Genome analysis of the Ash Dieback Fungus suggests a repeat-rich genome

2013-09-09T14:52:21Z (GMT) by Dan MacLean
<p>The TGAC KW1 assembly of Hymenoscyphus pseudoalbidus / Chalara fraxinea was analysed to display:</p> <p> </p> <p>1 (outer black ring) - scaffolds of length >= 10 kbp</p> <p>2 (blue stacks) - gene models</p> <p>3 (blue heatmap) - gene density in 10 kbp windows</p> <p>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)</p> <p>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)</p> <p> </p> <p>6 (pink line plot) - uniquely mapped read covereage. Maximum plotted = 300, minimum plotted = 80</p> <p>7 (pink line plot) - GC percent. Black line = 50% GC, light grey area = 50% - 30 % GC, dark grey area = > 30% GC. </p> <p>Maximum plotted = 60% GC, minimum plotted = 20% GC</p> <p>8 (green stacks) - Repeat Masker matches.</p> <p> </p> <p>The genome assembly contains numerous low GC, high coverage, repeat rich regions, with low overall gene density. This suggests an assembly with collapsed repeats.</p>