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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

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Functional Annotation Workflow for Fungal Transcriptomes.

Nagisa Morihara¹, Hidemasa Bono^1,2

¹Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8528, Hiroshima, Japan.

Journal of Fungi (Basel, Switzerland)

|February 26, 2026

Summary

This summary is machine-generated.

This study introduces a new fungal-specific functional annotation workflow for RNA sequencing (RNA-seq) data. It enables rapid, accurate transcript analysis, even without reference genomes, aiding fungal research and applications.

Keywords:

RNA sequencing full-length transcript sequencing functional annotation shiitake mushroom soybean rust transcriptome profiling

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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

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Area of Science:

Fungal genomics
Transcriptomics
Bioinformatics

Background:

Functional annotation of fungal transcriptomes is challenging due to limited reference genomes for non-model species.
Existing tools often lack fungal specificity and require reference genomes, hindering analysis of novel fungal species.
RNA sequencing (RNA-seq) provides rapid transcriptome profiling but requires robust annotation methods.

Purpose of the Study:

To develop a fungal-specific functional annotation workflow for RNA sequencing (RNA-seq) data.
To enable rapid and accurate functional analyses independent of reference genome availability.
To improve functional detection resolution compared to existing annotation tools.

Main Methods:

Development of a fungal-specific annotation workflow.
Application of the workflow to RNA-seq and full-length transcript sequencing (Iso-Seq) data from *Lentinula edodes* (shiitake mushroom) and *Phakopsora pachyrhizi* (Asian soybean rust).
Evaluation of annotation accuracy and functional enrichment detection.

Main Results:

The workflow successfully annotated over 96% of protein-coding transcripts.
Demonstrated applicability to both RNA-seq and Iso-Seq data.
Achieved higher-resolution functional detection and identified potential targets for genome editing.

Conclusions:

The developed workflow facilitates rapid and accurate functional annotation of fungal transcriptomes.
It is applicable to various fungal species, including those without reference genomes.
The workflow aids in discovering functionally important transcripts for biotechnological applications.