PMID:31246152 The Synchytrium endobioticum AvrSen1 Triggers a Hypersensitive Response in Sen1 Potatoes While Natural Variants Evade Detection.

[CuzickA]

curation link
https://canto.phi-base.org/curs/59484877a87d5786

Author contacted PHI-base and requested article to be curated.
I have had a go at curating this paper into PHI-Canto and added queries into the comment section of the annotations.

The pathogen 'mutant' genotypes have been identified as natural strain variants (and grouped into pathotypes).
This has caused difficulties in the past for PHI-base curation and a temporary evidence code for 'natural variation was created' rather than deletion etc.
In PHI-Canto do we need to specify whether the genotype arose from natural strain variation or was created within the lab?

Just to note:
Pathogen AvrSen1 triggers an HR in the presence of host Resistance gene Sen1.
Sen1 has not yet been isolated so there is no uniprot. Presence or absence of the Sen1 locus in the host strain is determined by markers generated from mapping populations.

@ValWood please check this session when you have time.

[CuzickA]

The lower two metagenotypes above with also need the 'NV' tag when it is available.
pombase/canto#2346

[CuzickA]

After discussion today with @ValWood and Kim H-K we decided to remove AE disease_caused Potato wart

It is misleading as the potato wart disease is observed on tubers and there are no expts in the paper showing disease. The Expt are based on leaves exhibiting an HR or not.

As discussed in pombase/canto#2206 we would prefer another curation type for capturing 'disease'. Therefore I will remove these AE from this session and document in record in
https://docs.google.com/spreadsheets/d/1806Vhv58ngmql-Z5fIEl7k0BxGx4CQoqamlOYvNwYSk/edit?usp=sharing

Also NTR: compatible interaction, functional host resistance gene present
Def: A pathogen host interaction phenotype where the gene-for-gene relationship between the pathogen and plant host results in disease susceptibility. The ability of a host to be resistant to a pathogen, via the recognition of a pathogen effector by a specific host resistance gene, is present. (The presence of a function pathogen effector is unknown due to a lack of data showing whether it is able to cause disease).

[CuzickA]

From PHI-base/phipo#299

The term below, developed for the avrSen1/Sen1 paper will now need further review. We have changed the function of an effector from 'to cause disease' to 'be recognised by host R gene'.

PHIPO_EXT:0000029 compatible interaction, functional host resistance gene present

A pathogen host interaction phenotype where the gene-for-gene relationship between the pathogen and plant host results in disease susceptibility. The ability of a host to be resistant to a pathogen, via the recognition of a pathogen effector by a specific host resistance gene, is present. (The presence of a functional pathogen effector is unknown due to a lack of data showing whether it is able to cause disease).

I think we could obsolete this 2-component term and use the newly updated 3-component terms - to discuss in the next Gene-for-gene curation meeting.

New PHIPO_EXT already mocked up within the curation session comments

[CuzickA]

Screen shot of annotations as a record prior to next set of edits

Updates below with PHIPO_EXT terms edited to record 'effector recognition by host R gene' rather than 'effector ability to cause disease'

@ValWood another one to look at whilst reviewing the biotrophic GfG AE

We need the 'natural variant' description tag for this session.

[CuzickA]

Just used new Disease name curation type to add the general disease info on potato tubers that seemed to be missing from this session.

[CuzickA]

Should these WT metagenotype also be annotated under disease?
Rules
WT metagenotype with a compatible/disease outcome for all strain combinations and for each gene (to hang off PHI5 gene page)

[CuzickA]

I think I will leave out the additional disease curation annotations above and just leave it at one metagenotype disease annotation for now.

This session still needs a review for capturing the GfG AE and the NV tag.

Approving session for now but leaving ticket open.

[CuzickA]

Can't curate control metagenotypes as all metagenotypes are WT with natural variation. See #96