DOI: 10.5061/dryad.cnp5hqcf3
title: Gene duplication captures morph-specific promoter usage in the evolution of aphid wing dimorphisms

description: Understanding how morphology evolves requires identifying the types of
 mutations that contribute to changes in development. We integrated
 comparative genomics and transcriptomics to reconstruct the evolution and
 regulation of follistatin paralogs in relation to the evolution of
 aphid-winged and wingless morphs. We discover that different pea aphid
 follistatin duplicates play an essential molecular role in both the male
 and female wing dimorphisms, linking the genetic and environmental control
 of morph determination in each sex, respectively. We also find that an
 ancestral follistatin gene likely had multiple promoters and that the
 follistatin duplicates that evolved wingless-specific expression retained
 only the ancestral wingless-specific promoter. Our work provides a roadmap
 for how alternative promoter usage and subsequent gene duplication can
 enable the evolution of animal form.
description: # Gene duplication ultimately captures morph-specific promoter usage in
 the evolution of aphid wing dimorphisms
 [https://doi.org/10.5061/dryad.cnp5hqcf3](https://doi.org/10.5061/dryad.cnp5hqcf3) ## Description of the data and file structure These data include the RNA-Seq output files like the differentially expressed genes by instar and sex and normalized read counts. They also include final output files for genome annotations, corrected scaffolds, and follistatin tree alignment files. ### Files and variables #### File: Data\_S1\_-\_pisum\_rnaseq\_DEgenes\_byinstar\_andsex.csv **Description:**, Gene list of differentially expressed genes sorted from DESeq2 analysis. ##### Variables * sex: sex denotes female or male samples * instar comparison: instar stages being compared. numbers correspond to stages being compared, e.g., "l21" is the stage 2 to stage 1 comparison, with the winged/wingless morph being contrasted * genes: gives the annotation ID from the reference annotation file #### File: Data\_S2\_-\_pisum\_rnaseq\_normalized\_counts.tsv **Description:** Output normalized read counts for pea aphid RNA-Seq data from the DESeq2 pipeline. #### File: Data\_S3\_-\_follistatin\_gene\_tree\_alignment.fasta **Description:** Alignment file for the follistatin paralogs gene tree coding region. #### File: Data\_S4\_-\_v3\_XChrWithApi-wlinsert-scaffold.fa **Description:** Correction of the genome annotation for the api region on the X chromosome. #### File: Data\_S5\_-\_HS2\_v3annotation\_edited\_wFs3\_fixed.gtf **Description:** Modified genome annotation of v3 pea aphid reference genome with the scaffold from DataS4 #### File: Data\_S6\_-\_foxglove\_flye\_fs\_contigs.fa **Description:** Contig assemblies of *Aulacorthum solani* for the follistatin paralogs. #### File: Data\_S7\_-\_church\_fsContigs\_chur.fa **Description:** Contig assemblies of *Acyrthosiphon churchillense* for the follistatin paralogs. #### File: Table\_S1\_-\_genomic\_intervals\_of\_follistatins\_used.xlsx **Description:** A reference to the regions of available genomes and the intervals where follistatin paralogs were identified. ##### Variables * Species corresponds to aphid species used * Region denotes paralog * Genome source names the reference/source sequence * Scaffold specifies the name of the scaffold in the annotation * Start/End gives the interval on that scaffold * Notes include peripheral comments #### File: Table\_S2\_-\_accessions\_of\_genomic\_files.xlsx **Description:** Information of source genomic files used in comparative analyses ##### Variables * Species gives the Latin aphid species name * Line gives the strain name when available * Type gives the sequencing source * HybPiper specifies whether the sequence was used as "queries" or "target" * Source gives the source of the genomic files with the NCBI SRA accession when available #### File: Table\_S3\_-\_rnaseq\_accessions.xlsx **Description:** Specifies the source of RNA-Seq data from alternative splicing analysis ##### Variables * Species describes the aphid species * Line is the strain when specified * Source denotes where the data came from * Dev Stages include the nymphal states of the data * Sex specifies which samples were available * Wing Morphs correspond to winged and wingless data * replicates specify study design * total samples gives the number of files available * Notes adds additional comments ## Access information NA