PMID: 25758923 Functional analysis of the Fusarium graminearum phosphatome

[MPiovesana]

Curated by @MPiovesana.

https://canto.phi-base.org/curs/17124e4e388efe19

[MPiovesana]

The focus of this paper is to assess the phenotypes of mutant strains generated by deleting the phosphatases of Fusarium graminearum in the wild type PH-1 background. Among the phenotypes assessed, the susceptibility of deletion strains to fungicides (FK506, carbendazim and JS399-19) is tested; however, these results are only presented in supporting material (Table S2). Of 71 deletion mutants analysed, only two displayed an altered phenotype to a fungicide treatment (FG10302 and FG09532, which displayed sensitivity to FK506 (also known as tacrolimus). Therefore, I decided to only annotate the phenotypes associated with the FG10302delta and FG09532delta.

[MPiovesana]

Uniprot IDs: After identifying the reference proteome UP000070720 of F. graminearum on Uniprot, I searched for FG10302 and FG09532. The following Uniprot IDs were returned with this search: FG09532 = I1RYS3 FG10302 = I1S0R5

[MPiovesana]

Curation of antifungal susceptibility phenotypes: the sensitivity of deletion lines FG09532Δ and FG10302Δ to the antifungal tacrolimus was recorded with a new suggested PHIPO term (sensitive to tacrolimus (FK506)). I also recorded their normal growth on carbendazim with the new suggested term "normal growth on carbendazim". I could not locate the common name of the third antifungal tested (JS399-19); thus, I have not annotated the phenotypes associated with this compound (both lines display normal growth). Would it be relevant to add these annotations as well?

[MPiovesana]

Other phenotypes: I also curated other phenotypes associated with these single altered genotypes, including their reduced mycelial growth ("decreased hyphal growth"), reduced conidium production ("decreased number of asexual spores"), and altered production of DON (new suggested terms "increased production of deoxynivalenol (DON)" and "abolished production of deoxynivalenol (DON)").

AC: See below for DON

[MPiovesana]

Metagenotype annotations: the authors also test the pathogenicity of these deletion lines by infecting flowering wheat heads with conidial suspensions. I recorded the wt metagenotype control ("presence of pathogen-associated host lesions") and the altered metagenotypes ("decreased extent of pathogen-associated host lesions"). I am not sure if these are the best terms to describe the disease caused by F. graminearum on wheat heads, but after searching the list of PHIPO terms, these seemed appropriate.

The wheat cultivar used for this experiment is not provided by the authors, so I selected "unknown strain". Authors mention the assay was performed as described by Jiang et al, 2011, where I found details of experimental conditions; should I also consider the wheat cultivar used in this reference?

[MPiovesana]

Curation completed pending review.

[MPiovesana]

NOTE: throughout the text, typo instances are present where mutant strain FG09532Δ is referenced as FG05932 instead. Careful when reading text to avoid confusion.

[CuzickA]

I think these DON annotations need to move from pathogen phenotypes to PHI phenotypes as the pathogen was inoculated onto wheat kernels

Now changed to

[CuzickA]

Session now checked and edits made

AE alteration in archetype N/A as gene deletion study

Needs 1) PHIPO terms (added to PHIPO ticket) 2) PHI-ECO term (added to PHI-ECO term creator)

And then it will be ready to approve.

[CuzickA]

Hi @jseager7, I have a question about the PHI4 -> PHI5 data migration relating to this publication.

What happens when a publication is curated in both PHI4 and then a subset of the data is also curated in PHI-Canto? Which data will be displayed in PHI5?

[jseager7]

@CuzickA Currently the PHI-Canto curation supersedes all curation from PHI-base 4 for a publication. It may be technically possible to merge the curation, but this would have to be done on a case-by-case basis since it presumably won't be appropriate in all cases.

[CuzickA]

@CuzickA Currently the PHI-Canto curation supersedes all curation from PHI-base 4 for a publication. It may be technically possible to merge the curation, but this would have to be done on a case-by-case basis since it presumably won't be appropriate in all cases.

Thanks @jseager7, it might be worth keeping a note in your transfer files that this publication may require a curated data merge.

[CuzickA]

PHIPO term added.

Session approved, closing ticket.

[CuzickA]

Added disease annotation