Epigenetic Stress and Long-Read cDNA Sequencing of Sunflower (Helianthus annuus L.) Revealed the Origin of Plant Retrotranscriptome

Transposable elements (TEs) contribute not only to genome diversity but also to transcriptome diversity in plants. To unravel the sources of LTR retrotransposon (RTE) transcripts in sunflower, we exploited a recently developed transposon activation method (TEgenesis) along with long-read cDNA Nanopore sequencing. This approach allows for identifying 56 RTE transcripts from different genomic loci including full-length and non-autonomous RTEs. Using the mobilome analysis, we provided a new set of expressed and transpositional active sunflower RTEs for fu-ture studies. Among them, a Ty3 Gypsy RTE called SUNTY3 exhibited ongoing transposition ac-tivity, as detected by eccDNA analysis. We showed that the sunflower genome contains a diverse set of non-autonomous RTEs encoding a single RTE protein, including previously described TR-GAG as well as new categories, TR-RT-RH, TR-RH, and TR-INT-RT. Our results demonstrate that 40% of loci for RTE-related transcripts lack their LTR sequences and resemble conventional eucaryotic genes encoding RTE-related proteins with unknown function. It was evident based on phylogenetic analysis that three solo-RTEs encode GAG (HadGAG1-3) fused to a host protein. These HadGAG proteins have homologs found in other plant species, potentially indicating GAG domestication. Ultimately, we found that the sunflower retrotranscriptome originated from the transcription of active RTEs, non-autonomous RTEs, and gene-like RTE transcripts including those encoding domesticated proteins.