Comprehensive analysis of both long and short read transcriptomes of a clonal and a seed-propagated model plant species reveal the prerequisites for transcriptional activation of autonomous and non-autonomous transposons in plants

Abstract Background Transposable element (TE) transcription is a precursor to its mobilisation in host genomes. However, the characteristics of expressed TE loci, the identification of self-competent transposon loci contributing to new insertions, and the genomic conditions permitting their mobilisation remain largely unknown. Results Using Vitis vinifera embryogenic callus, we explored the impact of biotic stressors on transposon transcription through the exposure of the callus to live cultures of an endemic grapevine yeast, Hanseniaspora uvarum. We found that only 1.7%-2.5% of total annotated TE loci were transcribed, of which 5%-10% of these were full-length, and the expressed TE loci exhibited a strong location bias towards expressed genes. These tendencies were also observed in Arabidopsis thaliana wild-type and ibm2, but not in ddm1 mutant. Moreover, differentially expressed TE loci in the grapevine model tended to share expression patterns with co-localised differentially expressed genes. Utilising nanopore cDNA sequencing, we found a strong correlation between the inclusion of intronic TEs in gene transcripts and the presence of premature termination codons in these transcripts. Finally, we identified low levels of full-length transcripts deriving from structurally autonomous TE loci in the grapevine model. Conclusion Our observations in two disparate plant models representing clonally and seed propagated plant species reveal a closely connected transcriptional relationship between TEs and co-localised genes, particularly when the epigenetic silencing system is intact. We found that the stress treatment alone was insufficient to induce large-scale full-length transcription from structurally competent TE loci, a necessity for non-autonomous and autonomous mobilisation.