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Sequence-based classification and identification of Fungi.

David Hibbett1, Kessy Abarenkov, Urmas Kõljalg

  • 1a Biology Department, Clark University, Worcester, Massachusetts 01610.

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PubMed
Summary

Integrating molecular data is key for fungal research. Advances in sequencing, data standards, and taxonomic practices are needed for comprehensive fungal sequence-based classification and identification (SBCI).

Keywords:
biodiversity informaticsmetagenomicsmolecular ecologynomenclaturesystematicstaxonomy

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Area of Science:

  • Fungal Taxonomy and Ecology
  • Genomics
  • Molecular Biology

Background:

  • Molecular methods have transformed fungal taxonomy and ecology, linking them to genomics and functional biology.
  • A gap exists between traditional specimen-based systematics and modern metagenomic/metatranscriptomic studies, hindering understanding of fungal community diversity and function.

Purpose of the Study:

  • To review current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi.
  • To highlight progress in prokaryotic SBCI and identify areas for fungal advancement.

Main Methods:

  • Review of existing literature and resources in fungal and prokaryotic sequence-based classification.
  • Analysis of current limitations and future opportunities in fungal molecular ecology and systematics.

Main Results:

  • Improvements in sequencing technologies (long-read, single-cell) are crucial for fungal molecular ecology.
  • Enhanced data quality and accessibility require standardized data/metadata and strict deposition policies.
  • Updates to nomenclatural rules are needed for valid publication of sequence-based fungal taxa.

Conclusions:

  • Realizing the full potential of fungal SBCI necessitates advancements in sequencing, data management, taxonomic practices, and nomenclatural rules.
  • Cultural shifts are essential to encourage SBCI adoption and recognize contributions to community resources.