From clonal diversity to transposon derived long non-coding RNA in trematode Himasthla elongata parthenogenetic generations

We investigated clonal diversity of parthenogenetic larvae, cercaria, with a simplified AFLP (SAFLP, Amplified fragment length polymorphism) method and explored the nature of diverse zones from electrophoretic patterns. LINE retroelements prevail in fragments analized. One of them was aligned to the spacer region in ORF2 of the CR1-like (LINE class) transposon and named CR1-renegade (CR1-rng). CR1-renegade exists in two types of transcripts: the long ones, containing reverse transcriptase and other domains, and the short ones, containing CR1-rng solely. Probes of CR1 reverse transcriptase (CR1-RT) and CR1-rng yielded strikingly different pictures in FISH physical mapping despite being fragments of CR1 transposons. The CR1-RT probe demonstrated dispersed signal distribution throughout the nuclei and all chromosomes while CR1-rng localized preferentially to the heterochromatic regions. We suppose that CR1-rng transcripts are related to lncRNA regulatory network.