Genome skimming for plant retrotransposon identification and expression analysis

Retrotransposons (repeated DNA sequences capable of moving across the genome) contribute considerably to the evolution of plant genomes. They are involved in determining variation of genome size, in structuring the chromatin, in altering the regulatory patterns of gene regions, also changing the epigenetic setting of DNA. Sequencing of genomic DNA at low coverage (also called genome skimming) and consequent sequence assembling is a practice that can be used in structural genomics to identify and collect retrotransposon sequences in eukaryotic genomes and to gain insights into plant genome structure and evolution. The replicative mechanism of retrotransposons starts with their transcription. Therefore, it is important to have strategies that allow whole genome analysis of their expression. Besides reporting many studies that use genome skimming and assembling for structural genomics, here we point out the use of genome skimming to produce a whole genome library of these elements, to be used as a reference for analysis of retrotransposon expression in RNA-seq libraries, evidencing pros and cons of such a strategy.