DOI: 10.5061/dryad.gf1vhhmsj
title: Data from: Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis

description: Polyploidization may precipitate dramatic changes to the genome, including
 chromosome rearrangements, gene loss, and changes in gene expression. In
 dioecious plants, the sex-determining mechanism may also be disrupted by
 polyploidization, with the potential evolution of hermaphroditism.
 However, while dioecy appears to have persisted through a ploidy
 transition in some species, it is unknown whether the newly formed
 polyploid maintained its sex-determining system uninterrupted, or whether
 dioecy re-evolved after a period of hermaphroditism. Here, we develop a
 bioinformatic pipeline using RNA-sequencing data from natural populations
 to demonstrate that the allopolyploid plant Mercurialis canariensis
 directly inherited its sex-determining region from one of its diploid
 progenitor species, M. annua, and likely remained dioecious throughout the
 transition. Interestingly, the sex-determining region of M. canariensis is
 smaller than that of its diploid progenitor, suggesting that the non -
 recombining region of M. annua expanded subsequent to the polyploid origin
 of M. canariensis. Furthermore, we find some evidence for sexual
 subfunctionalization of homeologous pairs, suggesting that polyploids may
 use gene duplicates created by polyploidization to resolve sexual
 antagonism.
description: ## Data files and pipeline for: Dioecy and chromosomal sex determination
 are maintained through allopolyploid speciation in the plant genus
 Mercurialis Melissa A. Toups, Beatriz Vicoso, and John R. Pannell PLoS
 Genetics, 2022 ### Main Data Files #### Transcriptomes: * DS24.HQ.fa - raw
 long read assembly computed by Lausanne Bioinformatics *
 DS24.HQ.fa.transdecoder.cds.NVTD.long - Long read assembly, longest
 isoform only, ORFs * SexDETector\_orfs.fa.long - transcriptome assembly of
 M. annua, filtered for longest isoform using Spice\_Finder.pl #### vcf
 files: * NP.raw.vcf - raw SNP file * NP.raw.cns - raw CNS file (vcf for
 all sites) #### Important Text Files: GenomicLG.Location.Transcripts.txt -
 genomic location of M. annua transcripts in the M. annua linkage map
 Column info: * Annua (ortholog name in Mercuralis annua genome) * target
 (scafflold in Mercurialis annua genome) * sd_lm (PAR - pseudoautosomal
 region, SL - sex-linked, Au - autosomal in Mercurialis annua genome) * LG
 - linkage group in Mercurialis annua genome * cm - linkage group position
 in male Mercurialis annua linkage map * cf- linkage group position in
 female Mercurialis annua linkage map * Female_list.txt & Male_list.txt
 - references samples that are female and male, respectively, in the vcfs
 #### Sample Information (see bioproject PRJNA835047 in SRA archive for
 sequences): DS\_18 RNA seq of M. canariensis: mature leaves from adult
 female DS\_33 RNA seq of M. canariensis: mature leaves from adult male
 DS\_19 RNA seq of M. canariensis: mature leaves from adult female DS\_11
 RNA seq of M. canariensis: mature leaves from adult male 206NP7F RNA seq
 of M. canariensis: mature leaves from adult female DS\_35 RNA seq of M.
 canariensis: mature leaves from adult male DS\_22 RNA seq of M.
 canariensis: mature leaves from adult female DS\_29 RNA seq of M.
 canariensis: mature leaves from adult male DS\_23 RNA seq of M.
 canariensis: mature leaves from adult female DS\_15 RNA seq of M.
 canariensis: mature leaves from adult male DS\_25 RNA seq of M.
 canariensis: mature leaves from adult female DS\_4 RNA seq of M.
 canariensis: mature leaves from adult male