Quercus tomentella (Island Oak)

Visual overview of genome assembly metrics

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K-mer spectra output generated from PacBio HiFi data without adapters using GenomeScope2.0. The bimodal pattern observed corresponds to a diploid genome and the k-mer profile matches that of high heterozygosity. K-mers covered at lower coverage and high frequency correspond to differences between haplotypes, whereas the higher coverage and slightly lower frequency correspond to the similarities between haplotypes.

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BlobToolKit snail plot showing a graphical representation of the quality metrics for the Quercus tomentella haplotype 1 (dhQueTome1.0.hap1). The first diagonal (~30 degrees) line represents the size of the longest scaffold; all other scaffolds are arranged in size-order moving clockwise around the plot and drawn in gray starting from the outside of the central plot. Dark and light orange arcs show the scaffold N50 and scaffold N90 values. The central light gray spiral shows the cumulative scaffold count with a white line at each order of magnitude. White regions in this area reflect the proportion of Ns in the assembly; the dark vs. light blue area around it shows mean, maximum and minimum GC vs. AT content at 0.1% intervals (Challis et al. 2020).

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Haplotype 1 and haplotype 2 assembly Omni-C contact maps generated with PretextSnapshot. Omni-C contact maps translate proximity of genomic regions in 3D space to contiguous linear organization. Each cell in the contact map corresponds to sequencing data supporting the linkage (or join) between two of such regions.

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Authors

Alayna Mead, Sorel T Fitz-Gibbon, Merly Escalona, Eric Beraut, Samuel Sacco, Mohan P A Marimuthu, Oanh Nguyen, Victoria L Sork

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