Data from: Mitochondrial genotype and phenotypic plasticity of gene expression in response to cold acclimation in killifish

AbstractAdjustments 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 notesUnique_Exon_Read_CountsRNA-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_LengthsReduced 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_IDsOrthologous GO annotations for the gene models in the F. heteroclitus genome assembly (http://marmot.bio.indiana.edu:7151/EvidentialGene/killifish/).KEGG_IDsOrthologous 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 scriptR 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.摘要：有氧代谢过程的调控是生物体响应环境变化的核心环节，该过程依赖核基因组与线粒体基因组的精密协同。线粒体基因型的种内差异可影响两个基因组的基因转录水平。据此推测，当生物体遭遇环境条件变化时，线粒体基因型变异可能与基因表达可塑性的差异存在关联。已知冷驯化可引发代谢响应，表现为线粒体数量与功能能力的提升，这提示低温环境在协调核与线粒体基因组功能时可能面临特殊挑战。本研究借助RNA测序（RNA-seq）技术，对携带线粒体基因型分离变异的大西洋鳉（*Fundulus heteroclitus*）肌肉组织开展全转录组基因表达分析。我们探究了5℃驯化下的基因表达可塑性，以及线粒体基因型对该可塑性的调控效应。冷驯化诱导的基因表达变化呈现出多类细胞功能相关基因的上调特征，涵盖剪接体与蛋白酶体过程相关基因；同时伴随细胞外基质、肌肉收缩及氧化磷酸化功能相关基因的下调。不同线粒体基因型的大西洋鳉个体间基因表达差异较小：14个基因呈现出线粒体基因型与驯化温度间的显著交互效应，另有3个基因仅表现出线粒体基因型的独立影响。上述结果表明，线粒体基因型变异对基因表达的影响较为温和，其中多数差异体现为环境变化所引发的可塑性差异。 使用说明： 1. 专属外显子读段计数（Unique_Exon_Read_Counts）：针对分别驯化于15℃或5℃环境、携带北方或南方线粒体基因型的大西洋鳉个体的RNA-seq读段计数数据。 2. 基因ID、名称与长度（Gene_IDs_Names_Lengths）：大西洋鳉基因组的简化基因模型信息，包含基因ID、基因名称及基因长度。相关数据取自大西洋鳉基因组组装结果（http://marmot.bio.indiana.edu:7151/EvidentialGene/killifish/）。 3. GO基因本体ID（GO_IDs）：取自该大西洋鳉基因组组装结果的基因模型的直系同源GO注释信息（http://marmot.bio.indiana.edu:7151/EvidentialGene/killifish/）。 4. KEGG通路ID（KEGG_IDs）：取自该大西洋鳉基因组组装结果的基因模型的直系同源KEGG注释信息（http://marmot.bio.indiana.edu:7151/EvidentialGene/killifish/）。 5. RNA-seq与富集分析R脚本（RNA-seq and enrichment analyses R script）：用于RNA-seq读段计数数据分析及GO/KEGG富集分析的R代码。本研究所有分析所用数据均可在本次Dryad提交的附属文件中获取。