WideEffHunter: An algorithm to predict canonical and non-canonical effectors in fungi and Oomycetes
Newer effectorome prediction algorithms are considering effectors that may not comply with the canonical characteristics of small, secreted, cysteine-rich proteins. The use of effector-related motifs and domains is an emerging strategy for effector identification, but its use has been limited to individual species, whether oomycete or fungal, and certain domains and motifs have only been associated with one or the other. The use of these strategies is important for the identification of novel, non-canonical effectors (NCEs) which we have found to constitute approximately 90% of the effectoromes. We produced an algorithm in Bash called WideEffHunter that is founded on integrating three key characteristics: the presence of effector motifs, effector domains and homology to validated existing effectors. Interestingly, we found similar numbers of effectors with motifs and domains within two different taxonomic kingdoms: fungi and oomycetes, indicating that with respect to their effector content, the two organisms may be more similar than previously believed. WideEffHunter can identify the entire effectorome (non-canonical and canonical effectors) of oomycetes and fungi whether pathogenic or non-pathogenic, unifying effector prediction in these two kingdoms as well as the two different lifestyles. The elucidation of complete effectoromes is a crucial step towards advancing effectoromics and disease management in agriculture. © 2022 by the authors.
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Subjects: | info:eu-repo/classification/Autores/EFFECTOROMICS, info:eu-repo/classification/Autores/EFFECTOR PREDICTION, info:eu-repo/classification/Autores/FUNGI AND OOMYCETES, info:eu-repo/classification/Autores/NON-CANONICAL EFFECTORS, info:eu-repo/classification/Autores/EFFECTOR-RELATED DOMAINS, info:eu-repo/classification/Autores/EFFECTOR-RELATED MOTIFS, info:eu-repo/classification/cti/2, info:eu-repo/classification/cti/24, info:eu-repo/classification/cti/2403, info:eu-repo/classification/cti/230221, |
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dig-cicy-1003-28192023-10-24T23:01:30Z WideEffHunter: An algorithm to predict canonical and non-canonical effectors in fungi and Oomycetes Karla Gisel Carreón Anguiano Jewel Todd Bartolomé Humberto Chí Manzanero Osvaldo Jhosimar Couoh Dzul Ignacio Rodrigo Islas Flores Blondy Beatriz Canto Canché 2022 info:eu-repo/semantics/article Newer effectorome prediction algorithms are considering effectors that may not comply with the canonical characteristics of small, secreted, cysteine-rich proteins. The use of effector-related motifs and domains is an emerging strategy for effector identification, but its use has been limited to individual species, whether oomycete or fungal, and certain domains and motifs have only been associated with one or the other. The use of these strategies is important for the identification of novel, non-canonical effectors (NCEs) which we have found to constitute approximately 90% of the effectoromes. We produced an algorithm in Bash called WideEffHunter that is founded on integrating three key characteristics: the presence of effector motifs, effector domains and homology to validated existing effectors. Interestingly, we found similar numbers of effectors with motifs and domains within two different taxonomic kingdoms: fungi and oomycetes, indicating that with respect to their effector content, the two organisms may be more similar than previously believed. WideEffHunter can identify the entire effectorome (non-canonical and canonical effectors) of oomycetes and fungi whether pathogenic or non-pathogenic, unifying effector prediction in these two kingdoms as well as the two different lifestyles. The elucidation of complete effectoromes is a crucial step towards advancing effectoromics and disease management in agriculture. © 2022 by the authors. info:eu-repo/classification/Autores/EFFECTOROMICS info:eu-repo/classification/Autores/EFFECTOR PREDICTION info:eu-repo/classification/Autores/FUNGI AND OOMYCETES info:eu-repo/classification/Autores/NON-CANONICAL EFFECTORS info:eu-repo/classification/Autores/EFFECTOR-RELATED DOMAINS info:eu-repo/classification/Autores/EFFECTOR-RELATED MOTIFS info:eu-repo/classification/cti/2 info:eu-repo/classification/cti/24 info:eu-repo/classification/cti/2403 info:eu-repo/classification/cti/230221 info:eu-repo/classification/cti/230221 International Journal of Molecular Sciences, 23(21), 13567, 2022. http://cicy.repositorioinstitucional.mx/jspui/handle/1003/2819 info:eu-repo/semantics/datasetDOI/https://doi.org/10.3390/ijms232113567 info:eu-repo/semantics/openAccess eng citation:Carreón-Anguiano, K.G.; Todd, J.N.A.; Chi-Manzanero, B.H.; Couoh-Dzul, O.J.; Islas-Flores, I.; Canto-Canché, B. WideEffHunter: An Algorithm to Predict Canonical and Non-Canonical Effectors in Fungi and Oomycetes. Int. J. Mol. Sci. 2022, 23, 13567.https://doi.org/10.3390/ ijms232113567 http://creativecommons.org/licenses/by-nc-nd/4.0 info:eu-repo/semantics/publishedVersion application/pdf |
