In the post-genomics era, non-model species like most Fagaceae still lack operational diversity resources for population genomics studies. Sequence data were produced from over 800 gene fragments covering ~530 kb across the genic partition of European oaks, in a discovery panel of 25 individuals from western and central Europe (11 Quercus petraea, 13 Q. robur, one Q. ilex as an outgroup). Regions targeted represented broad functional categories potentially involved in species ecological preferences, and a random set of genes. Using a high-quality dedicated pipeline, we provide a detailed characterization of these genic regions, which included over 14500 polymorphisms, with ~12500 SNPs -218 being triallelic-, over 1500 insertion-deletions, and ~200 novel di- and tri-nucleotide SSR loci. This catalog also provides various summary statistics within and among species, gene ontology information, and standard formats to assist loci choice for genotyping projects. The distribution of nucleotide diversity (theta.pi)and differentiation (Fst) across genic regions are also described for the first time in those species, with a mean theta.pi close to ~0.0049 in Q. petraea and to ~0.0045 in Q. robur across random regions, and a mean Fst ~0.13 across SNPs. The magnitude of diversity across genes is within the range estimated for long-term perennial outcrossers, and can be considered relatively high in the plant kingdom, with an estimate across the genome of 41 to 51 million SNPs expected in both species. Individuals with typical species morphology were more easily assigned to their corresponding genetic cluster for Q. robur than for Q. petraea, revealing higher or more recent introgression in Q. petraea and a stronger species integration in Q. robur in this particular discovery panel. We also observed robust patterns of a slightly but significantly higher diversity in Q. petraea, across a random gene set and in the abiotic stress functional category, and a heterogeneous landscape of both diversity and differentiation. To explain these patterns, we discuss an alternative and non-exclusive hypothesis of stronger selective constraints in Q. robur, the most pioneering species in oak forest stand dynamics, additionally to the recognized and documented introgression history in both species despite their strong reproductive barriers. The quality of the data provided here and their representativity in terms of species genomic diversity make them useful for possible applications in medium-scale landscape and molecular ecology projects. Moreover, they can serve as reference resources for validation purposes in larger-scale resequencing projects. This type of project is preferentially recommended in oaks in contrast to SNP array development, given the large nucleotide variation and the low levels of linkage disequilibrium revealed.

中文翻译：

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来自遗传区域的高质量SNP突显了欧洲白橡树（栎栎和Q. robur）的渗入模式。

在后基因组学时代，像大多数菊科这样的非模式物种仍然缺乏用于人口基因组学研究的可操作多样性资源。在覆盖欧洲橡树的基因分区的约530 kb的800多个基因片段中产生了序列数据，这是一个来自西欧和中欧的25个个体的发现组（11个栎属，13个罗伯勒霉，一个Q. ilex）作为一个小组）。目标区域代表了可能与物种生态偏好有关的广泛功能类别，以及一组随机基因。使用高质量的专用管线，我们提供了这些基因区域的详细表征，其中包括超过14500个多态性，其中〜12500个SNP -218是三核苷酸的，超过1500个插入缺失，以及〜200个新的二核苷酸和三核苷酸SSR基因座。该目录还提供了物种内部和物种之间的各种汇总统计信息，基因本体信息和标准格式，以协助基因分型项目的基因座选择。核苷酸多样性（分布theta.pi）和分化（的Fst跨越基因区域）也用于那些物种首次描述，平均theta.pi接近0.0049〜在问：佩特拉行省和0.0045〜在问：栎跨越随机地区，平均的Fst跨越的SNP〜0.13。跨基因的多样性幅度在长期多年生异源杂交的估计范围内，并且在植物界中可以认为是相对较高的，整个基因组中估计这两个物种中有41至5100万个SNP。具有典型物种形态的个体更容易被分配给罗伯Q. petraea而不是其Q. petraea相应的遗传簇，这表明在Q. petraea中有更高或更多的近渗性和在Q. robur中更强的物种整合在这个特定的发现面板中。我们还观察到在随机基因集和非生物胁迫功能类别中，白蜡树Q. petraea多样性稍强但明显更高的稳健模式，以及多样性和分化的异质景观。为了解释这些模式，我们讨论了Q. robur中更强的选择约束的替代性和非排他性假设。，橡树林中最先驱的树种具有动态特性，除了公认的和有记录的两种树种的渗入历史外，尽管它们具有强大的繁殖障碍。这里提供的数据的质量及其在物种基因组多样性方面的代表性，使其可在中等规模的景观和分子生态项目中应用。而且，它们可以作为参考资源，用于大规模重测序项目中的验证。鉴于SNP阵列的开发，相对于SNP阵列开发，这种类型的项目优先推荐使用，因为存在较大的核苷酸变异和较低的连锁不平衡水平。