Modularity Facilitates Flexible Tuning of Plastic and Evolutionary Gene Expression Responses during Early Divergence.
Modularity Facilitates Flexible Tuning of Plastic and Evolutionary Gene Expression Responses during Early Divergence.
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DOI：
10.1093/gbe/evx278
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发表时间：
2018-01-01
影响因子：
3.3
通讯作者：
Primmer CR
中科院分区：
文献类型：
--
作者：
Mäkinen H;Sävilammi T;Papakostas S;Leder E;Vøllestad LA;Primmer CR
基因表达变化已被认为是适应不断变化的环境条件的重要驱动力。在分化的早期阶段，对复杂基因表达网络中可塑性和进化反应的相对作用知之甚少。大的基因表达数据集，加上在硅片上的方法，以确定共表达模块，现在使系统遗传学方法也在非模式物种更好地了解基因表达反应在早期分歧。在这里，我们将基因共表达分析与群体遗传学相结合，以小鲑鱼种群为模型系统，分离表达网络中的塑料和群体（进化）效应。我们发现，塑料和人口的影响是高度可变的6个模块之间，塑料的影响解释了更大比例的总特征基因的表达比人口的影响。使用QST-FST比较16，622个注释的转录本对群体效应进行更详细的分析，揭示了基因表达在模块内和整体水平上遵循中性预期。此外，两个模块表现出丰富的基因编码的早期发育性状，以前已被确定为重要的表型性状的热响应在同一模型系统中，表明共表达分析可以捕获表达模式的生态重要性状。我们认为，模块特定的反应可能有助于灵活调整表达水平，以当地的热条件。总的来说，我们的研究表明，可塑性和中性进化是该系统中热适应早期阶段基因表达差异的主要驱动因素。
Gene expression changes have been recognized as important drivers of adaptation to changing environmental conditions. Little is known about the relative roles of plastic and evolutionary responses in complex gene expression networks during the early stages of divergence. Large gene expression data sets coupled with in silico methods for identifying coexpressed modules now enable systems genetics approaches also in nonmodel species for better understanding of gene expression responses during early divergence. Here, we combined gene coexpression analyses with population genetics to separate plastic and population (evolutionary) effects in expression networks using small salmonid populations as a model system. We show that plastic and population effects were highly variable among the six identified modules and that the plastic effects explained larger proportion of the total eigengene expression than population effects. A more detailed analysis of the population effects using a QST - FST comparison across 16,622 annotated transcripts revealed that gene expression followed neutral expectations within modules and at the global level. Furthermore, two modules showed enrichment for genes coding for early developmental traits that have been previously identified as important phenotypic traits in thermal responses in the same model system indicating that coexpression analysis can capture expression patterns underlying ecologically important traits. We suggest that module-specific responses may facilitate the flexible tuning of expression levels to local thermal conditions. Overall, our study indicates that plasticity and neutral evolution are the main drivers of gene expression variance in the early stages of thermal adaptation in this system.
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影响因子：
4.3
作者：
Espinosa-Soto C;Wagner A
通讯作者：
Wagner A
影响因子：
3.3
作者：
Foll, Matthieu;Gaggiotti, Oscar
通讯作者：
Gaggiotti, Oscar
影响因子：
14.9
作者：
Cunningham F;Amode MR;Barrell D;Beal K;Billis K;Brent S;Carvalho-Silva D;Clapham P;Coates G;Fitzgerald S;Gil L;Girón CG;Gordon L;Hourlier T;Hunt SE;Janacek SH;Johnson N;Juettemann T;Kähäri AK;Keenan S;Martin FJ;Maurel T;McLaren W;Murphy DN;Nag R;Overduin B;Parker A;Patricio M;Perry E;Pignatelli M;Riat HS;Sheppard D;Taylor K;Thormann A;Vullo A;Wilder SP;Zadissa A;Aken BL;Birney E;Harrow J;Kinsella R;Muffato M;Ruffier M;Searle SM;Spudich G;Trevanion SJ;Yates A;Zerbino DR;Flicek P
通讯作者：
Flicek P
影响因子：
3.8
作者：
Forsman A
通讯作者：
Forsman A
DOI：
10.1139/cjfas-2013-0295
发表时间：
2014-01-01
影响因子：
2.4
作者：
Chezik, Kyle A.;Lester, Nigel P.;Venturelli, Paul A.
通讯作者：
Venturelli, Paul A.