Negative set used to identify enriched motif in effectors regulatory regions

As negative set, we selected 167 M. incognita genes from an Orthofinder analysis (Emms Kelly, 2019) previously performed on 64 genomes, including 62 nematodes and two outgroup tardigrade species (Grynberg et al., 2020). The selection criteria were as follows: (i) the vast majority (163 genes) came from orthogroups conserved in at least 80% of the species and 85% of the Tylenchida and did not form multigene families. Being widely conserved across nematodes, including in many non phytoparasitic species and not forming multigene families, these genes are more likely involved in core housekeeping functions than coding for effector proteins. (ii) four genes specific to root-knot nematodes but bearing no signal peptide for secretion, including one gene specific to M. incognita.