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info:eu-repo/classification/Autores/EFFECTOROMICS info:eu-repo/classification/Autores/EFFECTOR PREDICTION info:eu-repo/classification/Autores/FUNGI AND OOMYCETES info:eu-repo/classification/Autores/NON-CANONICAL EFFECTORS info:eu-repo/classification/Autores/EFFECTOR-RELATED DOMAINS info:eu-repo/classification/Autores/EFFECTOR-RELATED MOTIFS info:eu-repo/classification/cti/2 info:eu-repo/classification/cti/24 info:eu-repo/classification/cti/2403 info:eu-repo/classification/cti/230221 info:eu-repo/classification/cti/230221 info:eu-repo/classification/Autores/EFFECTOROMICS info:eu-repo/classification/Autores/EFFECTOR PREDICTION info:eu-repo/classification/Autores/FUNGI AND OOMYCETES info:eu-repo/classification/Autores/NON-CANONICAL EFFECTORS info:eu-repo/classification/Autores/EFFECTOR-RELATED DOMAINS info:eu-repo/classification/Autores/EFFECTOR-RELATED MOTIFS info:eu-repo/classification/cti/2 info:eu-repo/classification/cti/24 info:eu-repo/classification/cti/2403 info:eu-repo/classification/cti/230221 info:eu-repo/classification/cti/230221 |
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info:eu-repo/classification/Autores/EFFECTOROMICS info:eu-repo/classification/Autores/EFFECTOR PREDICTION info:eu-repo/classification/Autores/FUNGI AND OOMYCETES info:eu-repo/classification/Autores/NON-CANONICAL EFFECTORS info:eu-repo/classification/Autores/EFFECTOR-RELATED DOMAINS info:eu-repo/classification/Autores/EFFECTOR-RELATED MOTIFS info:eu-repo/classification/cti/2 info:eu-repo/classification/cti/24 info:eu-repo/classification/cti/2403 info:eu-repo/classification/cti/230221 info:eu-repo/classification/cti/230221 info:eu-repo/classification/Autores/EFFECTOROMICS info:eu-repo/classification/Autores/EFFECTOR PREDICTION info:eu-repo/classification/Autores/FUNGI AND OOMYCETES info:eu-repo/classification/Autores/NON-CANONICAL EFFECTORS info:eu-repo/classification/Autores/EFFECTOR-RELATED DOMAINS info:eu-repo/classification/Autores/EFFECTOR-RELATED MOTIFS info:eu-repo/classification/cti/2 info:eu-repo/classification/cti/24 info:eu-repo/classification/cti/2403 info:eu-repo/classification/cti/230221 info:eu-repo/classification/cti/230221 Karla Gisel Carreón Anguiano Jewel Todd Bartolomé Humberto Chí Manzanero Osvaldo Jhosimar Couoh Dzul Ignacio Rodrigo Islas Flores Blondy Beatriz Canto Canché WideEffHunter: An algorithm to predict canonical and non-canonical effectors in fungi and Oomycetes |
description |
Newer effectorome prediction algorithms are considering effectors that may not comply with the canonical characteristics of small, secreted, cysteine-rich proteins. The use of effector-related motifs and domains is an emerging strategy for effector identification, but its use has been limited to individual species, whether oomycete or fungal, and certain domains and motifs have only been associated with one or the other. The use of these strategies is important for the identification of novel, non-canonical effectors (NCEs) which we have found to constitute approximately 90% of the effectoromes. We produced an algorithm in Bash called WideEffHunter that is founded on integrating three key characteristics: the presence of effector motifs, effector domains and homology to validated existing effectors. Interestingly, we found similar numbers of effectors with motifs and domains within two different taxonomic kingdoms: fungi and oomycetes, indicating that with respect to their effector content, the two organisms may be more similar than previously believed. WideEffHunter can identify the entire effectorome (non-canonical and canonical effectors) of oomycetes and fungi whether pathogenic or non-pathogenic, unifying effector prediction in these two kingdoms as well as the two different lifestyles. The elucidation of complete effectoromes is a crucial step towards advancing effectoromics and disease management in agriculture. © 2022 by the authors. |
format |
info:eu-repo/semantics/article |
topic_facet |
info:eu-repo/classification/Autores/EFFECTOROMICS info:eu-repo/classification/Autores/EFFECTOR PREDICTION info:eu-repo/classification/Autores/FUNGI AND OOMYCETES info:eu-repo/classification/Autores/NON-CANONICAL EFFECTORS info:eu-repo/classification/Autores/EFFECTOR-RELATED DOMAINS info:eu-repo/classification/Autores/EFFECTOR-RELATED MOTIFS info:eu-repo/classification/cti/2 info:eu-repo/classification/cti/24 info:eu-repo/classification/cti/2403 info:eu-repo/classification/cti/230221 info:eu-repo/classification/cti/230221 |
author |
Karla Gisel Carreón Anguiano Jewel Todd Bartolomé Humberto Chí Manzanero Osvaldo Jhosimar Couoh Dzul Ignacio Rodrigo Islas Flores Blondy Beatriz Canto Canché |
author_facet |
Karla Gisel Carreón Anguiano Jewel Todd Bartolomé Humberto Chí Manzanero Osvaldo Jhosimar Couoh Dzul Ignacio Rodrigo Islas Flores Blondy Beatriz Canto Canché |
author_sort |
Karla Gisel Carreón Anguiano |
title |
WideEffHunter: An algorithm to predict canonical and non-canonical effectors in fungi and Oomycetes |
title_short |
WideEffHunter: An algorithm to predict canonical and non-canonical effectors in fungi and Oomycetes |
title_full |
WideEffHunter: An algorithm to predict canonical and non-canonical effectors in fungi and Oomycetes |
title_fullStr |
WideEffHunter: An algorithm to predict canonical and non-canonical effectors in fungi and Oomycetes |
title_full_unstemmed |
WideEffHunter: An algorithm to predict canonical and non-canonical effectors in fungi and Oomycetes |
title_sort |
wideeffhunter: an algorithm to predict canonical and non-canonical effectors in fungi and oomycetes |
url |
http://cicy.repositorioinstitucional.mx/jspui/handle/1003/2819 |
work_keys_str_mv |
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_version_ |
1781883621633687552 |