Genomic and transcriptomic landscapes of independent invasions of the Pacific Oyster Crassostrea gigas

Upon colonizing new habitats invasive species face a series of new selection pressures as a result of changing abiotic conditions and novel biotic interactions with native species. These new selection pressures can be accommodated by different mechanism that act on different levels and across different time scales: 1) By changing transcriptomic profiles species can react by plasticity within individual physiological limitations. 2) Invasive populations can adapt by fixing beneficial genetic variants in response to the newly encountered selection pressures. Here, we compare the genomic and transcriptomic landscapes of two independent invasions of the Pacific Oyster Crassostrea gigas into the North Sea. In detail, we combine high density full genome resequencing and low density ddRAD on the genomic level with RNAseq on the transcriptomic level to reveal outlier loci (SNPs) indicative of adaptation, as well as transcriptomic profiles from a translocation experiment to show immediate physiological reactions. The low congruence between differentially regulated genes and outlier loci indicates that different processes act on the different time scales. By contrasting population outlier loci and population specific transcriptomic profiles we can thus identify relevant processes acting during different phases of the invasive process, which will allow to take a glimpse at the traits and processes characterizing successful invasions. Raw dd-RAD data is submitted here, raw RNA-seq data are in ArrayExpress (E-MTAB-9186).

当入侵物种定植于新生境时，会因非生物环境的改变以及与本地物种间的新型生物互作，面临一系列全新的选择压力。这类全新的选择压力可通过多种作用于不同层级、跨不同时间尺度的机制加以应对：1) 借助改变转录组谱（transcriptomic profiles），物种可在个体生理耐受限度内通过表型可塑性做出响应；2) 入侵种群可通过固定有益遗传变异，以响应新遭遇的选择压力，从而实现适应性演化。本研究针对两次独立入侵至北海的太平洋牡蛎（Crassostrea gigas），比较其基因组与转录组图谱。具体而言，我们在基因组层面采用高密度全基因组重测序与低密度ddRAD测序，在转录组层面采用RNAseq测序，以筛选出指示适应性演化的选择性异常位点（单核苷酸多态性，SNPs）；同时结合易位实验得到的转录组谱，揭示物种的即时生理响应。差异表达基因与选择性异常位点之间的低一致性，表明不同过程作用于不同的时间尺度。通过对比种群特异性的选择性异常位点与种群特异性转录组谱，我们可识别入侵进程不同阶段发挥作用的关键过程，进而得以窥见支撑成功入侵的关键性状与核心机制。原始ddRAD测序数据已在此处提交，原始RNAseq测序数据存于ArrayExpress数据库（登录号：E-MTAB-9186）。