RT Journal
A1 Coronado-Zamora, Marta
A1 González, Josefa
T1 Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains
JF Genome Research 
JO Genome Research 
YR 2023 
FD September 01 
VO 33 
IS 9 
SP 1541 
OP 1553 
DO 10.1101/gr.277565.122 
UL http://genome.cshlp.org/content/33/9/1541.abstract 
AB Transcriptomes are dynamic, with cells, tissues, and body parts expressing particular sets of transcripts. Transposable elements (TEs) are a known source of transcriptome diversity; however, studies often focus on a particular type of chimeric transcript, analyze single body parts or cell types, or are based on incomplete TE annotations from a single reference genome. In this work, we have implemented a method based on de novo transcriptome assembly that minimizes the potential sources of errors while identifying a comprehensive set of gene–TE chimeras. We applied this method to the head, gut, and ovary dissected from five Drosophila melanogaster natural strains, with individual reference genomes available. We found that ∼19% of body part–specific transcripts are gene–TE chimeras. Overall, chimeric transcripts contribute a mean of 43% to the total gene expression, and they provide protein domains for DNA binding, catalytic activity, and DNA polymerase activity. Our comprehensive data set is a rich resource for follow-up analysis. Moreover, because TEs are present in virtually all species sequenced to date, their role in spatially restricted transcript expression is likely not exclusive to the species analyzed in this work.