Investigating the potential roles of intra-colonial genetic variability in Pocillopora corals using genomics

Intra-colonial genetic variability (IGV), the presence of more than one genotype in a single colony, has been increasingly studied in scleractinians, revealing its high prevalence. Several studies hypothesised that IGV brings benefits, but few have investigated its roles from a genetic perspective. Here, using genomic data (SNPs), we investigated these potential benefits in populations of the coral Pocillopora acuta from Reunion Island (southwestern Indian Ocean). Besides, as the detection of IGV depends on sequencing and bioinformatics errors, we first explored the impact of the bioinformatics pipeline on its detection. Then, SNPs and genes variable within colonies were characterised. While most of the tested bioinformatics parameters did not significantly impact the detection of IGV, filtering on genotype depth of coverage strongly improved its detection by reducing genotyping errors. Mosaicism and chimerism, the two processes leading to IGV (the first through somatic mutations, the second through fusion of distinct organisms), were found in 7 and 12% of the colonies, respectively. Both processes led to several intra-colonial allelic differences, but most were non-coding or silent. However, 7% of the differences were non-silent and found in genes involved in a high diversity of biological processes, some of which directly linked to responses to environmental stresses. IGV, therefore, appears as a source of genetic diversity and genetic plasticity, increasing the adaptive potential of colonies. Such benefits undoubtedly play an important role in the maintenance and the evolution of scleractinian populations and appear crucial for the future of coral reefs in the context of ongoing global changes. This deposit contains the data related to Oury N, Magalon H (2024) Investigating the potential roles of intra-colonial genetic variability in Pocillopora corals using genomics. See 0_README.txt for more content details.菌落内遗传变异（Intra-colonial genetic variability, IGV）指单个菌落中存在多种基因型的现象，近年来在石珊瑚（scleractinians）中的相关研究日益增多，结果显示其发生率颇高。多项研究推测IGV具有益处，但极少有研究从遗传层面探究其具体作用。本研究利用单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）基因组数据，针对来自西南印度洋留尼汪岛的尖杯珊瑚（Pocillopora acuta）种群展开分析，以探究IGV的潜在益处。此外，鉴于IGV的检测依赖测序与生物信息学分析误差，我们首先探究了生物信息学流程对IGV检测的影响；随后对菌落内的可变SNPs与基因进行特征刻画。尽管多数测试的生物信息学参数对IGV的检测无显著影响，但基于基因型覆盖深度的过滤可通过降低基因分型误差，显著提升IGV的检测效能。分别有7%和12%的菌落呈现镶嵌现象（mosaicism）与嵌合现象（chimerism）——前者通过体细胞突变产生，后者通过不同个体融合产生——二者均为引发IGV的过程。两类过程均导致多种菌落内等位基因差异，但多数差异位于非编码区或为沉默突变。然而，7%的差异为非同义突变，且存在于参与多种生物过程的基因中，其中部分过程直接与环境胁迫响应相关。因此，IGV可作为遗传多样性与遗传可塑性的来源，提升菌落的适应潜力。这类益处无疑对石珊瑚种群的维持与演化具有重要意义，在当前持续的全球变化背景下，对珊瑚礁的未来发展至关重要。 本数据集包含Oury N、Magalon H（2024）发表的《利用基因组学探究杯形珊瑚菌落内遗传变异的潜在作用》相关研究数据。有关更多内容细节，请参阅0_README.txt文件。