PMID: 28456312 Characterization of boscalid-resistance conferring mutations in the SdhB subunit of respiratory complex II and impact on fitness and mycotoxin production in Penicillium expansum laboratory strains

[MPiovesana]

Discussion ticket opened by @MPiovesana

[MPiovesana]

This paper had been assigned as potentially curatable in the Excel spreadsheet. Here, authors generate laboratory mutant strains of Penicillium expansum by exposing a wild type strain to UV irradiation. Fifteen mutant isolates are identified and used for further experiments. In addition to characterising the antifungal susceptibility of these strains, authors proceed to sequence a fragment of the target gene SdhB to identify potential mutations. As presented in Table 4, some of the mutants display a point mutation at position 272 (numbering according to B. cinerea SdhB gene), while others retain the same amino acid (His) as the wild type at this position. As all fifteen mutants investigated display resistance to boscalid, but only a few harbour the aa substitution at position 272, antifungal resistance must be associated with other mutations which were not identified by the authors of the study.

As such, I believe this paper cannot be curated into PHI-Canto, as we the underlying mutations associated with boscalid resistance are unknown.

[MPiovesana]

Question: @CuzickA In several papers encountered during literature screening, mutant strains identified on the basis of their susceptibility/resistance to an antifungal compound are generated in the laboratory by similar methods (UV irradiation, induction of spontaneous mutants by exposure to antifungal on plates, etc). In these cases, authors sometimes compare whole genome sequencing information of the parental and mutant strains, allowing the identification of all SNPs present in mutant lines. Those mutations which are thought to be associated with the chemical resistance phenotype are also validated by complementation of the wild type / parental strain via gene replacement, for example, allowing a direct link between mutation and phenotype to be established. Alternatively, authors perform genetic crosses to observe the co-segregation of a mutant allele and the chemical antifungal resistance phenotype, another way to establish the correlation between allele and phenotype.

In other cases, however, after mutants are generated by directed evolution/mutagenesis, etc, authors proceed to identify mutations in candidate / target genes, but this is not followed by any experiment to validate the link between mutation and phenotype. Despite the likelihood of the two being connected, especially, in those cases where the target gene is known for a given fungicide, I wonder how confident we can be in curating these genotypes.

Should we formulate something to be included in user help text / FAQ regarding this issue? I believe that it can be confusing for community members who are not used to curating papers to identify which instances / experiments allow for curation. This paper could be used as an example.

[MPiovesana]

@CuzickA I think perhaps discussion of the question raised above could be interesting as we are currently drafting FAQ and user help text.

[MPiovesana]

@CuzickA Following the discussion above, this paper is assigned in Excel spreadsheet as non-curatable and I believe this ticket can be closed.