PMID:24913566 Molecular mechanism of resistance of Fusarium fujikuroi to benzimidazole fungicides.

MPiovesana commented 1 year ago

Curated by @MPiovesana https://canto.phi-base.org/curs/57500a0e921e0d10#

MPiovesana commented 1 year ago

In this paper three wild type strains of Fusarium fujikuroi are characterised based on their sensitivity to the fungicide carbendazim (MBC). Authors sequence the β2Tub gene of these strains, and identify mutations present in the sensitive (YC3), moderately resistant (YCA) and highly resistant (YC4201) strains. Deletion lines of β2Tub are generated and phenotypically characterised. Complementation lines are also generated by re-introducing the β2Tub gene in each respective background. The genotypes of the deletion lines were curated in this session.

MPiovesana commented 1 year ago

Uniprot IDs: authors provide the GenBank accession numbers for the β2Tub sequence of all three strains, which were used to retrieve respective Uniprot IDs:

KF771181 = W5RZY1 (β2Tub of sensitive strain YC3) KF771182 = W5RYV3 (β2Tub of moderate resistant strain YCA) KF771183 = W5RZ16 (β2Tub of highly resistant strain YC4201)

By using all three IDs in the curation session, it was possible to create individual deletion lines to record the phenotypes of all mutants described in the study.

AC: see comment below about needing to use one reference proteome uniprot id.

MPiovesana commented 1 year ago

Strains: strains YC3, YCA and YC4201 were manually added to the session.

MPiovesana commented 1 year ago

Genotype creation: deletion lines of β2Tub were created for all three strains, and a description of aa residues on positions of interest (codons 198 and 200) were added in brackets in the allele name. Codon 235 is also described in Table 1, but mutations in this codon are synonymous and, therefore, do not lead to aa change. Wild type alleles for all three strains were also created for metagenotype purposes.

AC: genotypes changed to use reference proteome uniprot. In the case of the deletion mutants the natural variation of aa residues were removed as this gene id deleted. changed to ![Uploading image.png…]()

MPiovesana commented 1 year ago

Genotype annotations: the following PHIPO terms were used: sensitive to carbendazim decreased rate of hyphae formation decreased number of asexual spores

MPiovesana commented 1 year ago

Metagenotypes: metagenotypes were created including wt and deletion alleles of β2Tub and tomato (S. lycopersicum in PHI-Canto; referred to as Lycopersicon esculentum in the paper. Both names refer to the same species to the best of my knowledge) cv. Kaisa. Control metagenotypes were assigned PHIPO term presence of pathogen-associated host lesions, and deletion metagenotypes with decreased extent of pathogen-associated host lesions.

MPiovesana commented 1 year ago

Curation completed pending review.

CuzickA commented 1 year ago

Uniprot IDs: authors provide the GenBank accession numbers for the β2Tub sequence of all three strains, which were used to retrieve respective Uniprot IDs:

KF771181 = W5RZY1 (β2Tub of sensitive strain YC3) KF771182 = W5RYV3 (β2Tub of moderate resistant strain YCA) KF771183 = W5RZ16 (β2Tub of highly resistant strain YC4201)

By using all three IDs in the curation session, it was possible to create individual deletion lines to record the phenotypes of all mutants described in the study.

We will need to use the same 'reference proteome' UniProt id for all the annotations in this session so that they are available on one PHI5 gene page.

Sessions annotating the same gene use P53374 https://www.uniprot.org/uniprotkb/P53374/entry see https://github.com/PHI-base/curation/issues/195 and https://github.com/PHI-base/curation/issues/194

I will update the UniProt id in the session.

CuzickA commented 1 year ago