A whole genome analysis of long-terminal-repeat retrotransposon transcription in leaves of Populus trichocarpa L. Subjected to different stresses

Long terminal repeat retrotransposons have a main role in shaping the structure of plant genomes. We used available genomic resources to study as several factors affect the expression of long terminal repeat retrotransposons in Populus trichocarpa. Such factors included redundancy of a retrotransposon in the genome, chromosomal localization, “genotype” of the retrotransposon, and changes in the environment. Overall, we identified and annotated 828 full-length retrotransposons, and analyzed their abundance in the genome. Then, we measured their expression in leaves of plants subjected to several stresses (drought, cold, heat, and salt) as well as in control plants. Our analyses showed that the expression of retrotransposons was generally low, especially that of abundant elements. The transcription of an element was found to be only slightly dependent on its chromosomal localization, rather it depended on the super-family and the lineage to which the retrotransposon belonged. Finally, some retrotransposons were specifically activated by different environmental stresses.