M. incognita predicted secreted proteins

To identify putative secreted proteins in the M. incognita protein set (Blanc-Mathieu et al. 2017), we searched for predicted signal peptides (SP) for secretion using SignalP v4 (Petersen, Brunak, von Heijne, Nielsen, 2011). This program improves the differentiation between transmembrane regions present in the N-terminal part of a protein and the presence of a peptide signal. In order to further eliminate this potential problem, predicted signal peptides were cropped, with the remaining part of the proteins subjected to TMHMM (Krogh, Larsson, von Heijne, Sonnhammer, 2001) for prediction of transmembrane regions. Proteins bearing a predicted SP and no transmembrane region were considered as putative secreted proteins. A separate list of predicted secreted proteins specific to plant-parasitic nematode species, according to orthofinder is also provided.