High-quality SNPs from genic regions highlight introgression patterns among European white oaks (Quercus petraea and Q. robur)

In the post-genomics era, non-model species like most Fagaceae still lack operational diversity resources for population genomics studies. Sanger sequences were produced from over 800 gene fragments covering ~530 kb across the genic partition of European oaks in a range-wide sampling of 25 individuals (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 and differenti..., The data here are the original Sanger sequences (*.ab1 trace files) obtained from a discovery panel of 25 Quercus individuals sampled across a large part of both species geographic range (13 from Quercus robur, 11 from Quercus petraea, 1 from Quercus ilex). These sequences represent amplicons for gene fragments associated with 759 reference contigs from the assembly provided in Appendix S2 of the lang et al. manuscript in BioRxiv (https://www.biorxiv.org/content/10.1101/388447v1).

Each subfolder can contain more than one fragment from the same reference contig and most fragments but not all are overlapping. More than 85% of the fragments yielded at least 12 high-quality sequences. All subfolders contain at least one sequence that is of very good Sanger quality.

Leaves from individuals were sampled and stored in silica gel. DNA extraction was performed following Guichoux et al. (2013, DOI : 10.1111/mec.12125). DNA quality and concentration were assessed with a Nanodrop spectrophotomete..., The additional file ab1.id includes the names of  to the 50608 *.ab1 trace files distributed across the 759 folders
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