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Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health

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FunFun: ITS-based functional annotator of fungal communities.

Danil V Krivonos¹, Dmitry N Konanov¹, Elena N Ilina¹

¹Research Institute for Systems Biology and Medicine (RISBM) Moscow Russia.

Ecology and Evolution

|March 13, 2023

Summary

FunFun enables functional gene content evaluation from fungal ITS sequencing data, overcoming limitations of traditional methods for individual fungi and mycobiomes.

Keywords:

bioinformatics fungal community fungi

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Area of Science:

Mycology
Genomics
Bioinformatics

Background:

Fungi are crucial in biology, producing useful compounds and causing diseases.
Fungal functional capabilities are linked to gene content, typically assessed via whole-genome sequencing.
Whole-genome sequencing is infrequent; ITS amplicon sequencing is common for fungal taxonomy but lacks functional annotation.

Purpose of the Study:

To develop an instrument, FunFun, for evaluating gene content from ITS sequencing data.
To enable functional annotation for individual fungi and mycobiomes without whole-genome sequencing.

Main Methods:

FunFun utilizes a modified K-nearest neighbors algorithm.
The tool accepts ITS1, ITS2, or full ITS cluster (ITS1-5.8S-ITS2) sequences as input.
It is a command-line instrument installed via pip and validated using a shuffle-split approach.

Main Results:

FunFun accurately predicts gene content and functional capabilities from ITS sequencing data.
The instrument provides high accuracy in predicting the most variable fungal functions.
Validated performance using a shuffle-split approach.

Conclusions:

FunFun is a valuable tool for fungal community analysis and functional capability assessment.
It bridges the gap between taxonomic identification using ITS sequencing and functional insights.
Enables broader functional studies in mycology where whole-genome data is unavailable.