Data from: Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis
Data files
Feb 13, 2024 version files 10.06 GB
-
DS24.HQ.fa
-
DS24.HQ.fa.transdecoder.cds.NVTD.long
-
Female_list.txt
-
GenomicLG.Location.Transcripts.txt
-
Male_list.txt
-
NP.raw.cns
-
NP.raw.vcf
-
README.md
-
SexDETector_orfs.fa.long
Abstract
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.
README
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