Plastome of Quercus xanthoclada and comparison of genomic diversity among selected Quercus species using genome skimming

The genus Quercus L. contains several of the most economically important species for timber production in the Northern Hemisphere. It was one of the first genera described but genetic diversity at a global scale within and among oak species remains unclear, despite numerous regional or species-specific assessments. To evaluate global plastid diversity in oaks, we sequenced the complete chloroplast of Quercus xanthoclada, and compared its sequence those available from other main taxonomic groups in Quercus. We quantify genomic divergence among oaks and performed a sliding window analysis to detect the most variable regions among members of the various clades, as well as divergent regions occurring in specific pairs of species. We identified private and shared SNPs among oaks species and sections, and stress the need for a large global assessment of the genetic diversity in this economically and ecologically important genus.