10.5061/DRYAD.J449C
Eyres, Isobel
University of Sheffield
Jaquiéry, Julie
French National Centre for Scientific Research
Sugio, Akiko
Institute for Genetics, Environment and Plant Protection
Duvaux, Ludovic
University of Sheffield
Gharbi, Karim
University of Edinburgh
Zhou, Jing-Jiang
Rothamsted Research
Legeai, Fabrice
Institute for Genetics, Environment and Plant Protection
Nelson, Michaela
University of York
Simon, Jean-Christophe
Institute for Genetics, Environment and Plant Protection
Smadja, Carole M.
French National Centre for Scientific Research
Butlin, Roger
University of Sheffield
Ferrari, Julia
University of York
Data from: Differential gene expression according to race and host plant
in the pea aphid
Dryad
dataset
2016
Acyrthosiphon pisum
Acyrthosiphon pisum
2016-07-28T21:48:03Z
2016-07-28T21:48:03Z
en
https://doi.org/10.1111/mec.13771
6024448 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Host-race formation in phytophagous insects is thought to provide the
opportunity for local adaptation and subsequent ecological speciation.
Studying gene expression differences amongst host races may help to
identify phenotypes under (or resulting from) divergent selection and
their genetic, molecular and physiological bases. The pea aphid
(Acyrthosiphon pisum) comprises host races specializing on numerous plants
in the Fabaceae and provides a unique system for examining the early
stages of diversification along a gradient of genetic and associated
adaptive divergence. In this study, we examine transcriptome-wide gene
expression both in response to environment and across pea aphid races
selected to cover the range of genetic divergence reported in this species
complex. We identify changes in expression in response to host plant,
indicating the importance of gene expression in aphid–plant interactions.
Races can be distinguished on the basis of gene expression, and higher
numbers of differentially expressed genes are apparent between more
divergent races; these expression differences between host races may
result from genetic drift and reproductive isolation and possibly
divergent selection. Expression differences related to plant adaptation
include a subset of chemosensory and salivary genes. Genes showing
expression changes in response to host plant do not make up a large
portion of between-race expression differences, providing confirmation of
previous studies’ findings that genes involved in expression differences
between diverging populations or species are not necessarily those showing
initial plasticity in the face of environmental change.
raw_countScript used to calculate the number of reads mapped to each gene
from the Official Gene Set annotation from AphidBase (Legeai et al. 2010),
by summing each read that overlaps at least one exon of any particular
gene.A. pisum raw countsTranscriptome data from 52 aphid genotypes, reared
both on Vicia faba and on their preferred host plant. Illumina sequencing
performed using HiSeq2000 using 75 bp paired-end reads (v3 chemistry).
Reads mapped to the pea aphid reference genome (IAGC) for each sample
separately using TopHat2 (v2.08). The number of reads mapped to each gene
from the Official Gene Set annotation from AphidBase
(http://aphidbase.com/) was calculated by summing each read that overlaps
at least one exon of any particular gene. Read counts reported for 36,401
genes.ApisumRawCounts.csv