DOI: 10.5061/dryad.w6m905qzj
title: Data from: Phylogenomics resolves key relationships in Rumex and uncovers a dynamic history of independently evolving sex chromosomes

description: 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.
description: Samples for live tissue were sourced from the USDA GRIN network
 (USDA Agricultural Research Service), the Southwest China Wildlife
 Germplasm Genobank (http://www.genobank.org/), and the collections from
 Spencer Barrett’s lab, totaling 10 species. Plants were grown under
 glasshouse conditions between 2018 and 2020. Because many Rumex species
 are perennials, we collected leaf, bud, and pollen tissue
 opportunistically based on availability. Leaf and bud tissue were
 collected directly into LN2 using sterilized forceps. Pollen was collected
 using keif boxes (WACKY WILLYS,Inc. BC, Canada) and either frozen in LN2
 or germinated prior to sequencing using the medium developed in Adhikari
 & Campbell (1998).  We used Trinity v2.11.0
 (Grabherr et al. 2011) with each of the 10 species to create a
 transcriptome assembly for the sequencing libraries (representing a single
 tissue/individual combination). These assemblies were combined for each
 species and then reduced to representative species-wide transcriptomes
 using the traa2cds.pl script from EvidentialGene (Gilbert 2013) and
 retaining the primary transcript for each gene model.
description: # Rumex transcriptome assembly cds filtered to main transcripts
 [https://doi.org/10.5061/dryad.w6m905qzj](https://doi.org/10.5061/dryad.w6m905qzj) ## Description of the data and file structure Transcriptome assembly from RNA-Seq of leaf, bud, and pollen tissue. ### Files and variables #### File: rumex\_cds\_filtered\_assemblies.zip **Description:** This zip folder contains 11 fasta files, representing the 10 assembled Rumex transcriptomes plus the coding sequences from a previously published genome annotation of Rumex *hastatulus*. ## Code/software All code required to replicate analysis of the transcriptomic data is available at [https://github.com/mhibbins/RumexComparative](https://github.com/mhibbins/RumexComparative). ## Access information Other publicly accessible locations of the data: * Raw RNA-Seq reads uploaded to SRA under BioProject PRJNA698922 Data was derived from the following sources: * n/a