PMID:27644008 Characterisation of Ramularia collo-cygni laboratory mutants resistant to succinate dehydrogenase inhibitors

[jingluodatacurator]

Curated by @jingluodatacurator

https://canto.phi-base.org/curs/46cc4ab2f530d7cf

[jingluodatacurator]

Hi @CuzickA, I have curated 4 laboratory generated mutants (AA subst. by UV mutagenesis) resistant to boscalid (with highest severity of RF increase).
I'm not sure if I should also curate the mutants to all the other four fungicides?

[CuzickA]

Hi @jingluodatacurator, were the other four fungicides mentioned in the abstract? As a general rule we are trying to report on the information from the title and abstract of the publication.

[jingluodatacurator]

Hi @CuzickA, the title includes them all I think as it says '..mutants resistant to SDH Inhibitors'.

[CuzickA]

Sounds like it might be useful to include them then please @jingluodatacurator

[CuzickA]

It looks like this sessions needs a few more annotations once @jingluodatacurator has her email and GitHub access restored.

[CuzickA]

tagging @jingluodatacurator

[jingluodatacurator]

Hi @CuzickA, I have added all the other four fungicides (bixafen, isopyrazam, carboxin and fluopyram) for each mutant (Mutant 1, 11, 7 and 8) but not for Mutant 2 because.. (section 3.3 in the Result)

'Mut2, which had no detectable mutations in SdhB, C or D, showed a moderate level of resistance to isopyrazam (RF=31.55) and bixafen (RF=24.51). For the remaining three active ingredients, no differences in sensitivity were observed compared with the DK05 and the UK field population (boscalid RF=1.532, fluopyram RF=1.177, carboxin RF=2.752) (Table 4).'

Let me know if get this correct please.

[jingluodatacurator]

Curation completed and pending review @CuzickA

[CuzickA]

Used author given genbank ids to search for uniprots
'Full SdhB, SdhC and SdhD sequences can be found
in the GenBank database under the accession numbers KU758973,
KU758974 and KU758975 respectively'
SdhB https://www.uniprot.org/uniprotkb/A0A1S6KZ79/entry
SdhC https://www.uniprot.org/uniprotkb/A0A1S6KZ87/entry

Genotypes look good

[CuzickA]

This one should be 'normal growth on isopyrazam' if no differences were observed between mutant and wild type.

[CuzickA]

Likewise, this one would also be 'normal growth on carboxin'

[CuzickA]

Current Chemistry pathogen phenotypes now checked.

Next steps

1. new PHIPO terms (DONE 03_10_2023)
2. new PHI-ECO terms (DONE 03_10_2023)
3. add in AE alteration in archetype DONE see below

[CuzickA]

Hi @jingluodatacurator, I think there are a few more annotations that could be made for this paper. These annotations would also help you become more familiar with making 'non-chemistry' annotations using PHI-Canto.

1. Pathogen phenotype
   Maybe just the 14 dpi in vitro growth (without chemical)
   
   These are the current hyphal growth terms in PHIPO, we may to suggest a new term for 'increased rate of hyphae formation'
   

2. Pathogen host interaction phenotype
   Need to make metagenotypes for the wild type and mutant pathogens inoculated onto barley (untreated with chemical).
   Annotate with 'presence of pathogen-associated host lesions'. Same phenotype was seen with both wild type and mutant pathogen
   

Please try to have a go at making these annotations and then we can discuss any issues :-)

[CuzickA]

AE alteration_in_archetype

Ramularia collo-cygni

SdhB(aaS217L)[Not assayed] 'S228L; SdhB; PYRNTE'
SdhB(aaN224I)[Not assayed] 'N235I; SdhB; PYRNTE'
SdhC(aaH142R)[Not assayed] 'H134R; SdhC; PYRNTE'
SdhC(aaH142Q)[Not assayed] 'H134Q; SdhC; PYRNTE'

From Nichola's S file

[CuzickA]

AE alteration_in_archetype

Needs checking by Nichola.

Question: Target site name 'SdhB', 'SdhC' or 'SdhBCD'?
Maybe it is best keep them separate as Mair et al 2016 has three Sdh tables, one each for B, C and D.

NH (18_10_2023) Yes, keep these separate.

[jingluodatacurator]

Hi @jingluodatacurator, I think there are a few more annotations that could be made for this paper. These annotations would also help you become more familiar with making 'non-chemistry' annotations using PHI-Canto.

1. Pathogen phenotype
   Maybe just the 14 dpi in vitro growth (without chemical)
   
   These are the current hyphal growth terms in PHIPO, we may to suggest a new term for 'increased rate of hyphae formation'
   
2. Pathogen host interaction phenotype
   Need to make metagenotypes for the wild type and mutant pathogens inoculated onto barley (untreated with chemical).
   Annotate with 'presence of pathogen-associated host lesions'. Same phenotype was seen with both wild type and mutant pathogen
   

Please try to have a go at making these annotations and then we can discuss any issues :-)

Thanks @CuzickA, I may need some help on these annotations. Maybe we could discuss it in tomorrow's meeting.

