Detection of active LTR retrotransposons via eccDNA analysis in Helianthus annuus L., Arabidopsis thaliana and triticale

Pavel Merkulov; Murad Omarov; Sofya Gvaramiya; Ilya Kirov
All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
LTR retrotransposons present a subclass of mobile genetic elements and can produce extrachromosomal circular DNA (eccDNA) as a byproduct of their life cycle. Recent studies showed that the amount of LTR retrotransposon eccDNA molecules is individual for each element and often correlates with the transposition ability. In this way, eccDNA can be used for experimental detection of active retrotransposons in plants as an alternative to whole-genome sequencing. In our study, we aimed to reveal active retrotransposons in Arabidopsis thaliana, H. annuus, and triticale (x Triticosecale Wittmack). We performed an eccDNA enrichment followed by inverse PCR with specific primers. In H. annuus & triticale we detected two LTR retrotransposons (named Gagarin & MIG, respectively) producing eccDNA molecules. Using RT-PCR analysis and direct RNA Nanopore sequencing we also detected different isoforms for these retrotransposons.Merkulov-Poster-A1-Novosibirsk-page