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Functional annotation of a divergent genome using sequence and structure-based similarity.

Dennis Svedberg1,2, Rahel R Winiger1, Alexandra Berg1,2

  • 1Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden.

BMC Genomics
|January 3, 2024
PubMed
Summary

We developed ANNOTEX, a novel tool combining sequence and structure data for accurate gene function annotation in microsporidia. This approach enhances understanding of these challenging intracellular pathogens and their genomes.

Keywords:
Functional annotationGenomeMicrosporidiaPolar tube proteinsRicin B lectinsStructural similarityVairimorpha necatrix

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Area of Science:

  • Genomics
  • Structural Biology
  • Bioinformatics

Background:

  • Microsporidia possess highly streamlined genomes, posing challenges for traditional gene annotation due to high sequence divergence.
  • Many microsporidian genes remain functionally uncharacterized, hindering biological understanding.
  • Advances in protein structure prediction and databases offer new avenues for functional gene annotation.

Purpose of the Study:

  • To develop and validate a novel workflow for functional gene annotation in microsporidian genomes.
  • To improve the accuracy and comprehensiveness of genome annotation for divergent organisms.
  • To characterize the genome of the microsporidian Vairimorpha necatrix.

Main Methods:

  • A workflow combining sequence and structure-based annotation using the ANNOTEX (Annotation Extension for ChimeraX) plugin was established.
  • Protein structure predictions were generated using ColabFold and searched against the PDB and AlphaFold databases with Foldseek.
  • Manual curation integrated sequence and structure-based evidence for enhanced annotation quality.

Main Results:

  • The workflow was applied to the Vairimorpha necatrix genome, annotating 3080 protein-coding sequences with high RNA sequencing confirmation.
  • Functional annotation accuracy and quality were significantly improved compared to traditional methods.
  • The study provided a comprehensive genome description for V. necatrix and identified functions for previously uncharacterized genes in Encephalitozoon cuniculi.

Conclusions:

  • A new functional annotation tool, ANNOTEX, was developed for divergent organisms like microsporidia.
  • The structure-based annotation approach provides a valuable template for studying other divergent species.
  • This work enhances the understanding of V. necatrix, an uncharacterized intracellular pathogen.