Mining for putative effectors in the Chalara fraxinea KW1 genome

The contributors

Daniel Bunting (Nuffield student), Kentaro Yoshida and Diane Saunders at TSL.

The material

We used the C. fraxinea KW1 predicted proteome (data/ash_dieback/chalara_fraxinea/Kenninghall_wood_KW1/annotations/Gene_predictions/TGAC_Chalara_fraxinea_ass_s1v1_ann_v1.1) as a basis to mine for candidate effectors.

The analysis

  1. First, the predicted proteome of C. fraxinea KW1 was searched for potential secreted proteins using SignalP2 with parameters described in [1]. Transmembrane domain containing proteins and proteins with mitochondrial signal peptides were removed using TMHMM [2] and TargetP [3], respectively.
  2. We then clustered all proteins using TribeMCL [4], following the methods described in [5]. We identified clusters of proteins (known as tribes) that contained at least one secreted protein. These 593 tribes were then used for all further analysis.
  3. Next, we annotated the protein tribes for known effector features as described in [6].
  4. Finally, we assigned an e-value to each feature within a tribe using the method described in [7] in order to rank tribes based on their likelihood of containing effector proteins.

A spreadsheet that contains the above analysis is available at (data/ash_dieback/chalara_fraxinea/Kenninghall_wood_KW1/annotations/Effector_mining).


Figure 1. Pipeline used to mine for potential effector proteins in C. fraxinea KW1 isolate. Programs are indicated in red.

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