This project is about search of mobile elements in trematode Himasthla elongata transcriptome
Repetitive DNA makes up a large fraction of a eukaryotic genomes, and some repetitive elements, transposons, are able to move within the genome. Transposons are powerful forces of genetic change and have played a significant role in the evolution of many genomes. Transposons seem to cause genetic polymorphism in trematodes. Therefore, this project is one of the steps for investigation of transposon functions.
Identification transposable elements in Himasthla elongata transcriptome using different tools and comparative analysis of their results
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Filtering raw reads using BBTools, Trimmomatic;
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Transcriptome assembly using rnaSPAdes;
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Identification and classification of transposable elements using different tools (RepeatModeller, RepeatMasker, Repeatexplorer2)
- To get more information about RepeatModeller results go to "RepeatModeller_output" folder
- To get more information about RepeaMasker results go to "RepeatModeller_output"
- To get more information about Repeat Explorer2 results go to "repeat_explorer_output"
- To get more information about quality assessment of transcriptome assembly go to "rnaQ_report"
- To get file with transcripts abundance in TPM go to "quantification"
For de novo transposons identification we used RepeatModeller tool which includes RepeatScout, RECON, and Tandem Repeat Finder.
To classify transposons we used RepeatMasker with databases from GIRI with multiple types of libraries
To identify de novo and classify modile elements in raw reads we used Repeat Explorer from Galaxy server
In general, using RepeatModeller+Repeatmasker combination we got following results:
According to RepeatMasker search, based on RepeatModeller generated library the most abundant transposon families are RTE-BovB, CR1 and Gypsy. All these families belong to class I (retrotransposons).
RepeatExplorer reported about 10 percents of repetitive elements in the H. elongata transcriptome. Only 0,01% fell on Bel-Pao elements, 1.03 - Gypsy and 0.09 - Satellites.
Thus, RepetExplorer turned out to be a less effective tool in the annotation of mobile elements