Analysis of the Chalara genome suggests that it is AT repeat rich

The Contributor

Dan MacLean

The Analysis

I analysed the TGAC KW1 assembly of Hymenoscyphus pseudoalbidus / Chalara fraxinea  to display various features of the assembly. Click for larger image

 

preview_1194882

  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.
  8. Maximum plotted = 60% GC, minimum plotted = 20% GC
  9.  (green stacks) – Repeat Masker matches.

 

http://figshare.com/articles/Genome_analysis_of_the_Ash_Dieback_Fungus_suggests_a_repeat_rich_genome/791640

The interpretation

The genome assembly contains numerous low GC, high coverage, repeat rich regions, with low overall gene density. This suggests an assembly with collapsed repeats of a genome that is overall rich in repeats.

Cite this:

http://dx.doi.org/10.6084/m9.figshare.791640