DOI: 10.5061/dryad.s7h44j14h
title: Widespread recombination suppression facilitates plant sex chromosome evolution

description: Classical models suggest that recombination rates on sex chromosomes
 evolve in a stepwise manner to localize sexually antagonistic variants in
 the sex in which they are beneficial, thereby lowering rates of
 recombination between X and Y chromosomes. However, it is also possible
 that sex chromosome formation occurs in regions with pre-existing
 recombination suppression. To evaluate these possibilities, we constructed
 linkage maps and a chromosome-scale genome assembly for the dioecious
 plant Rumex hastatulus. This species has a polymorphic karyotype with a
 young neo-sex chromosome, resulting from a Robertsonian fusion between the
 X chromosome and an autosome, in part of its geographical range. We
 identified the shared and neo-sex chromosome using comparative genetic
 maps of the two cytotypes. We found that sex-linked regions of both the
 ancestral and the neo-sex chromosome are embedded in large regions of low
 recombination. Furthermore, our comparison of the recombination landscape
 of the neo-sex chromosome to its autosomal homologue indicates that low
 recombination rates preceded sex linkage. These patterns are not unique to
 the sex chromosomes; all chromosomes were characterized by massive regions
 of suppressed recombination spanning most of each chromosome. This
 represents an extreme case of the periphery-biased recombination seen in
 other systems with large chromosomes. Across all chromosomes, gene and
 repetitive sequence density correlated with recombination rate, with
 patterns of variation differing between repetitive element type. Our
 findings suggest that ancestrally low rates of recombination may
 facilitate the formation and subsequent evolution of heteromorphic sex
 chromosomes.
description: The data here include a whole-genome assembly from Dovetail
 Genomics of a <em>Rumex hastatulus</em> male from
 the XX/XY-cytotype population, an .agp file relating that assembly to a
 linkage map, a pseudomolecule assembly, a repeat-filtered gene annotation,
 and a repeat annotation. ### Genome assembly
     ### Primary assembly <br>       
  hastate_28Sep2018_nbKXS.fasta # Whole-genome assembly received from
 Dovetail Genomics of a TX (XX/XY-cytotype) male       
  no_eq_no_sc_DEGAPPEDhastate_28Sep2018_nbKXS.fasta # The genome assembly
 received from Dovetail Genomics with special characters (line breaks
 within scaffolds, and semicolons and equals signs in scaffold headers)
 removed, because some programs don't expect those characters in
 fastas<br>     <br>     ### Secondary assembly<br>   
  <br>         CHRR_genome.agp # The .agp file relating our linkage
 groups to the scaffolds in the primary assembly. LG identities are as
 follows: A1 = L.7, A2 = L.8, A3 = L.5, A4 = L.3, X = L.10<br>       
  <br>         CHRR_integrated.fa # Pseudomolecules assembled from
 the linkage groups<br>          ### Genome
 annotation<br>     <br>     ### Gene annotations<br>   
      <br>         goodGenes.chrom.gff # Current Augustus genome
 annotation, positioned relative to the linkage maps<br>   
  <br>     ### Repeat annotations<br>         <br>       
  LG.repeats.gff # Repeat annotation, positioned relative to the linkage
 maps