Disparate responses to salinity across species and organizational levels in anchialine shrimps

Abstract:<br>Environmentally-induced plasticity in gene expression is one of the underlying mechanisms of adaptation to habitats with variable environments. For example, euryhaline crustaceans show predictable changes in the expression of ion-transporter genes during salinity transfers, although studies have typically been limited to specific genes, taxa, and ecosystems of interest. Here, we investigated responses to salinity change at multiple organizational levels in five species of shrimps representing at least three independent invasions of the anchialine ecosystem, defined as habitats with marine and freshwater influences with spatial and temporal fluctuations in salinity. Although all five species were generally strong osmoregulators, salinity-induced changes in gill physiology and gene expression were highly species-specific. While some species exhibited patterns similar to previously studied euryhaline crustaceans, instances of distinct and atypical patterns were recovered from closely related species. Species-specific patterns were found when examining: 1) numbers and identities of differentially expressed genes, 2) salinity-induced expression of genes predicted a priori to play a role in osmoregulation, and 3) salinity-induced expression of orthologs shared among all species. Notably, ion transport genes were unchanged in the atyid Halocaridina rubra while ones normally associated with vision and light perception were among those most highly upregulated. Potential reasons for species-specific patterns are discussed, including variation among anchialine habitats in salinity regimes and divergent evolution in anchialine taxa. Underexplored mechanisms of osmoregulation in crustaceans revealed here by the application of transcriptomic approaches to ecologically and taxonomically understudied systems are also explored.<br>Supplementary datasets and information:<br>Here:<br>you will find all the supplementary information referred to in the paper (tables, methods, figures are in the file SI_101319.pdf) as well as two different datasets on gene expression, which are described in the pdf and in the README sheets of the datasets.

摘要：环境诱导的基因表达可塑性是适应多变生境的核心机制之一。例如，广盐性甲壳动物（euryhaline crustaceans）在盐度转移过程中会呈现离子转运基因表达的可预测变化，但过往研究通常仅局限于特定基因、类群与目标生态系统。本研究针对代表至少3次独立锚穴生态系统（anchialine ecosystem）入侵事件的5种虾类展开研究，从多个组织水平探究其对盐度变化的响应——锚穴生态系统被定义为兼具海水与淡水影响、盐度随时空波动的生境。
尽管5个物种总体均为优秀的渗透压调节者，但盐度诱导的鳃生理变化与基因表达模式具有极强的物种特异性。部分物种的响应模式与此前研究的广盐性甲壳动物相似，但近缘类群中也发现了独特且非典型的响应模式。在以下三个维度均观察到物种特异性模式：1）差异表达基因（differentially expressed genes）的数量与种类；2）被先验预测参与渗透压调节的基因的盐度诱导表达情况；3）所有物种共有的直系同源基因（orthologs）的盐度诱导表达模式。
值得注意的是，匙指虾科的红色盲虾（Halocaridina rubra）中离子转运基因的表达未发生显著变化，而通常与视觉及光感知相关的基因则是上调幅度最高的基因之一。本文讨论了物种特异性模式的潜在成因，包括锚穴生境盐度条件的类群间差异，以及锚穴类群的趋异演化。本研究将转录组学方法（transcriptomic approaches）应用于生态与分类学上研究不足的类群系统，揭示了甲壳动物渗透压调节中尚未被充分探索的机制，相关内容也在文中进行了探讨。

补充数据集与信息：
本文包含论文提及的全部补充资料（表格、研究方法、图表均收录于文件SI_101319.pdf），同时包含两组独立的基因表达数据集，相关说明详见该PDF文件及各数据集的README文档。