Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis

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 - re..., , , ## 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)
*...