Functional annotation of a divergent genome using sequence and structure-based homology. DOI Creative Commons
Dennis Svedberg, Rahel R. Winiger, Alexandra Berg

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Авг. 28, 2023

Abstract Background Microsporidia are a large taxon of intracellular pathogens characterized by extraordinarily streamlined genomes with unusually high sequence divergence and many species-specific adaptations. These unique factors pose challenges for traditional genome annotation methods based on homology. As result, the microsporidian sequenced to date contain numerous genes unknown function. Recent innovations in rapid accurate structure prediction comparison, together growing amount data structural databases, provide new opportunities assist functional newly genomes. Results In this study, we established workflow that combines structure-based gene approaches employing ChimeraX plugin, allowing visual inspection manual curation. We employed high-quality telomere-to-telomere tetraploid Vairimorpha necatrix . First, 3080 predicted open reading frames, which 89 % were confirmed RNA sequencing data, used as input. Next, ColabFold was create protein predictions, followed Foldseek search matching PDB AlphaFold databases. The subsequent curation, using hits, increased accuracy quality compared results only tools. Our resulted comprehensive description V. genome, along summary most prevalent groups, such ricin B lectin family. addition, test our tool, identified functions several previously uncharacterized Encephalitozoon cuniculi genes. Conclusion tool divergent organisms employ it sequenced, shed light pathogen Lepidoptera. addition approach can serve valuable template studying other or similarly species.

Язык: Английский

Functional annotation of a divergent genome using sequence and structure-based homology. DOI Creative Commons
Dennis Svedberg, Rahel R. Winiger, Alexandra Berg

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Авг. 28, 2023

Abstract Background Microsporidia are a large taxon of intracellular pathogens characterized by extraordinarily streamlined genomes with unusually high sequence divergence and many species-specific adaptations. These unique factors pose challenges for traditional genome annotation methods based on homology. As result, the microsporidian sequenced to date contain numerous genes unknown function. Recent innovations in rapid accurate structure prediction comparison, together growing amount data structural databases, provide new opportunities assist functional newly genomes. Results In this study, we established workflow that combines structure-based gene approaches employing ChimeraX plugin, allowing visual inspection manual curation. We employed high-quality telomere-to-telomere tetraploid Vairimorpha necatrix . First, 3080 predicted open reading frames, which 89 % were confirmed RNA sequencing data, used as input. Next, ColabFold was create protein predictions, followed Foldseek search matching PDB AlphaFold databases. The subsequent curation, using hits, increased accuracy quality compared results only tools. Our resulted comprehensive description V. genome, along summary most prevalent groups, such ricin B lectin family. addition, test our tool, identified functions several previously uncharacterized Encephalitozoon cuniculi genes. Conclusion tool divergent organisms employ it sequenced, shed light pathogen Lepidoptera. addition approach can serve valuable template studying other or similarly species.

Язык: Английский

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