UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, 97744, St Denis Cedex 09, La Réunion, France.
Laboratoire Cogitamus, Paris, France.
Sci Rep. 2024 Mar 18;14(1):6437. doi: 10.1038/s41598-024-57136-5.
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). 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 were 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.
种内遗传变异（IGV），即在单个群体中存在多种基因型，在石珊瑚中越来越受到关注，其高发生率也得到了揭示。一些研究假设 IGV 带来了益处，但很少从遗传角度研究其作用。在这里，我们使用基因组数据（SNP）研究了留尼汪岛（印度洋西南部）的鹿角珊瑚 Pocillopora acuta 种群中可能存在的这些益处。由于 IGV 的检测取决于测序和生物信息学错误，我们首先探讨了生物信息学管道对其检测的影响。然后，我们对种内的 SNP 和基因变异进行了特征分析。虽然大多数测试的生物信息学参数对 IGV 的检测没有显著影响，但过滤基因型覆盖深度可以通过减少基因分型错误来显著提高 IGV 的检测。嵌合体和嵌合性（导致 IGV 的两种过程，第一种是通过体细胞突变，第二种是通过不同生物体的融合）分别在 7%和 12%的群体中发现。这两种过程都导致了几个种内等位基因差异，但大多数是非编码或沉默的。然而，7%的差异是非沉默的，存在于参与多种生物过程的基因中，其中一些直接与对环境压力的反应有关。因此，IGV 是遗传多样性和遗传可塑性的来源，增加了群体的适应潜力。这些益处无疑在石珊瑚种群的维持和进化中发挥了重要作用，在全球变化背景下，对珊瑚礁的未来至关重要。
