DOI: 10.5061/dryad.g1jwstqnd
title: Data from: Changes in gene expression during female reproductive development in a colour polymorphic insect

description: Pleiotropy (multiple phenotypic effects of single genes) and epistasis
 (gene interaction) have key roles in the development of complex
 phenotypes, especially in polymorphic taxa. The development of discrete
 and heritable phenotypic polymorphisms often emerges from major-effect
 genes that interact with other loci and have pleiotropic effects on
 multiple traits. We quantified gene expression changes during ontogenetic
 colour development in a polymorphic insect (damselfly: Ischnura elegans),
 with three heritable female morphs, one being a male mimic. This female
 colour polymorphism is maintained by male mating harassment and sexual
 conflict. Using transcriptome sequencing and de novo assembly, we
 demonstrate that all three morphs downregulate gene expression during
 early colour development. The morphs become increasingly differentiated
 during sexual maturation and when developing adult colouration. These
 different ontogenetic trajectories arise because the male-mimic shows
 accelerated (heterochronic) development, compared to the other female
 morphs. Many loci with regulatory functions in reproductive development
 are differentially regulated in the male-mimic, including upstream and
 downstream regulators of ecdysone signalling and transcription factors
 potentially influencing sexual differentiation. Our results suggest that
 long-term sexual conflict does not only maintain this polymorphism, but
 has also modulated the evolution of gene expression profiles during colour
 development of these sympatric female morphs.
description: This dataset contains data for gene expression analyses,
 reproductive failure data and maturation time data for the common bluetail
 damselfly <em>Ischnura elegans</em>. The data for gene
 expression analyses includes a transcriptome (Trinity.fasta) and
 gene-level counts (counts.txt). These files stem from RNA-Seq data
 collected from whole bodies of field-caught individuals and individuals
 raised in outdoor mesocosms. Raw RNA-Seq reads are available through
 NCBI’s Sequence Read Archives (BioProject # PRJNA624641). The
 transcriptome, based on all 83 samples, was assembled in TRINITY after
 quality control and trimming. Gene-level counts for the 27 samples in the
 experimental design (Exp_design.csv) were then obtained by mapping the
 reads on the transcriptome and clustering transcripts based on sequence
 and expression similarity in CORSET. After excluding
 lowly expressed transcripts, transcripts were blasted against the
 non-redundant database in NCBI. Blast hits were then mapped to Gene
 Ontology (GO) terms using Blast2GO. The resulting file contains
 transcript-level annotations (blast2go_mapping_20180521_1147.txt). Gene
 ontology terms were then extracted for each gene cluster and are also
 included in this dataset (AnnotationsByCluster.txt).
 The gene-level counts (counts.txt), experimental design
 (Exp_design.csv) and gene-level ontology terms (AnnotationsByCluster.txt)
 are used in differential expression analyses, vector correlation analyses
 and GO enrichment analyses presented in this study. All these analyses can
 be reproduced using the R Markdown script IschnuraColourDevelopment.Rmd.
 This study also examines in more detail a subset of differentially
 expressed genes. The GO names and descriptions of this gene subset
 (DEG_Gos_expanded.tsv) are also included in the dataset. This file is also
 used in the R Markdown script to identify genes with gene regulatory
 functions among the subset of interest. Reproductive
 failure data (Rep_Failure.csv) come from field-collected individuals that
 were caught while mating and brought into an indoor laboratory for
 ovipostion. Eggs were then photographed and counted. Reproductive failure
 data were collected between 2001 and 2017 in 18 natural populations of
 <i>I. elegans</i> in Southern Sweden. Finally, colour
 maturation data (Morph_Maturation.csv) was collected from field-caught
 females which were raised in outdoor mesocosms in the summers of
 2015-2017. Females were marked with wing colour codes and monitored daily
 to determine the duration of colour transitions. These two data files are
 also used in the R Markdown script for this study.