The Gene and Repetitive Element Landscape of the Rye Genome

In the genomics era, the rye genome has been given as little attention by researchers as no other entity in the most renowned triad of cereal crops in the tribe Triticeae: wheat, barley, and rye. Some of the reasons behind this neglection are due to the large size of rye’s genome and its abundance of various classes of repetitive DNA sequences. Despite substantial progress in sequencing and assembling methods, most of its genomic regions, which are made of alternating families of tandem repeats and transposable elements, lie ahead of the undertakers like uncharted dungeons. This chapter outlines the history of research into the molecular organization of the rye genome, from insights into the structure of the repetitive DNA sequences to the recently published annotated chromosome-scale genome assembly. In contrast to previous attempts (Martis et al, Plant Cell 25:3685–3698, 2013; Bauer et al, Plant J 89:853–869, 2017), which were focused on some parts of the rye genome, ours is trying to give a holistic understanding of the genome of this economically important cereal crop. To this end, we will consider the most complete set of classes of DNA sequences and see how their molecular structure and abundance are linked to their chromosomal locations.