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

Montero‐Vargas Maripaz; Escudero‐Leyva Efraín; Díaz‐Valerio StefaniChaverri Priscila

首页> 外文期刊>Current Protocols in Microbiology >Step‐by‐Step Pipeline for the Ecological Analysis of Endophytic Fungi using ITS nrDNA Data

【24h】

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

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

获取原文

获取原文并翻译 | 示例

掌桥外文数据库（机构版） >>

开具论文收录证明 >>

文献代查 >>

页面导航

摘要
著录项
相关主题

摘要

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

著录项

来源
《Current Protocols in Microbiology》 |2020年第1期|n/a-n/a|共14页
作者
Montero‐Vargas Maripaz; Escudero‐Leyva Efraín; Díaz‐Valerio StefaniChaverri Priscila;
展开▼
作者单位

Colaboratorio Nacional de Computación Avanzada (CNCA)CeNAT‐CONARESan José,Costa Rica;

Escuela de Biología and Centro de Investigaciones en Productos Naturales (CIPRONA)Universidad de Costa RicaSan José,Costa Rica;

展开▼
收录信息
原文格式 PDF
正文语种英语
中图分类微生物学;
关键词
database; ecological guilds; fungal communities; fungi; ITS region; phylogenetics;

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

摘要

著录项

相关主题

期刊订阅