Adjustments of aerobic metabolic processes are critical components of organismal responses to environmental change that require tight co-ordination between the nuclear and mitochondrial genomes. Intraspecific differences in mitochondrial genotype can affect gene transcription in both genomes. Thus, variation in mitochondrial genotype may be associated with differences in the plasticity of gene expression when organisms are faced with changes in environmental conditions. Cold acclimation is known to result in metabolic responses involving increases in mitochondrial amount and capacity, suggesting that low temperatures may pose a particular challenge when co-ordinating the functions of the nuclear and mitochondrial genomes. In this study, we utilized RNA-seq to assess transcriptome-wide gene expression in the muscle of Atlantic killifish (Fundulus heteroclitus) from a population that contains segregating variation in mitochondrial genotype. We examined gene expression plasticity in response to 5°C acclimation and the effects of mitochondrial genotype on this plasticity. Cold acclimation resulted in changes in gene expression consistent with up-regulation of genes involved in many cellular functions, including spliceosomal and proteasomal processes, and with down-regulation of genes involved in extracellular matrix, muscle contraction and oxidative phosphorylation functions. There were few differences in gene expression between killifish with different mitochondrial genotypes: 14 genes demonstrated significant interactions between mitochondrial genotype and acclimation temperature and 3 genes demonstrated effects of mitochondrial genotype alone. These results indicate that variation in mitochondrial genotype has modest effects on gene expression; the majority of which are revealed as differences in plasticity as a result of environmental change.
Usage Notes:
Unique_Exon_Read_Counts
RNA-seq read count data for killifish individuals with northern or southern mitochondrial genotypes that were acclimated to either 15 or 5 degrees Celsius.
Gene_IDs_Names_Lengths
Reduced gene model information for the Fundulus heteroclitus genome containing gene IDs, gene names and gene lengths. Information was obtained from the F. heteroclitus genome assembly (http://marmot.bio.indiana.edu:7151/EvidentialGene/killifish/).
GO_IDs
Orthologous GO annotations for the gene models in the F. heteroclitus genome assembly (http://marmot.bio.indiana.edu:7151/EvidentialGene/killifish/).
KEGG_IDs
Orthologous KEGG annotations for the gene models in the F. heteroclitus genome assembly (http://marmot.bio.indiana.edu:7151/EvidentialGene/killifish/).
RNA-seq and enrichment analyses R script
R code used for analysis of RNA-seq read count data and GO/KEGG enrichment analyses. All data used in these analyses are found in the additional files associated with this Dryad submission.