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。从淡水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、病原体暴露以及膳食脂质可获得性的改变。在洄游入海前，鲑鱼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。
本研究通过长期喂食实验，探究大西洋鲑在淡水与盐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的差异具有高度可塑性；而当鲑鱼进入海洋生活阶段时，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，肠道内负责脂质摄取的基因表达量则显著升高。此外，针对鲑科特有全基因组复制（salmonid specific whole-genome duplication）事件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率或重复基因调控保守性存在显著差异（p<0.05）；我们还发现极少数案例中，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，提示脂质代谢存在进化而来的预适应性优化。