Genome-wide analysis of highly expressed plant retrotransposons

Murad Omarov¹, Pavel Merkulov², Sofia Gvaramia³, Liza Kolganova⁴, Ilya Kirov^5
1All-Russia Research Institute of Agriculture biotechnology, muradok98@gmail.com
²All-Russia Research Institute of Agriculture biotechnology, paulmerkulov97@gmail.com
³All-Russia Research Institute of Agriculture biotechnology, sofia.gvaramia@gmail.com
⁴All-Russia Research Institute of Agriculture biotechnology, liza.colg@gmail.com
⁵All-Russia Research Institute of Agriculture biotechnology, kirovez@gmail.com

Retrotransposons (TEs) are mobile genomic elements capable of transposition via reverse transcription of RNA intermediate. Transcription and mobility of TEs in a cell are under strong epigenetic silencing being partially recovered during stress and some development stages. But recent studies cast doubt on this axiomatic statement, revealing many transcripts of TEs (retrotranscriptome) in somatic organs under non-stressed conditions. The composition and structure of plant retrotranscriptome are still not clear. Here, we developed a pipeline for transcribed TEs identification and applied it to 7 plant species using RNA-seq data from different organs and under different conditions. Our results showed that TEs transcription under non-stressed conditions is the widespread phenomenon in plants and expressed TEs possess some distinctive genomic features