Large-scale long terminal repeat insertions found to produce a significant set of novel transcripts in cotton

TEs (transposable elements), especially LTRs, are known to play an important role in determining the basic genome structure and influencing the expression of functional genes. Insertion of TE or LTR fragments may also create novel transcription start sites (TSSs) to initiate transcription in the host genome. New intergenic transcripts were thought to be created by terminal repeat retrotransposon insertions using a combination of de novo and homology-based strategy in maize.