Fungal effectors do not often exhibit conserved sequence similarity, however some effectors are only present a small number of species, which may be distantly related. A typical example of this is the ToxA effector which is found by orthology in only a handful of species (Pyrenophora tritici-repentis, Parastagonospora nodorum, and Bipolaris maydis). By predicting rare orthologous groups (ROGs) (with reciprocal best blastp hits), potential LGT events, and effector-like ROGs can be predicted (see menu above “ROG Predictions”).
The image above shows the taxonomic locations and frequency of effector-like ROGs produced by this study.
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Orthology was predicted with BLASTP and ProteinOrtho. Additional filters (signalP, EffectorP) were applied to predicted LGTs.
BLASTP – Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J., 1990. Basic local alignment search tool. Journal of molecular biology, 215(3), pp.403-410.
ProteinOrtho – Lechner, M., Findeiß, S., Steiner, L., Marz, M., Stadler, P.F. and Prohaska, S.J., 2011. Proteinortho: detection of (co-) orthologs in large-scale analysis. BMC bioinformatics, 12(1), p.1.
signalP – Petersen, T.N., Brunak, S., von Heijne, G. and Nielsen, H., 2011. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nature methods, 8(10), pp.785-786.
EffectorP – Sperschneider, J., Gardiner, D.M., Dodds, P.N., Tini, F., Covarelli, L., Singh, K.B., Manners, J.M. and Taylor, J.M., 2015. EffectorP: predicting fungal effector proteins from secretomes using machine learning. New Phytologist.