Little is known about the physiological responses and genetic mutations associated with reproductive isolation between species, especially for postmating prezygotic isolating barriers. Here, we examine changes in gene expression that accompany the expression of ‘unilateral incompatibility’ (UI)—a postmating prezygotic barrier in which fertilization is prevented by gamete rejection in the reproductive tract [in this case of pollen tubes (male gametophytes)] in one direction of a species cross, but is successful in the reciprocal crossing direction. We use whole-transcriptome sequencing of multiple developmental stages of male and female tissues in two Solanum species that exhibit UI to: (i) identify transcript differences between UI-competent and UI noncompetent tissues; (ii) characterize transcriptional changes specifically associated with the phenotypic expression of UI; and (iii) using these comparisons, evaluate the behaviour of a priori candidate loci for UI and identify new candidates for future manipulative work. In addition to describing transcriptome-wide changes in gene expression that accompany this isolating barrier, we identify at least five strong candidates for involvement in postmating prezygotic incompatibility between species. These include three novel candidates and two candidates that are strongly supported by prior developmental, functional, and quantitative trait locus mapping studies. These latter genes are known molecular players in the intraspecific expression of mate choice via genetic self-incompatibility, and our study supports prior evidence that these inter- and intraspecific postmating prezygotic reproductive behaviours share specific genetic and molecular mechanisms.
Commands used for data processing and analysis
Text file containing example commands used for data processing and analysis
commands.txt
Raw read count data
Tab-separated file with information on each locus for all 39 samples
de_master_list_v5.2.4_clean.txt
R linear model metadata file
Tab-separated file containing metadata for use in the R linear models
de_master_list_v5.2.4-metadata.txt
Annotation information for loci
Tab-separated file with gene annotations and coordinates. No coordinates or annotation are available for de novo assembled transcripts labelled "Unmap", "LycoD", or "PennD." Genes starting with Solyc##x are unannotated regions with reference coordinates.
de_master_list_v5.2.4_annot.txt
pileup_conv
Python script that converts pileup-format files to allele-specific SNP count text files.
Rmarkdown file for generating the Supplementary Methods, Figures and Tables
A Rmarkdown file that contains instructions for creating the supplementary information PDF with all supplementary figures, tables, and additional methods details.
solDX_report.Rmd
R source file
R source file that accompanies the Rmarkdown file to perform differential expression calculations
solDX_source.R
splitreads_tabulate
Python script that tabulates and collates the split-read pollen/style allele-based count files.
Style-specific unilateral incompatibility differential gene expression results
Tab-separated text file showing results of differential expression on genes showing strong differential expression in the style during UI.
style_alleleSpec.filtered.txt
Pollen-specific unilateral incompatibility differential gene expression results
Tab-separated text file showing results of differential expression on genes showing strong differential expression in the pollen during UI.
pollen_alleleSpec.filtered.txt
Pollen interspecific differential gene expresssion results
Tab-separated text file showing results of differential expression on genes showing expression differences between S. lycopersicum and S. pennellii pollen
pollen_tissue_comparison.filtered.txt
Unilateral incompatibility differential gene expression raw results
Tab-separated file output from R script showing differential expression results from a comparison of style+pollen tissue during unilateral incompatibility to pollinated and unpollinated styles
UI_R_lm1.rawtable
Unilateral incompatibility differential gene expression filtered results
UI_R_lm1.filtered.txt
test2f.meta
Pollen-specific test R metadata file
test2g.meta
Style-specific test R metadata file
http://www.ncbi.nlm.nih.gov/bioproject/PRJNA309342
BioProject id for all raw reads (http://www.ncbi.nlm.nih.gov/bioproject/PRJNA309342)