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Step‐by‐Step Pipeline for the Ecological Analysis of Endophytic Fungi using ITS nrDNA Data

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dc.creatorMontero Vargas, Maripaz
dc.creatorEscudero Leyva, Efraín
dc.creatorDíaz Valerio, Stefani
dc.creatorChaverri Echandi, Priscila
dc.date.accessioned2021-02-18T18:17:31Z
dc.date.available2021-02-18T18:17:31Z
dc.date.issued2020-01-07
dc.description.abstractThe nuclear ribosomal DNA internal transcribed spacer (ITS) is accepted as the genetic marker or barcode of choice for the identification of fungal samples. Here, we present a protocol to analyze fungal ITS data, from quality preprocessing of raw sequences to identification of operational taxonomic units (OTUs), taxonomic classification, and assignment of functional traits. The pipeline relies on well‐established and manually curated data collections, namely the UNITE database and the FUNGuild script. As an example, real ITS data from culturable endophytic fungi were analyzed, providing detailed descriptions for every step, parameter, and downstream analysis, and finishing with a phylogenetic analysis of the sequences and assigned ecological roles. This article constitutes a comprehensive guide for researchers that have little familiarity with bioinformatic analysis of essential steps required in further ecological studies of fungal communities. © 2020 by John Wiley & Sons, Inces_ES
dc.description.procedenceUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigaciones en Productos Naturales (CIPRONA)es_ES
dc.description.procedenceUCR::Vicerrectoría de Docencia::Ciencias Básicas::Facultad de Ciencias::Escuela de Biologíaes_ES
dc.description.sponsorshipCentro Nacional de Alta Tecnología/[]/CeNAT/Costa Ricaes_ES
dc.description.sponsorshipUniversidad de Costa Rica/[111-B7-176]/UCR/Costa Ricaes_ES
dc.description.sponsorshipUniversidad de Costa Rica/[809‐B9‐662]/UCR/Costa Ricaes_ES
dc.description.sponsorshipNational Sanitation Foundation/[DEB‐1638976]/NSF/Estados Unidoses_ES
dc.identifier.citationhttps://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpmc.96
dc.identifier.codproyecto111-B7-176
dc.identifier.codproyecto809‐B9‐662
dc.identifier.doi10.1002/cpmc.96
dc.identifier.issn1934-8533
dc.identifier.urihttps://hdl.handle.net/10669/82870
dc.language.isoenges_ES
dc.rightsacceso abierto
dc.sourceCurrent Protocols in Microbiology, vol.56(1)es_ES
dc.subjectDatabasees_ES
dc.subjectEcological guildses_ES
dc.subjectFungal communitieses_ES
dc.subjectFungies_ES
dc.subjectITS regiones_ES
dc.subjectPhylogeneticses_ES
dc.titleStep‐by‐Step Pipeline for the Ecological Analysis of Endophytic Fungi using ITS nrDNA Dataes_ES
dc.typeartículo original

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