DOI: 10.5061/dryad.f7m0cfxt8
title: Transcriptome assembly for: Genetic compensation rather than genetic assimilation drives the evolution of plasticity in response to mild warming across latitudes in a damselfly

description: Global warming is causing plastic and evolutionary changes in the
 phenotypes of ectotherms. Yet, we have limited knowledge on how the
 interplay between plasticity and evolution shapes thermal responses and
 underlying gene expression patterns. We assessed thermal reaction norm
 patterns across the transcriptome and identified associated molecular
 pathways in northern and southern populations of the damselfly Ischnura
 elegans. Larvae were reared in a common garden experiment at the mean
 summer water temperatures experienced at the northern (20 °C) and southern
 (24 °C) latitudes. This allowed a space-for-time substitution where the
 current gene expression levels at 24 °C in southern larvae are a proxy for
 the expected responses of northern larvae under gradual thermal evolution
 to the predicted 4 °C warming. Most differentially expressed genes showed
 fixed differences across temperatures between latitudes, suggesting that
 thermal genetic adaptation will mainly evolve through changes in
 constitutive gene expression. Northern populations also frequently showed
 plastic responses in gene expression to mild warming, while southern
 populations were much less responsive to temperature. Thermal responsive
 genes in northern populations showed to a large extent a pattern of
 genetic compensation, i.e. gene expression that was induced at 24 °C in
 northern populations remained at a lower constant level in southern
 populations, and were associated with metabolic and translation pathways.
 There was instead little evidence for genetic assimilation of an initial
 plastic response to mild warming. Our data therefore suggest that genetic
 compensation rather than genetic assimilation may drive the evolution of
 plasticity in response to mild warming in this damselfly species.
description: Pooled RNA samples (n=24) were sent to BGI, Hong Kong where 160
 bp libraries were constructed using the TruSeq technology. Next, the
 libraries were 101 bp Paired-End sequenced on a Hiseq4000 platform. Raw
 reads were visually inspected with FastQC version 0.11.5 (Andrews, 2010)
 and trimmed using Trimmomatic version 0.36 (Bolger et al. 2014) for
 adapter sequences. The trimmed reads were <i>de novo
 </i>assembled with Trinity version 2.2.0 (Grabherr et al., 2011)
 using default parameters (kmer length = 25). Duplicate
 transcripts were removed by clustering the assembly using CD-HIT-EST
 version 4.6.6 (Li & Godzik, 2006) at 95% sequence similarity
 resulting in an assembly containing only the representative sequences of
 the detected clusters. Furthermore, Repeatmasker version 4.0.6 was used to
 remove transcripts containing ribosomal RNA. The completeness of the
 assembly was assessed using Benchmarking Universal Single-Copy Orthologs
 (BUSCO) version 1.22 (Simão, Waterhouse, Ioannidis, Kriventseva, &
 Zdobnov, 2015) which measures the number of near-universal single-copy
 orthologs in the assembly that are stored in the Arthropods database from
 OrthoDB. Only transcripts with at least one read per million in at least
 two samples were kept.