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.