DOI: 10.5061/dryad.65k4n
title: Data from: The transcriptome response of Heliconius melpomene larvae to a novel host plant

description: In the warfare between herbivore and host plant, insects have evolved a
 variety of defensive mechanisms, including allelochemical transformation
 and excretion. Several studies have explored the transcriptome responses
 of insects after host plant shifts to understand these mechanisms. We
 investigated the plastic responses of Heliconius melpomene larvae feeding
 on a native host Passiflora menispermifolia and a less strongly defended
 nonhost species, Passiflora biflora. In total, 326 differentially
 expressed genes were identified, with a greater number upregulated on the
 more strongly defended native host. Functional annotation showed that
 detoxifying enzymes, transporters and components of peritrophic membrane
 were strongly represented. In total, 30 candidate detoxification genes
 were differentially expressed, with glutathione S-transferases (GSTs) and
 UDP-glucuronosyltransferases (UGTs) showing the highest proportion of
 differential expression, 27.3% and 17.3%, respectively. These
 differentially expressed detoxification genes were shown to evolve mainly
 under the influence of purifying selection, suggesting that protein-coding
 evolution has not played a major role in host adaptation. We found only
 one gene, GSTe3, with evidence of adaptive evolution at H40, which is
 around the G-site and might alter enzyme activity. Based on our
 transcriptome and molecular evolution analysis, we suggest that
 transcriptional plasticity of genes in a herbivore may play an important
 role in adaptation to a new host plant.
description: Fig. S1 Gene ontology
 classification of the postman butterfly genes expressed in the
 gut.GEG: gene expressed in
 the gut. GHG: gene highly expressed in the gut.Fig.
 S1.pdfFig. S2 Scatterplot of
 enriched pathways for DEGs in larval gut after host plant
 shift.The size and color of
 the dots represent the gene number and the range of the FDR value,
 respectively. Rich factor is the ratio of the differentially expressed
 gene number to the total gene number in a certain pathway. Four pathway
 databases were used in our analysis, including Kyoto Encyclopedia of Genes
 and Genomes (KEGG) pathway, Reactome, BioCyc and Protein Analysis Through
 Evolutionary Relationships (PANTHER).Fig.
 S2.pdfFig. S3 NJ tree and
 intron positions of HmelGST genes.Phase 0, 1, and 2
 introns are shown by black, blue, and red solid lines,
 respectively.Fig.
 S3.pdfFig. S4 Distributions of
 H. melpomene GST and UGT genes on chromosmes.Scaffold arrangement is
 based on the published linkage map (Heliconius Genome Consortium
 2012).Fig.
 S4.pdfFig. S5 Duplication
 mechanisms and conserved motif of UGT33 family in H.
 melpomene.MCScanX (max gaps = 50)
 was used to identify the segmental and tandem duplications of
 detoxification genes in H. melpomene. This annotated tree was predicted by
 the collinear and tandem relationships of the output from ‘family tree
 plotter of MCScanX’. The characters T and S on the nodes mean tandem and
 segmental duplications, respectively. All the UGT33 family members in Fig.
 4 were used to create sequence logo of signature region
 (http://weblogo.berkeley.edu/logo.cgi).Fig.
 S5.pdfFig. S6 Gene gain and
 loss of GSTs superfamily in Heliconius butterflies.The species tree was
 derived from a phylogeny based on independent nuclear and mitochondrial
 DNA sequences (Beltran et al. 2007). Each class of GSTs from 10 Heliconius
 species were reconstructed the NJ phylogenectic tree. Gene gain and loss
 was estimated with the method of Nam & Nei (2005).Fig.
 S6.pdfTable S1 Primer
 sequences used for quantitative PCR validation.Table
 S1.docxTable S2 Annotation and
 sequences of GST and UGT multigene families in H. melpomene and Danaus
 plexippus genome.Table
 S2.xlsxTable S3 Sequences of
 detoxifying genes were used for PAML analysis.Table
 S3.xlsxTable S4 Summary of
 reads and assembly of the gut transcriptomes in H.
 melpomene.“host” and “non”
 represent the samples from individuals reared with host and non host
 plant, respectively. The number after the sample name means
 replicates.Table
 S4.xlsxTable S5 Annotations and
 expression signals of 326 DEGs in larval gut after host plant
 shift.The protein sequences of
 all the genes were used as queries to Blastp search against nr database in
 NCBI (http://www.ncbi.nlm.nih.gov/). Transporter Classification DataBase
 (TCDB) was searched for the best hits of transporter genes (Saier et al.
 2009). Peritrophin and genes related to nutrient digestion were classified
 by search against PFAM database
 (http://pfam.xfam.org/).Table
 S5.xlsxTable S6 GO enrichment
 ananlysis of the differentially expressed genes.Table
 S6.xlsxTable S7 Orthologous
 divergence of detoxification genes among Heliconius
 butterflies.Table
 S7.xlsxTable S8 Differentially
 expressed genes detected by DESeq2 packageTable
 S8.xlsx