Identifying differentially expressed transposons across four life-cycle stages of Fasciola hepatica
Transposable elements (TEs) are highly repetitive mobile sequences, which play diverse roles in genome regulation. As well, it is expected that TEs participate in lncRNAs function. In trematodes, lncRNA might be involved in development processes and life cycle regulation. For future studies it is significant to explore connection between TEs expression and developmental stages.
Our study is devoted to detecting transposons in transcriptomes of four different life-cycle stages of F. hepatica and analyzing their differential expression across stages.
- Create mapping of RNA-seq data onto a list of transposons sequences
- Quantify expression from mappings for each transposon
- Normalize TE data using statistical approach
- Discover differentially expressed TEs on each stage of F. hepatica life cycle
F. hepatica RNA-seq data
List of F. hepatica TEs
As well we applied fasta file with repeatitive elements of F.hepatica genome, created earlier with help of RepeatMasker tool.
First of all, row reads of 4 developmental stages were downloaded and then filtered using Trimmomatic and FastQC for quality control. Differential expression analysis was performed with two separate methods: kallisto + sleuth and TEtools + DeSeq2. To analyze any TEs that show change in expression across the different stages, likelihood ratio test (LRT) was implemented. In the end lists of significant TEs (FDR>0.05), which are differentially expressed across developmental stages, was obtained. All steps can be found in lab notebook
- python v.3.6
- R v.3.4.4
- Trimmomatic v.0.36
- FastQC v.0.11.7
- kallisto v.0.44.0
- sleuth R package v.0.29.0
- TEtools v.3
- DeSeq2 R package v.1.18.1
Anna Solovyeva, Nickolay Panuyshev
- Vasconcelos EJR et al, 2017. The Schistosoma mansoni genome encodes thousands of long non-coding RNAs predicted to be functional at different parasite life-cycle stages. Sci Rep. 2017 Sep 5;7(1):10508. doi: 10.1038/s41598-017-10853-6.