On the unreliability of published DNA sequences

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.