Closed jingluodatacurator closed 11 months ago
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?
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.
Hi @CuzickA, the title includes them all I think as it says '..mutants resistant to SDH Inhibitors'.
Sounds like it might be useful to include them then please @jingluodatacurator
It looks like this sessions needs a few more annotations once @jingluodatacurator has her email and GitHub access restored.
tagging @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.
Curation completed and pending review @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
This one should be 'normal growth on isopyrazam' if no differences were observed between mutant and wild type.
Likewise, this one would also be 'normal growth on carboxin'
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
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 :-)
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
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.
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.
- 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'
- 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.
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
Hi @CuzickA, I can't quite understand what you have done here. Maybe we could discuss it in tomorrow's meeting too, thanks.
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
Hi @CuzickA, I can't quite understand what you have done here. Maybe we could discuss it in tomorrow's meeting too, thanks.
Hi @jingluodatacurator, this is information that I am adding in when I check the sessions. I have been working on this AE with Nichola. We are adding in the equivalent mutation position in the archetype species target site. Happy to discuss at tomorrow's meeting but for now I'll take care of making these entries and checking them through with Nichola.
Next steps 1) Additional annotations to be made for pathogen only and PHI phenotypes. (Jing) 2) Check AE alteration in archetype with Nichola. (AC)
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.
- 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'
- 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.
Hi @jingluodatacurator, I have reactivated the session so you should be able to go ahead and try adding in the new annotations. It would be great if you could have a go at this following the main PHI-Canto Help documentation and the Google FAQ document. We can then discuss any issues/sticking points when we meet tomorrow :-).
Hi @CuzickA, I'm not sure why I can't attach a snip image here?! I will email it to you now.
New pathogen phenotype annotations look fine
New PHI annotations
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
Feedback continued for @jingluodatacurator
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'
@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.
Now looks like this
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.
Note to self 1) Add host strain to list 2) Create new PHI-ECO term for '25 dpi' 3) Create new PHIPO term
Feedback on PHI annotations for @jingluodatacurator
- 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
- 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.
Hi @jingluodatacurator,
yes, this looks good for the wild type control metagenotype for SdhC
Next steps, edit the PHIPO terms and AEs
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.
Hi @jingluodatacurator, these look great
Note to self
- Add host strain to list
- Create new PHI-ECO term for '25 dpi'
- 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.
Terms now loaded into PHI-Canto.
Need AE archetype checking by Nichola and then session will be ready to approve.
AE archetype checked by Nichola and looks fine. Approving session and closing ticket.
Curated by @jingluodatacurator
https://canto.phi-base.org/curs/46cc4ab2f530d7cf