and Boleophthalmus pectinirostris)exist TEs ‘burst' time corresponding to the time of common ancestor species differentiation.Therefore,the hypothesis can be verified that there is a correlation between TEs ‘burst' and species differentiation.(2)To verify the applicability of the validated hypothesis in this study,primates,glires,birds,and amphibious/reptiles genome data were added to get a wider range of validation.The results show that among primates(Anthropoidea: Homo sapiens,Pan troglodytes,Gorilla gorilla,Pongo abelii,Nomascus leucogenys;Old world monkeys: Macaca mulatta,M.fascicularis,Papio anubis,Chlorocebus sabaeus;Prosimii: Eulemur macaco,Daubentonia madagascariensis,Otolemur garnettii),Tupaia belangeri,glires(Spermophilus tridecemlineatus,Jaculus jaculus,Microtus ochrogaster,Heterocephalus glaber,Cavia porcellus,Chinchilla lanigera,Octodon degus,Oryctolagus cuniculus),birds(Amazona vittata,Anas platyrhynchos,Columba livia,Ficedula albicollis,Geospiza fortis,Melopsittacus undulates,Pseudopodoces humilis,Scarlet macaw,Taeniopygia guttata,Zonotrichia albicollis,Falco peregrinus,F.cherrug),amphibious/reptiles(Chrysemys picta bellii,Chelonia mydas,Apalone spinifera,Pelodiscus sinensis)exist TEs ‘burst' time corresponding to the time of common ancestor species differentiation.So far,we have found evidence of a link between TEs ‘burst' and species differentiation in vertebrates.To sum up,fish TEs were studied step by step in this research.From the prediction of transposons in fish genomes to construct basic data,and through systematic comparative analysis,the TEs in fish genomes were summarized and the regularities were searched to obtain meaningful difference signals and clues.Based on the obtained clues,the hypothesis was proposed,and finally the evidence was noted that the activity of transposons was related to the species differentiation.