DOI: 10.5061/dryad.408ht
title: Data from: Plasticity in gene transcription explains the differential performance of two invasive fish species

description: Phenotypic plasticity buffers organisms from environmental change and is
 hypothesized to aid the initial establishment of non-indigenous species in
 novel environments and post-establishment range expansion. The genetic
 mechanisms that underpin phenotypically plastic traits are generally
 poorly characterized; however, there is strong evidence that modulation of
 gene transcription is an important component of these responses. Here we
 use RNA sequencing to examine the transcriptional basis of temperature
 tolerance for round and tubenose goby, two non-indigenous fish species
 that differ dramatically in the extent of their Great Lakes invasions
 despite similar invasion dates. We used generalized linear models of read
 count data to compare gene transcription responses of organisms exposed to
 increased and decreased water temperature from those at ambient
 conditions. We identify greater response in the magnitude of
 transcriptional changes for the more successful round goby compared with
 the less successful tubenose goby. Round goby transcriptional responses
 reflect alteration of biological function consistent with adaptive
 responses to maintain or regain homeostatic function in other species. In
 contrast, tubenose goby transcription patterns indicate a response to
 stressful conditions, but the pattern of change in biological functions do
 not match those expected for a return to homeostatic status.
 Transcriptional plasticity plays an important role in the acute thermal
 tolerance for these species; however, the impaired response to stress we
 demonstrate in the tubenose goby may contribute to their limited invasion
 success relative to the round goby. Transcriptional profiling allows the
 simultaneous assessment of the magnitude of transcriptional response as
 well as the biological functions involved in the response to environmental
 stress and is thus a valuable approach for evaluating invasion potential.
description: Round goby transcript
 count dataThis file was generated
 using Corset software to process BAM files of RNAseq reads mapped to a de
 novo assembled transcriptome for nine round goby and enumerate counts of
 reads per transcript as a proxy for transcript
 abundance.RG_counts.txtTubenose goby transcript count dataThis file was generated using Corset software to process BAM files of RNAseq reads mapped to a de novo assembled transcriptome for nine tubenose goby and enumerate counts of reads per transcript as a proxy for transcript abundance.TNG_counts.txtR code for round goby differential expression analysisRG_analysis.RR code for tubenose goby differential expression analysisTNG_analysis.RR code for analysis of shared orthologsThis R code uses information about the reciprocal best BLAST matches between round and tubenose goby transcripts to combine and analyze the count datasets for shared orthologs.RG_TNG_comparision.RReciprocal best hits between round and tubenose goby transcriptsThis file was generated by reciprocally BLASTing the translated longest open reading frame of one species on the other. Pairs of round and tubenose goby transcripts retained in this file are where the pair represent each others best match. This file is required for the analysis of shared orthologs.RBH_blastp_with_masking_and_sw.txtUnix shell script for transcriptome assembly and read mappingThis script was used to perform de novo transcriptome assembly and read mapping for both round and tubenose goby. Its inclusion is primarily to document specific parameters used for these analysis steps.goby_transcriptomics_unix_code.txt