[CuzickA]

New pathogen phenotype annotations look fine

[CuzickA]

New PHI annotations

[CuzickA]

Feedback on PHI annotations for @jingluodatacurator

1. The two metagenotypes with the altered pathogen inoculated onto the wild type host look pretty good. The wild type host 'H. vulgare' needs to have the strain/cultivar name added.
   From the text section 2.4 this is 'Optic'
   
   In this section, add 'optic' instead of 'wild type'
   
   

I have now made these changes with 'optic' as the wild type host strain/cultivar

2. For metagenotypes we also need to make a wild type control metagenotype, please see the help documentation https://canto.phi-base.org/docs/genotypes#metagenotype_management section 'Creating control metagenotypes'.
   Here is an example for SdhB
   

Jing, please have a go at creating the wild type control metagenotype for SdhC

[CuzickA]

Feedback continued for @jingluodatacurator

3. For the annotations here, we want to curate the pathogen inoculation onto host information without the chemistry.

Text from section 3.4.4.
'Disease symptoms, initial pepper-like spots expanding
to small, brown-to-blackish necrotic lesions, on the untreated
leaf segments were observed macroscopically from 25 DPI for all
three isolates used in this study (data not shown). This showed that
Mut11 and Mut7 could infect the host plant barley, reproduce successfully
by generating spores and complete their life cycle, further
suggesting that there was no measurable fitness penalty associated
with the target mutations conferring resistance to SDHIs.'

Note: this data is not shown, so we would remove 'Figure 4' and add 'Text p. 1192' to the 'Figure column'
From this text, I understand that the wild type and two pathogen mutants showed the same lesions in the host.
Therefore I would add the PHIPO term 'presence of pathogen-associated host lesions'

4. I have also changed the evidence code from 'other' to 'Macroscopic observation (qualitative observation)' as these lesions would be visible by eye.

@jingluodatacurator, please could you add/edit the PHIPO terms for the wild type and mutant SdhC inoculated onto barley (metagenotypes from 2 above).

The next set of comments with focus on the conditions and AEs.

[CuzickA]

5. Notes on conditions @jingluodatacurator
   
   i) We don't need to add 'leaf assay' here as this is not really a condition. A condition is adding a chemical, temperature etc. The AE infects tissue record the information about the 'leaf'
   ii) The text in the publication states that the disease symptoms were observed '25 dpi'. Therefore, I am changing '1 day post inoculation' to '25 days post inoculation' (note: the text is red as I will need to make a new ontology term)
   iii) Removing chemical
   iv) Also changed the light conditions to 'intermittent light' as seemed a better match (12 h light, 12 h dark cycles)

Now looks like this

[CuzickA]

6. notes on AEs for @jingluodatacurator
   i) Removing AEs severity and penetrance as not applicable.
   ii) For the mutant pathogen inoculated onto the wild type host we want to use the AE 'compared to'. We then add the corresponding wild type metagenotype. We can then add the AE infective ability 'unaffected pathogenicity' to the mutant metagenotype annotation as the wild type metagenotype and the mutant pathogen metagenotype have the same phenotype.
   This is what it wold look like
   
   

[CuzickA]

Session reactivated for @jingluodatacurator to make further changes.

In summary, read through above comments on the edits that I have made. Create the wild type metagenotype control for SdhC and make relevant annotations.

Please let me know if you have any follow up questions as I realise there is a lot to take on board here.

[CuzickA]

Note to self

1. Add host strain to list
2. Create new PHI-ECO term for '25 dpi'
3. Create new PHIPO term

[jingluodatacurator]

Feedback on PHI annotations for @jingluodatacurator

1. The two metagenotypes with the altered pathogen inoculated onto the wild type host look pretty good. The wild type host 'H. vulgare' needs to have the strain/cultivar name added.
   From the text section 2.4 this is 'Optic'
   
   In this section, add 'optic' instead of 'wild type'
   
   

I have now made these changes with 'optic' as the wild type host strain/cultivar

2. For metagenotypes we also need to make a wild type control metagenotype, please see the help documentation https://canto.phi-base.org/docs/genotypes#metagenotype_management section 'Creating control metagenotypes'.
   Here is an example for SdhB
   

Jing, please have a go at creating the wild type control metagenotype for SdhC

Hi @CuzickA, please check the wild type control metagenotype for SdhC been created, link below thanks.

https://canto.phi-base.org/curs/46cc4ab2f530d7cf

[CuzickA]

Hi @jingluodatacurator,

yes, this looks good for the wild type control metagenotype for SdhC

Next steps, edit the PHIPO terms and AEs

[jingluodatacurator]

Hi @jingluodatacurator,

yes, this looks good for the wild type control metagenotype for SdhC

Next steps, edit the PHIPO terms and AEs

Hi @CuzickA, PHIPO terms and AEs have been edited, please check on the link below thanks.

https://canto.phi-base.org/curs/46cc4ab2f530d7cf#

[CuzickA]

Hi @jingluodatacurator, these look great

[CuzickA]

Note to self

1. Add host strain to list
2. Create new PHI-ECO term for '25 dpi'
3. Create new PHIPO term

Above all done, just waiting for loading into PHI-Canto.
After this need AE archetype checking by Nichola and then session will be ready to approve.

[CuzickA]

Terms now loaded into PHI-Canto.

Need AE archetype checking by Nichola and then session will be ready to approve.

[CuzickA]

AE archetype checked by Nichola and looks fine. Approving session and closing ticket.