Data from: Phylogenomics resolves key relationships in Rumex and uncovers a dynamic history of independently evolving sex chromosomes

Sex chromosomes have evolved independently many times across eukaryotes.
Despite a considerable body of literature on sex chromosome evolution, the
causes and consequences of variation in their formation, degeneration, and
turnover remain poorly understood. Chromosomal rearrangements are thought
to play an important role in these processes by promoting or extending the
suppression of recombination on sex chromosomes. Sex chromosome variation
may also contribute to barriers to gene flow, limiting introgression among
species. Comparative approaches in groups with sexual system variation can
be valuable for understanding these questions. Rumex is a diverse genus of
flowering plants harboring significant sexual system and karyotypic
variation, including hermaphroditic and dioecious clades with XY (and XYY)
sex chromosomes. Previous disagreement in the phylogenetic relationships
among key species have rendered the history of sex chromosome evolution
uncertain. Resolving this history is important for investigating the
interplay of chromosomal rearrangements, introgression, and sex chromosome
evolution in the genus. Here, we use new transcriptome assemblies from 11
species representing major clades in the genus, along with a whole-genome
assembly generated for a key hermaphroditic species. Using phylogenomic
approaches, we find evidence for the independent evolution of sex
chromosomes across two major clades, and introgression from unsampled
lineages likely predating the formation of sex chromosomes in the genus.
Comparative genomic approaches revealed high rates of chromosomal
rearrangement, especially in dioecious species, with evidence for a
complex origin of the sex chromosomes through multiple chromosomal
fusions. However, we found no evidence of elevated rates of fusion on the
sex chromosomes in comparison with autosomes, providing no support for an
adaptive hypothesis of sex chromosome expansion due to sexually
antagonistic selection. Overall, our results highlight a complex history
of karyotypic evolution in Rumex, raising questions about the role that
chromosomal rearrangements might play in the evolution of large
heteromorphic sex chromosomes.