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{"title":"Step-by-Step Pipeline for the Ecological Analysis of Endophytic Fungi using ITS nrDNA Data","authors":"Maripaz Montero-Vargas, Efraín Escudero-Leyva, Stefani Díaz-Valerio, Priscila Chaverri","doi":"10.1002/cpmc.96","DOIUrl":null,"url":null,"abstract":"<p>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.</p><p><b>Basic Protocol 1</b>: Raw sequencing data processing</p><p><b>Support Protocol</b>: Building a BLAST database</p><p><b>Basic Protocol 2</b>: Obtaining information from databases</p><p><b>Basic Protocol 3</b>: Phylogenetic analysis</p>","PeriodicalId":39967,"journal":{"name":"Current Protocols in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2020-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpmc.96","citationCount":"1","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Current Protocols in Microbiology","FirstCategoryId":"1085","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/cpmc.96","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
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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.
Basic Protocol 1 : Raw sequencing data processing
Support Protocol : Building a BLAST database
Basic Protocol 2 : Obtaining information from databases
Basic Protocol 3 : Phylogenetic analysis
利用ITS nrDNA数据逐步进行内生真菌生态分析的流水线
核糖体DNA内转录间隔段(ITS)被公认为真菌样品鉴定的遗传标记或条形码的选择。在这里，我们提出了一种分析真菌ITS数据的方案，从原始序列的高质量预处理到操作分类单元(otu)的识别，分类分类和功能性状的分配。该管道依赖于完善的和人工管理的数据收集，即UNITE数据库和FUNGuild脚本。以可培养内生真菌的真实ITS数据为例，对其每个步骤、参数和下游分析进行了详细描述，并对序列和指定的生态作用进行了系统发育分析。这篇文章构成了一个全面的指南，为研究人员不熟悉的生物信息学分析的必要步骤，在进一步的生态真菌群落的研究。©2020 by John Wiley &基本协议1:原始测序数据处理支持协议:建立BLAST数据库基本协议2:从数据库中获取信息基本协议3:系统发育分析
本文章由计算机程序翻译，如有差异，请以英文原文为准。
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