Definition of the effector landscape across 13 Phytoplasma proteomes with LEAPH and EffectorComb

Abstract

BackgroundCrop pathogens are a major threat to plants health, reducing the yield and quality of agricultural production. Among them, the Candidatus Phytoplasma genus, a group of fastidious phloem-restricted bacteria, can parasite a wide variety of both ornamental and agro-economically important plants. Several aspects of the interaction with the plant host are still unclear but it was discovered that phytoplasmas secrete certain proteins (effectors) responsible for the symptoms associated with the disease. Identifying and characterizing these proteins is of prime importance for globally improving plant health in an environmentally friendly context. ResultsWe challenged the identification of phytoplasmas effectors by developing LEAPH, a novel machine-learning ensemble predictor for phytoplasmas pathogenicity proteins. The prediction core is composed of four models: Random Forest, XGBoost, Gaussian, and Multinomial Naive Bayes. The consensus prediction is achieved by a novel consensus prediction score. LEAPH was trained on 479 proteins from 53 phytoplasmas species, described by 30 features accounting for the biological complexity of these protein sequences. LEAPH achieved 97.49% accuracy, 95.26% precision, and 98.37% recall, ensuring a low false-positive rate and outperforming available state-of-the-art methods for putative effector prediction. The application of LEAPH to 13 phytoplasma proteomes yields a comprehensive landscape of 2089 putative pathogenicity proteins. We identified three classes of these proteins according to different secretion models: "classical", presenting a signal peptide, "classically-like" and "non-classical", lacking the canonical secretion signal. Importantly, LEAPH was able to identify 15 out of 17 known experimentally validated effectors belonging to the three classes. Furthermore, to help the selection of novel candidates for biological validation, we applied the Self-Organizing Maps algorithm and developed a shiny app called EffectorComb. Both tools would be a valuable resource to improve our understanding of effectors in plant-phytoplasmas interactions. ConclusionsLEAPH and EffectorComb app can be used to boost the characterization of putative effectors at both computational and experimental levels and can be employed in other phytopathological models. Both tools are available at https://github.com/Plant-Net/LEAPH-EffectorComb.git.