Afficher la notice abrégée

Comparison of Current Methods for Signal Peptide Prediction in Phytoplasmas

hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorGARCION, Christophe
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorBEVEN, Laure
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorFOISSAC, Xavier
dc.date.issued2021-03-25
dc.identifier.issn1664-302X
dc.description.abstractEnAlthough phytoplasma studies are still hampered by the lack of axenic cultivation methods, the availability of genome sequences allowed dramatic advances in the characterization of the virulence mechanisms deployed by phytoplasmas, and highlighted the detection of signal peptides as a crucial step to identify effectors secreted by phytoplasmas. However, various signal peptide prediction methods have been used to mine phytoplasma genomes, and no general evaluation of these methods is available so far for phytoplasma sequences. In this work, we compared the prediction performance of SignalP versions 3.0, 4.0, 4.1, 5.0 and Phobius on several sequence datasets originating from all deposited phytoplasma sequences. SignalP 4.1 with specific parameters showed the most exhaustive and consistent prediction ability. However, the configuration of SignalP 4.1 for increased sensitivity induced a much higher rate of false positives on transmembrane domains located at N-terminus. Moreover, sensitive signal peptide predictions could similarly be achieved by the transmembrane domain prediction ability of TMHMM and Phobius, due to the relatedness between signal peptides and transmembrane regions. Beyond the results presented herein, the datasets assembled in this study form a valuable benchmark to compare and evaluate signal peptide predictors in a field where experimental evidence of secretion is scarce. Additionally, this study illustrates the utility of comparative genomics to strengthen confidence in bioinformatic predictions.
dc.language.isoen
dc.publisherFrontiers Media
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subjectphytoplasme
dc.subjectbactérie phytopathogène
dc.subjectpathologie végétale
dc.subject.enbacteria
dc.subject.enMollicutes
dc.subject.enSignalP
dc.subject.enTMHMM
dc.subject.enPhobius
dc.subject.ensecretion
dc.subject.eneffector
dc.subject.entransmembrane domain
dc.title.enComparison of Current Methods for Signal Peptide Prediction in Phytoplasmas
dc.typeArticle de revue
dc.identifier.doi10.3389/fmicb.2021.661524
dc.subject.halSciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
dc.subject.halSciences du Vivant [q-bio]/Microbiologie et Parasitologie/Bactériologie
dc.subject.halSciences du Vivant [q-bio]
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale/Phytopathologie et phytopharmacie
bordeaux.journalFrontiers in Microbiology
bordeaux.page661524
bordeaux.volume12
bordeaux.peerReviewedoui
hal.identifierhal-03200258
hal.version1
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-03200258v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Frontiers%20in%20Microbiology&rft.date=2021-03-25&rft.volume=12&rft.spage=661524&rft.epage=661524&rft.eissn=1664-302X&rft.issn=1664-302X&rft.au=GARCION,%20Christophe&BEVEN,%20Laure&FOISSAC,%20Xavier&rft.genre=article


Fichier(s) constituant ce document

FichiersTailleFormatVue

Il n'y a pas de fichiers associés à ce document.

Ce document figure dans la(les) collection(s) suivante(s)

Afficher la notice abrégée