DOI: 10.5061/dryad.r3t28r6
title: Data from: Comparative proteomics of stenotopic caddisfly Crunoecia irrorata identifies acclimation strategies to warming

description: Species’ ecological preferences are often deduced from habitat
 characteristics thought to represent more or less optimal conditions for
 physiological functioning. Evolution has led to stenotopic and eurytopic
 species, the former having decreased niche breadths and lower tolerances
 to environmental variability. Species inhabiting freshwater springs are
 often described as being stenotopic specialists, adapted to the stable
 thermal conditions found in these habitats. Whether due to past local
 adaptation these species have evolved or have lost intra-generational
 adaptive mechanisms to cope with increasing thermal variability has, to
 our knowledge, never been investigated. By studying how the proteome of a
 stenotopic species changes as a result of increasing temperatures we
 investigate if the absence or attenuation of molecular mechanisms is
 indicative of local adaptation to freshwater springs. An understanding of
 compensatory mechanisms is especially relevant as spring-specialists will
 experience thermal conditions beyond their physiological limits due to
 climate change. In this study, the stenotopic species Crunoecia irrorata
 (Trichoptera: Lepidostomatidae, Curtis 1834) was acclimated to 10, 15 and
 20 °C for 168 h. We constructed a homology-based database, and via liquid
 chromatography-tandem mass spectrometry (LC-MS/MS)-based shotgun
 proteomics identified 1358 proteins. Differentially abundant proteins and
 protein norms of reaction revealed candidate proteins and molecular
 mechanisms facilitating compensatory responses such as trehalose
 metabolism, tracheal system alteration, and heat shock protein regulation.
 A species-specific understanding of compensatory physiologies challenges
 the characterization of species as having narrow tolerances to
 environmental variability if that characterization is based on occurrences
 and habitat characteristics alone.
description: Protein sequences of
 translated gene-prediction sequences of five Trichoptera
 speciesThis protein sequence
 file (FASTA format) contains in-silico translated gene prediction
 sequences of the following four Trichoptera species (DOIs leading to the
 original publication in which these data were generated are given in
 parentheses after the species name): Stenopsyche tienmushanensis
 (10.1093/gigascience/giy143), Glossosoma conformis
 (10.1016/j.scitotenv.2018.03.109), Sericostoma personatum
 (10.1111/mec.14292) and Limnephilus lunatus (10.1093/nar/gku983).
 Additionally the FASTA file contains in-silico predicted protein sequences
 of the transcriptome of Micropterna lateralis
 (10.1080/01650424.2016.1200727). For the bioinformatics pipeline on how
 these protein sequences were generated from the original data see Material
 & Methods in our publication. Additionally, the FASTA files contains
 heat shock protein sequences downloaded from NCBI (taxonomic scope
 Insecta, see publication). This file was used as a homology in-silico
 digested search space in MaxQuant to identify proteins in samples of
 Crunoecia irrorata reared at three different temperatures via
 LC-MS/MS.Trichoptera_PredictedProteinSequences.fastaBioinformatic commands used to construct the protein databaseThis file specifies the commands and parameters (utilizing e.g. TransDecoder, QIIME, blast, Unix commands) used to construct the amino-acid database used in MaxQuant as in-silico digested homology search space for protein identification and can be applied to the self-generated or publicly available genome and transcriptome sequences.Commands.pdf