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Fungal genomes: suffering with functional annotation errors.

Tapan Kumar Mohanta1, Ahmed Al-Harrasi2

  • 1Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman. nostoc.tapan@gmail.com.

IMA Fungus
|November 2, 2021
PubMed
Summary

Functional annotation errors in fungal proteomes are common, affecting proteins involved in calcium signaling and other pathways. These errors, including misidentified calcium-dependent protein kinases and WRKY transcription factors, compromise data accuracy and require urgent correction.

Keywords:
AnnotationCalcium dependent protein kinaseCalcium signalingFungal genomeFungiGenomeSelenoproteinWRKY

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Area of Science:

  • Genomics
  • Proteomics
  • Bioinformatics

Background:

  • Vast amounts of genome sequence data are publicly available, necessitating accurate functional annotation for effective research.
  • Functional annotation is crucial for researchers to optimally utilize accumulating genomic data.

Purpose of the Study:

  • To identify functional annotation errors in fungal proteome sequence data.
  • To investigate discrepancies in the annotation of proteins related to calcium signaling, transcription factors, and metabolic pathways.

Main Methods:

  • Analysis of proteome sequence data from 689 fungal species (7.15 million protein sequences).
  • Targeted analysis of proteins including calcium-dependent protein kinases (CDPKs), calmodulins (CaM), calmodulin-like (CML) proteins, WRKY transcription factors, and selenoproteins.
  • Utilized InterproScan for sequence analysis to verify functional domains.

Main Results:

  • Identified proteins annotated as CDPKs lacked calcium binding EF-hands.
  • Proteins annotated as selenoproteins did not contain the Sec (U) amino acid.
  • Discrepancies were found in CaM and CML proteins regarding the number of calcium binding EF-hands.
  • Fungal proteins were erroneously annotated as WRKY transcription factors despite lacking the characteristic WRKY domain.

Conclusions:

  • Significant functional annotation errors exist in fungal genome and proteome databases.
  • These inaccuracies pose a considerable concern for the scientific community.
  • Timely correction of these annotation errors is essential for reliable data interpretation.