Data from: Life-stage associated remodeling of lipid metabolism regulation in Atlantic salmon

Atlantic salmon migrates from rivers to sea to feed, grow and develop gonads before returning to spawn in freshwater. The transition to marine habitats is associated with dramatic changes in the environment, including water salinity, exposure to pathogens, and shift in dietary lipid availability. Many anticipatory changes in physiology occur before migration to sea, but little is known about the molecular nature of these changes.
Here we use a long term feeding experiment to study transcriptional regulation of lipid metabolism in Atlantic salmon gut and liver in both fresh- and saltwater. We find that lipid metabolism is highly plastic in response to differences in dietary lipid composition in freshwater, but then undergoes a marked shift when salmon transitions to the marine life-stage. Expression of genes in liver relating to lipogenesis and lipid transport decrease overall and become less responsive to diet, while genes for lipid uptake in gut become more highly expressed. Finally, analyses of evolutionary consequences of the salmonid specific whole-genome duplication on lipid metabolism reveals several pathways with significantly different (p<0.05) duplicate retention or duplicate regulatory conservation. We also find a limited number of cases where the whole genome duplication has resulted in an increased gene dosage.
Our results demonstrate the presence of a life-stage associated remodeling of lipid metabolism at the gene regulatory level, suggesting an evolved preparatory optimization of lipid metabolism

大西洋鲑（Atlantic salmon）会从河流洄游至海洋，以觅食、生长并发育性腺，随后返回淡水水域产卵。向海洋生境的转变伴随着环境的剧烈变化，包括水盐度改变、病原体暴露风险上升以及膳食脂质可获得性的转变。洄游至海洋前，鲑的生理会发生诸多预期性变化，但目前对这些变化的分子机制仍知之甚少。
本研究通过长期饲喂实验，探究了大西洋鲑在淡水与咸水环境下，肠道与肝脏中脂质代谢的转录调控机制。我们发现，在淡水环境中，脂质代谢对膳食脂质组成差异具有高度可塑性；而当鲑进入海洋生活阶段后，其脂质代谢会发生显著转变。肝脏中与脂肪生成、脂质转运相关的基因整体表达量下降，且对膳食的响应性降低；与此同时，肠道中参与脂质摄取的基因表达量则显著升高。此外，针对鲑科特异性全基因组复制（salmonid specific whole-genome duplication）对脂质代谢的进化影响分析显示，多条通路的重复基因保留或重复基因调控保守性存在显著差异（p<0.05）；我们还发现少量案例显示，全基因组复制导致了基因剂量的增加。
本研究结果证实，在基因调控层面存在与生活阶段相关的脂质代谢重塑现象，这表明脂质代谢存在进化而来的预适应性优化。