Fundamentally different repetitive element composition of sex chromosomes in Rumex acetosa.

BACKGROUND AND AIMS Dioecious species with well-established sex chromosomes are rare in the plant kingdom. Most sex chromosomes increase in size but no comprehensive analysis of the kind of sequences which drive this expansion has been presented. Here, we analyse sex chromosome structure in common sorrel (Rumex acetosa), a dioecious plant with XY1Y2 sex determination, and we provide the first chromosome specific repeatome analysis for a plant species possessing sex chromosomes. METHODS We flow-sorted and separately sequenced sex chromosomes and autosomes in R. acetosa using the two-dimensional Fluorescence In Situ Hybridization in Suspension (FISHIS) method and Illumina sequencing. We identified and quantified individual repeats using RepeatExplorer, Tandem Repeat Finder and the Tandem Repeats Analysis Program. We employed Fluorescence In Situ Hybridization (FISH) to analyse chromosome localisation of satellites and transposons. KEY RESULTS We identified a number of novel satellites, which have, in a fashion similar to previously known satellites, significantly expanded on the Y chromosome but not as much on the X nor on autosomes. Additionally, the size increase of Y chromosomes is caused by non-LTR and LTR retrotransposons, while only the latter ones contribute to the enlargement of the X chromosome. However, the X chromosome is populated by different LTR retrotransposon lineages than Y chromosomes. CONCLUSIONS The X and Y chromosomes significantly diverged in terms of repeat composition. The lack of recombination probably contributed to the expansion of diverse satellites and microsatellites and faster fixation of newly inserted transposable elements (TEs) on the Y chromosomes. In addition, X and Y chromosomes, despite similar total counts of TEs, significantly differ in the representation of individual TE lineages, which indicates that transposons proliferate preferentially either in the paternal or maternal lineage.