Abstract

This tutorial is for you if you are a mycologist using metabarcoding data to understand the fungal composition of soil samples. In particular, this tutorial and its downstream applications will be of most interest to mycorrhizal scientists. Society for the Protection of Underground Networks (SPUN) is a research and advocacy organisation that uses Illumina sequencing of environmental environmental DNA (eDNA) from soil samples to identify mycorrhizal fungi. At SPUN, we use both Internal Transcribed Spacer 2 (ITS2) and Small Subunit (RNA) (SSU) amplicon sequencing to identify ectomycorrhizal and arbuscular mycorrhizal fungi, respectively. This tutorial focuses on the ITS2 sequencing used to identify Mycorrhizal fungi (MF).

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

• What is the fungal community composition in a given soil sample?

Learning Objectives

• Understand the files needed for running LotuS2
• Learn to use datasets from Zenodo in a Galaxy tool
• Learn to upload data files to Galaxy
• Learn to run the Galaxy LotuS2 tool and what the parameters mean
• Understand the output files from LotuS2
• Understand the structure of the mapping file needed by LotuS2 to link sample metadata to a pair of FASTQ files