DOI: 10.5061/dryad.8d724
title: Data from: Gene duplication and gene expression changes play a role in the evolution of candidate pollen feeding genes in Heliconius butterflies

description: Heliconius possess a unique ability among butterflies to feed on pollen.
 Pollen feeding significantly extends their lifespan, and is thought to
 have been important to the diversification of the genus. We used RNA
 sequencing to examine feeding-related gene expression in the mouthparts of
 four species of Heliconius and one non-pollen feeding species, Eueides
 isabella. We hypothesized that genes involved in morphology and protein
 metabolism might be upregulated in Heliconius because they have longer
 proboscides than Eueides, and because pollen contains more protein than
 nectar. Using de novo transcriptome assemblies, we tested these hypotheses
 by comparing gene expression in mouthparts against antennae and legs. We
 first looked for genes upregulated in mouthparts across all five species
 and discovered several hundred genes, many of which had functional
 annotations involving metabolism of proteins (cocoonase), lipids and
 carbohydrates. We then looked specifically within Heliconius where we
 found eleven common upregulated genes with roles in morphology (CPR
 cuticle proteins), behavior (takeout-like), and metabolism
 (luciferase-like). Closer examination of these candidates revealed that
 cocoonase underwent several duplications along the lineage leading to
 heliconiine butterflies, including two Heliconius-specific duplications.
 Luciferase-like genes also underwent duplication within lepidopterans, and
 upregulation in Heliconius mouthparts. Reverse-transcription PCR confirmed
 that three cocoonases, a peptidase and one luciferase-like gene are
 expressed in the proboscis with little to no expression in labial palps
 and salivary glands. Our results suggest pollen feeding, like other
 dietary specializations, was likely facilitated by adaptive expansions of
 pre-existing genes—and that the butterfly proboscis is involved in
 digestive enzyme production.
description: Annotation file of open
 reading frames from 5 butterfly speciesThis is an annotation
 file for open reading frames (ORFs) from five species of heliconiine
 butterflies. The file includes ORFs from all five species, top BLAST hits,
 and the ortholog group the ORF belongs to. Column headers are as follows:
 "Row#" (row number), "Seq_ID" (sequence ID, including:
 3 letter species code [Eis = Eueides isabella, Hdo = Heliconius doris, Her
 = Heliconius erato, Hmel = Heliconius melpomene, Hsa = Heliconius sara],
 Trinity 'gene' contig ID [e.g., compXXXX_cX], and ORF
 coordinates within contig), "H-ID" (hit ID), "H-Eval"
 (hit e-value), "H-Desc" (hit description), "H-Species"
 (hit species), "H-Type" (hit type), "H-Tag" (hit
 database), "H-Len" (hit length), and "OM"
 (orthocluster membership). NOTE: The program TCW produces two BLAST hits:
 1. Best e-value, 2. best e-value with best evidence. The ones presented
 here are number 2.Annotation_file_of_ORFs_from_5_species_incl_speciesID_and_orthocluster_membership.txtEueides isabella Trinity assemblyThis is a fasta format file containing all mRNA contigs for Eueides isabella. The assembly was performed in Trinity version "20130216" and is a raw output that includes all assembled contigs (see Table 1 for contig counts). Assembly was carried out as described in the Methods section of the publication.Eueides_isabella_Trinity_assembly_Dryad.fastaHeliconius doris Trinity assemblyThis is a fasta format file containing all mRNA contigs for Heliconius doris. The assembly was performed in Trinity version "20130216" and is a raw output that includes all assembled contigs (see Table 1 for contig counts). Assembly was carried out as described in the Methods section of the publication.Heliconius_doris_Trinity_assembly_Dryad.fastaHeliconius erato Trinity assemblyThis is a fasta format file containing all mRNA contigs for Heliconius erato. The assembly was performed in Trinity version "20130216" and is a raw output that includes all assembled contigs (see Table 1 for contig counts). Assembly was carried out as described in the Methods section of the publication.Heliconius_erato_Trinity_assembly_Dryad.fastaHeliconius melpomene Trinity assemblyThis is a fasta format file containing all mRNA contigs for Heliconius melpomene. The assembly was performed in Trinity version "20130216" and is a raw output that includes all assembled contigs (see Table 1 for contig counts). Assembly was carried out as described in the Methods section of the publication.Heliconius_melpomene_Trinity_assembly_Dryad.fastaHeliconius sara Trinity assemblyThis is a fasta format file containing all mRNA contigs for Heliconius sara. The assembly was performed in Trinity version "20130216" and is a raw output that includes all assembled contigs (see Table 1 for contig counts). Assembly was carried out as described in the Methods section of the publication.Heliconius_sara_Trinity_assembly_Dryad.fastaEueides isabella RSEM mapped count dataFile is count data (expression level) output of Trinity contigs from RSEM for Eueides isabella. Column headers contain species name, sex (M or F), specimen ID (see Table S1 for details), and tissue type ("ant" = antennae, "leg" = legs, and "mou" = mouthparts).Eueides_isabella_RSEMmapped_count_data_3tissues_2sexes.txtHeliconius doris RSEM mapped count dataFile is count data (expression level) output of Trinity contigs from RSEM for Heliconius doris. Column headers contain species name, sex (M or F), specimen ID (see Table S1 for details), and tissue type ("ant" = antennae, "leg" = legs, and "mou" = mouthparts).Heliconius_doris_RSEMmapped_count_data_3tissues_2sexes.txtHeliconius erato RSEM mapped count dataFile is count data (expression level) output of Trinity contigs from RSEM for Heliconius erato. Column headers contain species name, sex (M or F), specimen ID (see Table S1 for details), and tissue type ("ant" = antennae, "leg" = legs, and "mou" = mouthparts).Heliconius_erato_RSEMmapped_count_data_3tissues_2sexes.txtHeliconius melpomene RSEM mapped count dataFile is count data (expression level) output of Trinity contigs from RSEM for Heliconius melpomene. Column headers contain sex (M or F), tissue type ("ant" = antennae, "leg" = legs, and "mou" = mouthparts), and sample number. See Table S1 for specimen IDs. Samples labelled "1" are the result of merging two technical replicates (see Methods section of paper for details).Heliconius_melpomene_RSEMmapped_count_data_3tissues_2sexes.txtHeliconius sara RSEM mapped count dataFile is count data (expression level) output of Trinity contigs from RSEM for Heliconius sara. Column headers contain species name, sex (M or F), specimen ID (see Table S1 for details), and tissue type ("ant" = antennae, "leg" = legs, and "mou" = mouthparts).Heliconius_sara_RSEMmapped_count_data_3tissues_2sexes.txt