Category Archives: Update

Rare Ortholog effector candidates added

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.

If you use this data cite this URL and check back here soon for upcoming publication details.

 

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.