Cyanocitta stelleri (Steller’s Jay)
Visual overview of genome assembly metrics
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 low (<1%) heterozygosity. The left-hand peak at lower coverage and frequency derives from k-mers in heterozygous regions, while the higher coverage right hand peak k-mers stem from homozygous regions.
BlobToolKit Snail plot shows quality metrics for the primary assembly of the Steller’s jay (Cyanocitta stelleri) genome. The plot circle represents the full size of the assembly. From the inside-out, the central plot covers length-related metrics. The red 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 versus light blue area around it shows mean, maximum, and minimum GC vs. AT content at 0.1% intervals.
Hi-C contact maps for the primary and alternate assemblies generated using PretextSnapshot. Hi-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 2 such regions. d) Jupiter plot comparing higher level synteny and degree of completeness between the New Caledonian crow (Corvus moneduloides) genome and the Steller’s jay genome. Crow chromosomes are on the left (colored) and jay scaffolds are on the right (light gray).
Authors
Phred M Benham, Carla Cicero, Devon A DeRaad, John E McCormack, Robert K Wayne, Merly Escalona, Eric Beraut, Mohan P A Marimuthu, Oanh Nguyen, Michael W Nachman, Rauri C K Bowie