Identification And Evolutionary Analysis Of Tc1/Mariner Transposons In Fish Genomes

Transposable elements(TEs)are interspersed DNA fragments that can be moved and widely distributed in the genome of eukaryotes.TEs can be classified in two main class,based on their transposition mechanism: RNA transposons('copy and paste')and DNA transposons('cut and paste').As genome data continue to be published,more and more studies have found that TEs play an important role in the process of biological evolution.Tc1/Mariner transposons belong to class ? transposable elements,which are abundant in fish and amphibians.As the oldest group of vertebrates,fish can be traced back to the Cambrian period about 500 million years ago.After a long period of evolution,the number of fish has exceeded 30,000 species.Since the Tc1/Mariner transposons has an ultra-high proportion in most fish genomes,some researchers have become interested in the study of Tc1/Mariner transposons in fish.At present,the study of Tc1/Mariner transposons in most fish only stay at the level of superfamily,and there are not many reports on their specific classification,structural characteristics and evolutionary analysis.In this paper,we selected 30 fish genomes,including 2 Agnatha fish,1 Chondrichthyes fish,1 Sarcopterygii fish and 26 Actinopterygii fish for the identification and evolutionary analysis of Tc1/Mariner transposons.The main research results are as follows:1.Identification and content analysis of Tc1/Mariner transposons in fishIn order to more accurately identify Tc1/Mariner transposons in the fish genomes,we annotated both de novo and homology-based approaches.Through the statistics and classification of the obtained sequences,we finally identified a total of 761 Tc1/Mariner family sequences in the 30 fish genomes,of which 267 were autonomous family.RepeatMasker was used to annotate and count the transposons of 30 fish.The results showed that the content of Tc1/Mariner transposons in different fish varied greatly(0.04%-9.46%).Compared with other fish,Tc1/Mariner transposons of freshwater fish,such as Ictalurus punctatus(9.46%),Danio rerio(8.93%),Silurus meridionalis(8.54%)and so on,are relatively high;Except for Amphiprion ocellaris,the content of Tc1/Mariner transposons in marine fish(0.04% to 0.85%)was generally lower than that of freshwater fish(0.95% to 9.46%)and diadromous fish(1.70% to 9.46%).Pearson correlation analysis showed that there was no significant correlation between the content of Tc1/Mariner transposons and genome size.2.Characteristic analysis of Tc1/Mariner transposons in fishBased on the structural and phylogenetic analysis of the catalytic region of the transposase,all identified autonomous Tc1/Mariner transposons are mainly divided into 8 different subgroups: Tc1(DD34E),DD35 E,DD36E,DD37 E,DD38E,mariner(DD34D),pogo(DD30-32 D and DD35D)and rosa(DD41D),in which the Tc1 is found in virtually all teleost species.Tc1/Mariner family of some ancient fish such as Agnatha,Chondrichthyes,and Sarcopterygii fish are different from those of Actinopterygii.DD46 D was found in the Lethenteron camtschaticum;pogo(DD30-32D)and mariner transposons were found only in Latimeria chalumnae.In addition,maT was also found in A.ocellaris.The phylogenetic relationship of most transposons is basically the same as that of species.In addition,correlation analysis showed no significant correlation between Tc1/Mariner family diversity(family number)and genome size.3.Amplification time of Tc1/Mariner transposons in fishTo explore the historical dynamics of Tc1/Mariner transposons evolution,we analyzed the insertion time of Tc1/Mariner transposons in the 30 fish genomes.The results indicated that the Tc1/Mariner transposons of most fish was 'single peak' amplification,and the related species had similar TEs history.The autonomous Tc1/Mariner transposons has an expansion mainly in 1 Mya,while the non-autonomous Tc1/Mariner transposons has been amplified mainly in 3-2 Mya.Through comparison analysis,it was found that most of the fish(such as I.punctatus,S.asotus,S.meridionalis,Astyanax mexicanus and Nothobranchius furzeri,etc.)matched a large number of transcriptome data,indicating Tc1/Mariner transposons of most fish may have been transcribed in the near future.In summary,our study found that most fish have a 'burst' event in the near future.4.Distribution and function analysis of Tc1/Mariner transposons in fishThrough the analysis of transposons,it was found that the Tc1/Mariner transposons mainly exists in the intron of the gene in the 30 fish genomes,and there are also a few distributions in the flanking gene(<5kb).4 fish genomes with high content of Tc1/Mariner transposons(I.punctatus,S.salar,D.rerio and A.mexicanus)were selected for GO enrichment analysis of Tc1/Mariner transposons.The results showed that all the 4 fish were significantly enriched in the term of ATP binding(GO: 0005524).In addition,I.punctatus,S.salar,D.rerio and A.mexicanus are also mainly enriched in integrin-mediated signaling pathway(GO: 0007229),nervous system development(GO: 0007399),transmembrane transport(GO: 0055085),microtubule-based movement(GO: 0007018)and so on.These enrichment analyses indicated that the transposons near the genes may be related to the regulation and metabolism of functional genes in fish.In summary,this study enriches the data on transposons taxonomy by identifying,classifying and characterizing Tc1/Mariner transposons in the 30 fish genomes.Through comparative genomics analysis,the structure,amplification pattern and distribution of Tc1/Mariner transposons were clarified in fish.In addition,we also carried out enrichment analysis of neighboring genes in some fish,which laid the foundation for further research on the function of the Tc1/Mariner transposons.