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Step‐by‐Step Pipeline for the Ecological Analysis of Endophytic Fungi using ITS nrDNA Data
dc.creator | Montero Vargas, Maripaz | |
dc.creator | Escudero Leyva, Efraín | |
dc.creator | Díaz Valerio, Stefani | |
dc.creator | Chaverri Echandi, Priscila | |
dc.date.accessioned | 2021-02-18T18:17:31Z | |
dc.date.available | 2021-02-18T18:17:31Z | |
dc.date.issued | 2020-01-07 | |
dc.identifier.citation | https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpmc.96 | |
dc.identifier.issn | 1934-8533 | |
dc.identifier.uri | https://hdl.handle.net/10669/82870 | |
dc.description.abstract | The 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, Inc | es_ES |
dc.description.sponsorship | Centro Nacional de Alta Tecnología/[]/CeNAT/Costa Rica | es_ES |
dc.description.sponsorship | Universidad de Costa Rica/[111-B7-176]/UCR/Costa Rica | es_ES |
dc.description.sponsorship | Universidad de Costa Rica/[809‐B9‐662]/UCR/Costa Rica | es_ES |
dc.description.sponsorship | National Sanitation Foundation/[DEB‐1638976]/NSF/Estados Unidos | es_ES |
dc.language.iso | eng | es_ES |
dc.source | Current Protocols in Microbiology, vol.56(1) | es_ES |
dc.subject | Database | es_ES |
dc.subject | Ecological guilds | es_ES |
dc.subject | Fungal communities | es_ES |
dc.subject | Fungi | es_ES |
dc.subject | ITS region | es_ES |
dc.subject | Phylogenetics | es_ES |
dc.title | Step‐by‐Step Pipeline for the Ecological Analysis of Endophytic Fungi using ITS nrDNA Data | es_ES |
dc.type | artículo original | |
dc.identifier.doi | 10.1002/cpmc.96 | |
dc.description.procedence | UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigaciones en Productos Naturales (CIPRONA) | es_ES |
dc.description.procedence | UCR::Vicerrectoría de Docencia::Ciencias Básicas::Facultad de Ciencias::Escuela de Biología | es_ES |
dc.identifier.codproyecto | 111-B7-176 | |
dc.identifier.codproyecto | 809‐B9‐662 |
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Biología [1616]