DOI: 10.5061/dryad.j3s5r
title: Data from: Molecular mechanisms of postmating prezygotic reproductive isolation uncovered by transcriptome analysis

description: 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.
description: Commands used for data
 processing and analysisText file containing
 example commands used for data processing and analysiscommands.txtRaw read count dataTab-separated file with information on each locus for all 39 samplesde_master_list_v5.2.4_clean.txtR linear model metadata fileTab-separated file containing metadata for use in the R linear modelsde_master_list_v5.2.4-metadata.txtAnnotation information for lociTab-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.txtpileup_convPython script that converts pileup-format files to allele-specific SNP count text files.Rmarkdown file for generating the Supplementary Methods, Figures and TablesA Rmarkdown file that contains instructions for creating the supplementary information PDF with all supplementary figures, tables, and additional methods details.solDX_report.RmdR source fileR source file that accompanies the Rmarkdown file to perform differential expression calculationssolDX_source.Rsplitreads_tabulatePython script that tabulates and collates the split-read pollen/style allele-based count files.Style-specific unilateral incompatibility differential gene expression resultsTab-separated text file showing results of differential expression on genes showing strong differential expression in the style during UI.style_alleleSpec.filtered.txtPollen-specific unilateral incompatibility differential gene expression resultsTab-separated text file showing results of differential expression on genes showing strong differential expression in the pollen during UI.pollen_alleleSpec.filtered.txtPollen interspecific differential gene expresssion resultsTab-separated text file showing results of differential expression on genes showing expression differences between S. lycopersicum and S. pennellii pollenpollen_tissue_comparison.filtered.txtUnilateral incompatibility differential gene expression raw resultsTab-separated file output from R script showing differential expression results from a comparison of style+pollen tissue during unilateral incompatibility to pollinated and unpollinated stylesUI_R_lm1.rawtableUnilateral incompatibility differential gene expression filtered resultsUI_R_lm1.filtered.txttest2f.metaPollen-specific test R metadata filetest2g.metaStyle-specific test R metadata filehttp://www.ncbi.nlm.nih.gov/bioproject/PRJNA309342BioProject id for all raw reads (http://www.ncbi.nlm.nih.gov/bioproject/PRJNA309342)