Genome analysis of the Ash Dieback Fungus suggests a repeat-rich genome
The TGAC KW1 assembly of Hymenoscyphus pseudoalbidus / Chalara fraxinea was analysed to display:
1 (outer black ring) - scaffolds of length >= 10 kbp
2 (blue stacks) - gene models
3 (blue heatmap) - gene density in 10 kbp windows
4 (line plot) - aligned distance between paired end read for library with 196 bp insert size (< 31 bp - 5th percentile - rendered in orange, > 351 bp - 95th percentile - rendered in blue)
5 (line plot) - aligned distance between paired end read for library with 570 bp insert size (< 265 bp - 5th percentile - rendered in orange, > 2313 bp - 95th percentile - rendered in blue) Thresholds calculated as per (https://github.com/danmaclean/h_pseu_analysis/blob/master/circos/scripts/assess_insert_size_distributions.md)
6 (pink line plot) - uniquely mapped read covereage. Maximum plotted = 300, minimum plotted = 80
7 (pink line plot) - GC percent. Black line = 50% GC, light grey area = 50% - 30 % GC, dark grey area = > 30% GC.
Maximum plotted = 60% GC, minimum plotted = 20% GC
8 (green stacks) - Repeat Masker matches.
The genome assembly contains numerous low GC, high coverage, repeat rich regions, with low overall gene density. This suggests an assembly with collapsed repeats.
