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Rare Event Detection Using Error-corrected DNA and RNA Sequencing
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On the unreliability of published DNA sequences.

Paul D Bridge1,2,3, Peter J Roberts2, Brian M Spooner2

  • 1School of Biological and Chemical Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK.

The New Phytologist
|April 20, 2021
PubMed
Summary

Published fungal nucleic acid sequences, particularly ribosomal RNA (rRNA) gene sequences, may have significant reliability issues. Our analysis indicates up to 20% of these crucial genetic markers could be inaccurate, impacting fungal research.

Keywords:
DNA sequencesdatabasesfungireliabilityribosomal RNAsystematics

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Area of Science:

  • Mycology
  • Molecular Biology
  • Bioinformatics

Background:

  • Ribosomal RNA (rRNA) gene sequences are vital for fungal phylogeny, evolution, and identification in non-culture based studies.
  • Public-access databases host a large volume of fungal nucleic acid sequences used in research.
  • Ensuring the reliability of these publicly available sequences is critical for scientific integrity.

Purpose of the Study:

  • To critically re-evaluate the reliability of published fungal nucleic acid sequences.
  • To assess the accuracy of ribosomal RNA (rRNA) gene sequences commonly used in fungal research.
  • To quantify potential unreliability in publicly available fungal genetic data.

Main Methods:

  • Re-evaluation of 206 named fungal nucleic acid sequences from public databases.
  • Focus on sequences from the ribosomal RNA (rRNA) gene cluster, including internal transcribed spacer (ITS) and small subunit rRNA.
  • Selection of fungal groups (Amanita, Phoma, Helotiales) with sequences from multiple laboratories to mitigate sample bias.

Main Results:

  • Up to 20% of available rRNA sequences for the studied fungal groups may be unreliable.
  • This level of unreliability was observed across different fungal genera and orders.
  • Informal observations support the quantitative findings on sequence reliability.

Conclusions:

  • A significant proportion of publicly available fungal rRNA gene sequences may be unreliable.
  • The findings highlight a potential issue impacting fungal evolutionary studies and identification.
  • Researchers should exercise caution when utilizing public fungal sequence data and consider validation.