Signs of local adaptation by genetic selection and isolation promoted by extreme temperature and salinity in the Mediterranean seagrass Posidonia oceanica

Adaptation to local conditions is known to occur in seagrasses, however, knowledge of the genetic basis underlying this phenomenon remains scarce. Here, we analyzed Posidonia oceanica from six sites within and around the Stagnone di Marsala, a semi-enclosed coastal lagoon where salinity and temperature exceed the generally described tolerance thresholds of the species. Sea surface temperatures (SSTs) were measured and plant samples were collected for the assessment of morphology, flowering rate and for screening genome-wide polymorphisms using double digest restriction-site-associated DNA sequencing. Results demonstrated more extreme SSTs and salinity levels inside the lagoon than the outer lagoon regions. Morphological results showed significantly fewer and shorter leaves and reduced rhizome growth of P. oceanica from the inner lagoon and past flowering events were recorded only for a meadow farthest away from the lagoon. Using an array of 51,329 SNPs, we revealed a clear genetic struc..., Ninety-five ddRAD-seq library construction and sequencing were conducted at IGATech (Udine, Italy) using an IGATech custom protocol, with minor modifications with respect to Peterson’s double digest restriction-site associated DNA preparation (Peterson et al., 2012). To ensure the quality of sequencing outcomes, for each site, one sample was randomly selected and sequenced twice. The final number of biological replicates for each site was n = 14 for OpenSea-C and n = 15 for the other sites (i.e. North-basin, South-basin, OpenSea-A, OpenSea-B, and OpenSea-D), respectively (i.e. 89 unique samples + 6 technical replicates). In short, gDNA was double digested with both SphI and MboI endonucleases (New England BioLabs). Fragmented DNA was purified with AMPureXP beads (Agencourt) and subsequently ligated with T4 DNA ligase (New England BioLabs). Samples were pooled on multiplexing batches and bead purified as before and then they were size-selected and underwent several purification steps. dd..., , # Raw sequencing data and VCF files --- This dataset contains raw sequencing files and vcf files of a field experiment on the seagrass *Posidonia oceanic*. Samples were collected from six sites within and around the Stagnone di Marsala, a semi-enclosed coastal lagoon where salinity and temperature exceed the generally described tolerance thresholds of the species. This study aimed at better understanding the genetic basis of local adaptation in *P. oceanica* to extreme temperature and salinity. The screening of genome-wide polymorphisms using double digest restriction-site-associated DNA sequencing revealed a clear genetic structure among the study sites and confirmed the genetic isolation and high clonality of the innermost site. Fourteen outlier loci were identified and annotated with several proteins including those relate to plant stress response, protein transport and regulators of plant-specific developmental events. Especially, five outlier loci showed maximum allele frequency...海草已被证实可发生本地适应，但目前对该现象背后的遗传基础仍缺乏深入认知。本研究针对马尔萨拉斯塔格诺内潟湖（Stagnone di Marsala，一处半封闭沿岸潟湖，其盐度与温度均超出该物种已报道的耐受阈值）内部及周边6个采样点的波西多尼亚海草（Posidonia oceanica）展开分析。研究人员测定了海表温度（Sea Surface Temperatures, SST），并采集植物样本以评估其形态学特征与开花率，同时利用双酶切限制性位点关联DNA测序（double digest restriction-site-associated DNA sequencing, ddRAD-seq）筛选全基因组多态性位点。结果表明，潟湖内部的海表温度与盐度水平显著高于潟湖外围区域。形态学分析结果显示，采自潟湖内部的波西多尼亚海草叶片数量更少、长度更短，且根茎生长受到明显抑制；过往开花事件仅在距离潟湖最远的海草床中被记录到。本研究利用包含51329个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）的位点阵列，揭示了清晰的遗传结构...。 95份ddRAD-seq文库的构建与测序工作在位于意大利乌迪内的IGATech公司完成，采用IGATech定制实验方案，仅对Peterson等人2012年提出的双酶切限制性位点关联DNA制备流程进行了小幅优化。为保障测序结果质量，每个采样点随机选取1份样本进行两次重复测序。各采样点的生物学重复数最终为：OpenSea-C组14份，其余5个采样点（北盆、南盆、OpenSea-A、OpenSea-B及OpenSea-D）各15份，总计89份独特样本与6份技术重复样本。简言之，基因组DNA（gDNA）经SphI与MboI两种限制性内切酶（新英格兰生物实验室，New England BioLabs）双酶切；酶切后的DNA片段使用Agencourt AMPureXP磁珠纯化，随后通过T4 DNA连接酶（新英格兰生物实验室，New England BioLabs）进行接头连接；样本按多重测序批次混合后再次进行磁珠纯化，继而进行片段大小筛选并经多轮纯化步骤。dd..., , # 原始测序数据与VCF文件 本数据集包含波西多尼亚海草野外实验的原始测序文件与VCF文件。样本采集自马尔萨拉斯塔格诺内潟湖及其周边的6个采样点，该半封闭沿岸潟湖的盐度与温度均超出该物种已报道的耐受阈值。本研究旨在深入解析波西多尼亚海草应对极端温度与盐度的本地适应遗传基础。 利用双酶切限制性位点关联DNA测序筛选全基因组多态性的结果显示，各采样点间存在显著的遗传结构，并证实了潟湖最内部采样点的遗传隔离性与高克隆性。本研究共鉴定并注释了14个离群位点，其功能涉及植物胁迫响应、蛋白质运输以及植物特异性发育事件调控等；其中5个离群位点的等位基因频率...