Identification And Evolutionary Analysis Of MITE Transposons In Fish Genomes

Transposable elements(TEs)are a class of DNA repeat sequences that can move through the genome.They are mainly divided into two types,one is a retrotransposon(RNA transposon)transposed in a "copy and paste" manner.The other type is a DNA transposon transposed in a "cut and paste" manner.Miniature inverted-repeat transposable elements(MITEs)are a group of short and non-autonomous DNA transposons.They are typically 50 to 800 bp in length with a typical terminal inverted repeat(TIR)and target repeat(TSD)at both ends of the sequence.MITEs have high copy numbers in the vertebrate genomes and are usually preferentially inserted into or near genes.At present there is a clear understanding of the content,diversity,distribution and transposition mechanism of MITEs.The number of species of the fish(more than 30,000 species)accounts for more than half of the total number of vertebrate species,and fish is also an important component of marine and freshwater ecosystems.Fishes include Agnatha,Chondrichthyes,Sarcopterygii and Actinopterygii.Gene replication is very frequent in the evolutionary history of fish.The replicated genes and genomes can influence fish evolution and speciation.Fish genome data is being published one after another with the development of next-generation sequencing technology,which provides an opportunity for the development of our research.Transposons are highly abundant in the fish genome,such as 58% transposons of the zebrafish genome.Therefore,transposons are an important part of the fish genomes.MITEs are a special class of transposons.Currently,plants,insects,and viruses have related MITEs libraries,but there is no systematic prediction for fish MITE transposons.Therefore,it will contribute to the in-depth research on fish to accurately annotate and analyze the MITE transposons of fish genomes.In this study,we selected 34 representative fishes’ genomes,including 3 kinds of Agnatha,2 kinds of Chondrichthyes,1 kind of Sarcopterygii,28 kinds of Actinopterygii,and lancelet.We used bioinformatics methods to identify and compare genomics of MITEs in the genomes of these species.The main findings are as follows:(1)Identification,classification and content of MITEs in fish genomesWe downloaded genomes data from NCBI.MITEs in the fish genome were predicted by software such as MITE-Hunter,and we constructed a consensus sequence of MITEs.After that,the predicted MITEs are classified by TIR,TSD sequence characteristics.The results showed that the MITEs super families contained in the fish genome included Tc1-Mariner,PHIS,P,Kobolok,PiggyBac,hAT,Ginger,CMC,Merlin,Sola2,and the Tc1-Mariner superfamily accounted for the majority.We analyzed the relationship between MITEs content and the genome size of the corresponding species,revealing that there is no correlation between them.(2)Amplification pattern of MITEs in the genomesThe insertion time of the full-length copies in the genome were calculated according to Kimura 2 parameter distances.We found that MITEs have one or two bursts of amplification during the evolution of fish species.TEs burst in most species occurred between 0.5 and 2 million years ago.The expansion of MITEs is similar for species which have close phylogenetic relationships.The Agnatha(Eptatretus burger,Lethenteron camtschaticum,Petromyzon marinus),Chondrichthyes(Leucoraja erinacea)and Sarcopterygii(Latimeria chalumnae)have reached the peak of amplification in 1.5-0.5 million years ago.The most recent amplification of fish in Actinopterygii peaked between 2.5-1.5 million years ago.Some species experienced two bursts of MITEs,such as Oreochromis niloticus,Astyanax mexicanus,Danio rerio,Sinocyclocheilus rhinocerous and Paramormyrops kingsleyae.We searched for long copies with identical TIR sequences in MITEs in the corresponding fish genome,because MITEs require amplification with them.A total of 72 autonomous TEs were found in 14 fish genomes,including the Tc1-Mariner and hAT superfamily of DNA transposons TIR class,most of which are Tc1-Mariner with DD34 E structure.(3)Analysis of MITEs proximity genes in fish genomesOnly 25 annotated information files were available for MITEs insertion sites and proximity gene analysis in selected 35 species.The results show that MITEs are primarily inserted into the 3’ and 5’ ends of the gene in the fish genomes.At the same time,it was found that MITEs were inserted inside the gene,and multiple MITEs were inserted into the exons of the genes.In addition,MITEs in different fish genomes were inserted into the same gene,indicating that the target sites of fish MITEs have a certain similarity.The genes inserted by MITEs were subjected to GO enrichment analysis according to the corresponding annotation information database of each species in AnnotationHub.The GO enrichment results of only 12 species were obtained since many of the genes inserted by MITEs are new unexplained ones.From the results,Danio rerio,Ictalurus punctatus,Nothobranchius furzeri and Salmo salar are enriched for pathways associated with GTPase activity.Paramormyrops kingsleyae and Oryzias latipes are enriched in a pathway associated with ATPase activity.Astyanax mexicanus and Nothobranchius furzeri are enriched in the pathway of gene kinase activity.In summary,this study predicted MITEs of some fish genomes,constructed MITEs consensus sequences and classified MITEs.The relationship between genome size and MITEs content was also analyzed.The insertion time of MITEs was calculated to study the amplification of MITEs in the fish genome,and the insertion location of MITEs was analyzed to explore the function of MITEs-related genes.The results enriched the data of vertebrate MITEs and supplemented the lack of research on the evolution of fish MITEs.This work also helps to promote functional studies of fish genomes MITEs.