Signatures of Compositionally Non-Homogenous Domains (CNHD) in draft Chalara genome.

Read and assembly sequences were analysed to calculate GC content in reads and different genomic feature types. This figure shows that the gDNA reads and contigs/scaffolds have a skewed, almost bimodal GC content. The skew is absent from RNA sequence and gene feature sequences, indicating a difference in GC content in the non-genic regions of the genome.

Scaffolds over 250 kbp long, namely

Cf746836_TGAC_s1v1_scaffold_945
Cf746836_TGAC_s1v1_scaffold_1167
Cf746836_TGAC_s1v1_scaffold_1170
Cf746836_TGAC_s1v1_scaffold_1201
Cf746836_TGAC_s1v1_scaffold_1232
Cf746836_TGAC_s1v1_scaffold_1249
Cf746836_TGAC_s1v1_scaffold_1479
Cf746836_TGAC_s1v1_scaffold_1507
Cf746836_TGAC_s1v1_scaffold_1550
Cf746836_TGAC_s1v1_scaffold_1659

were then analysed for the presence of small Compositionally Non-Homogenous Domains (GC-rich regions) using IsoPlotter 2.3. in Elhaik et al. This figure shows each of the scaffolds as black bars in which the white regions indicate statistically significant regions of non-homoegeneity, according to the method in in Elhaik et al.

These plots show in greater detail the changes in GC percent across these scaffolds. Many show strong drops in the GC content.

The pattern of GC poor patches observed here is reminiscent of the ‘isochore-like’ regions observed around the regions carrying effector genes in Leptosphaeria maculan’s that are believed to be involved in the plasticity of that organisms genome and may contribute to increased evolutionary potential and an ability to change hosts quickly see Raffaele and Kamoun, 2012.