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7 results for “Quercus xanthoclada”
Data from: 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.
Figure 4 from: Hinsinger DD, Strijk JS (2019) Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming. PhytoKeys 132: 75-89. https://doi.org/10.3897/phytokeys.132.36365
Figure 4 mVISTA percent identity plot comparing the four Quercus chloroplast genomes with Q. xanthoclada as a reference. Vertical scale indicates the percentage of identity ranging from 50% to 100%. Coding regions are in blue and non-coding regions are in pink.
Figure 3 from: Hinsinger DD, Strijk JS (2019) Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming. PhytoKeys 132: 75-89. https://doi.org/10.3897/phytokeys.132.36365
Figure 3 Sliding window analysis of the whole plastomes of five oak species. (window length: 500 bp, step size: 250 bp). X-axis: position of the mid-point of the window, Y-axis: number of SNPs (solid line) and indels (dashed line) positions of each window in bp. Coding regions and directions of transcription are indicated by arrows, inverted repeats by grey areas. Putative barcode loci are highlighted for SNPs and indels. For readability, only a few major genes are indicated.
Figure 2 from: Hinsinger DD, Strijk JS (2019) Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming. PhytoKeys 132: 75-89. https://doi.org/10.3897/phytokeys.132.36365
Figure 2 ML phylogenetic tree of the nine selected plastomes in GenBank, plus the plastome of Quercus xanthoclada. The tree is rooted with Trigonobalanus doichangensis. Bootstraps (1000 replicates) are shown at the nodes, values below 50% not shown. Scale in substitution per site.
Figure 1 from: Hinsinger DD, Strijk JS (2019) Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming. PhytoKeys 132: 75-89. https://doi.org/10.3897/phytokeys.132.36365
Figure 1 Circular gene map of the plastid genome of Quercus xanthoclada. Genes drawn within the circle are transcribed clockwise, while those drawn outside are transcribed counter clockwise. Genes are colour-coded according to their functional groups.
Figure 5 from: Hinsinger DD, Strijk JS (2019) Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming. PhytoKeys 132: 75-89. https://doi.org/10.3897/phytokeys.132.36365
Figure 5 Venn diagram showing the private and shared SNPs amongst the five oak species. Each area is coloured according to the relative number of shared SNPs in this area.
Data from: Plastome of Quercus xanthoclada and comparison of genomic diversity among selected Quercus species using genome skimming
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