Bioinformatics Analysis Of Helitron Transposons In Plant Genomes

Helitron transposons are a type of DNA transposons that can be transposed by rolling circle replication.It is inclined to insert into the vicinity of a gene,especially has an important feature of autonomously capturing gene fragments.Therefore,they contributed greatly to genome evolution and regulation of gene expression.However,because this type of transposons was discovered only 19 years ago,the study of Helitron transposons is still not completely clear in terms of annotation and identification methods,insertion time and origin.In this study,bioinformatics calculations combined with Python and Perl script programs were used to annotate and identify Helitron transposons in 302 plant genomes that have been published,and their structures,insertion time,location characteristics,and gene capture feature were extensively analyzed.The main results are as follows:1.Identification and content analysis of Helitron transposons in plant genomesIn order to fully identify Helitrons in the sequenced plant genomes,we used a combined method with Helitron Scanner program and the Python and Perl scripts.A total of 984459 Helitrons were identified,and the species with the highest number was Triticum dicoccoides,which has 129,122 Helitrons.The lowest was found in Galdieria sulphuraria,with only two Helitrons.The average length of Helitrons in the 302 plant genomes was 8650 bp,and the average Helitron density was 3.47 per Mb.The Helitrons were accounting for 3.00% of the whole genome averagely.The results also showed that the content of Helitron transposons in different species varied widely,with an average density ranging between 0.02 per Mb-28.83 per Mb.The species with the highest genome abundance of Helitron is maize,with the ratio of 24.69%,and the lowest is Vitis aestivalis,accounting for 0.002% of the genome.Among different plant groups,monocotyledons have the highest Helitron content,and the average content of Helitron transposons in Gramineae is much higher than in the other families.Correlation analysis between the number and total length of Helitron transposons and genome size revealed that they were both positively correlated,indicating that the insertion of Helitron is one of the factors for the expansion of plant genomes.2.Conservative structure analysis of Helitron transposons at 5 'and 3' ends in plant genomesOur analysis of each 50 bp sequence at the 5' and 3' ends of Helitron transposon showed that most Helitrons had a conserved 5'-TC start and 3'-CTRR end.The 5'-end was rich in A and T bases,and GC content at the stem-loop structure at the 3 'end was high.Helitron in different plant groups at the end of the base composition was consistent with the basic structure.Only dicotyledons did not strictly follow the terminal characteristics of 5'-TC and 3'-CTRR,and the first two sites at the 5 'end and the last four loci at the 3' end showed a difference of less than 0.5%,suggesting that dicotyledons were more tolerant to the end sequences of Helitron transposons.3.Expansion time of Helitron transposons in plant genomeIn order to elucidate the insertion and expansion patterns of Helitron transposons in plant genomes,we calculated the insertion time of 158,302 Helitron transposons from 204 plant genomes using the Kimura two-parameter model.The results showed that Helitron transposon had experienced two rapid expansion periods,with the first expansion occurring between 25-19 million years ago and peaking at 22 million years ago.The second expansion occurred in the last 4 million years,peaking at about 200,000 years ago,and 77.1% of Helitron transposons were inserted into plant genomes at this stage.The two expansions of Helitron were accompanied by the third genome-wide replication event of the plant group,indicating that Helitron transposons in existing plant genomes may have been produced by the third genome-wide replication event.4.Analysis of Helitron transposon insertion positions and adjacent genes in the genomes of Brassicaceae and SolanaceaeTo understand the location pattern of Helitron insertion in plant genomes,we selected 18 species from the Brassicaceae and Solanaceae plants with annotated documents,and analyzed the Helitron insertion position and the function of neighboring genes.The results showed that the insertion of Helitron in plant genomes was quite different among different plant groups.For example,about 69%-89.7% of Helitrons in the genomes of Brassicaceae plant were inserted into the flanking region of gene,while this frequency of solanaceae plants was relatively low,with only 14.46-38.65%.We analyzed the genomic characteristics of these species and found that this difference might be due to the content of repetitive sequences in the genome.GO enrichment analysis of these neighboring genes showed that Helitron insertion position was random in the function selection of neighboring genes,and did not show obvious common preference.5.Analysis of Helitron transposon gene capture in the genomes of Brassicaceae and SolanaceaeAnalysis of Helitron transposon captured genes from 18 species of Brassicaceae and Solanaceae shows that 38.29%-45.76% of Helitron transposons in Brassicaceae had captured complete genes,while only 4.22%-15.99% in Solanaceae.GO enrichment analysis was performed on the captured genes,and 6 of the 9 species obtained the results were enriched to the term related to metal ion binding.This result might be related to the need for binding of divalent metal ions to the Rep domain required for Helitron transposition.In summary,this study fully identified Helitron transposons in the genomes of 302 plant species,explored their content,terminal structure and insertion time in different plant groups,and focused on analyzing the Brassicaceae and Solanaceae plant Helitron insertion location preferences and gene capture,the function of related genes was also enriched.The results have greatly enriched the plant transposon database and provided important basic data for the study of the origin and evolution of Helitron transposons in plant genomes.