PMID:30732567 Molecular characterization of carbendazim resistance of Fusarium species complex that causes sugarcane pokkah boeng disease

[MPiovesana]

Curated by @MPiovesana https://canto.phi-base.org/curs/8c52e5b463d36d1b

[MPiovesana]

Laboratory-induced mutants of Fusarium spp display increased resistance to the fungicide carbendazim. One of the mutants is derived from wild type strain SJ51 (Fusarium verticillioides) and carries a point mutation in one of the β-tubulin genes (FVER_09254). A second mutant is derived from wild type strain HC30 (Fusarium proliferatum), and also carries a point mutation in a β-tubulin gene (FPRO_07779). The fitness and pathogenicity of the mutant lines are analysed.

[MPiovesana]

Uniprot ID: although the authors provide gene IDs for the β-tubulin genes of F. verticillioides and F. proliferatum, these do not return any ID when used to search Uniprot. I also searched NCBI with these, and although the search returns gene entries, I could link those to Uniprot entries. Thus, I used the protein sequences displayed in Additional File 3, Figure S1 (amino acid alignments) to perform BLAST searches in Uniprot. With this search, the following IDs were retrieved:

β-tubulin Fusarium verticillioides = W7M0I3

β-tubulin Fusarium proliferatum = P53374 (this one was trickier as no result for Fusarium proliferatum was returned. After a google search I found that F. proliferatum is also known as Giberella fujikuroi, and thus this ID was selected. The length and the sequence of the protein match the one used in this study). AC: Also used in https://github.com/PHI-base/curation/issues/195 :-)

[MPiovesana]

Strains: strains HC30 (F. proliferatum/fujikuroi) and SJ51 (F. verticillioides) were manually added to the session.

AC: Now added in PHI-Canto

[MPiovesana]

Genotype creation: amino acid substitution allele types were created to represent the genotypes of the laboratory-induced mutants.

Genotype annotations: the chemical resistance, temperature sensitivity and pathogenicity of the mutant isolates were recorded with the following PHIPO terms:

resistance to carbendazim normal growth on carbendazim (suggested; could not find higher level term 'chemical phenotype' to suggest child term, so I made suggestion to 'increased sensitivity to chemical'. Term used to record the normal growth of HC30-derived mutant on carbendazim in low temperature, in contrast to standard and high temperatures) normal hyphal growth

Metagenoype annotations: the control and mutant metagenotypes composed of Fusarium spp pathogens and sugarcane (host) were recorded with PHIPO term 'presence of pathogen-associated host lesions'. The unaffected virulence of the mutant lines were highlighted with annotation extensions.

[MPiovesana]

Curation completed pending review.

[CuzickA]

Session checked and all looks fine. Just waiting for a new PHIPO term.

[CuzickA]

No alteration in archetype info found in Nichola's S file.

[CuzickA]

Try FRAST

[CuzickA]

β-tubulin Fusarium verticillioides /moniliformis FVER_09254

β-tubulin Fusarium fujikuroi / proliferatum FPRO_07779

Searching Genbank, cannot find obvious gene sequences.

AA sequence available in Additional file 3 but not in a copy and pasteable format.

I'm not sure how to proceed with looking up the archetype AE information for this one.

[CuzickA]

After discussion with Nichola 1)gene id prefixes incorrect in paper FVER->FVEG and FPRO->FPRN. 2) Look up FVEG_09254 and FPRN_07779 in genbank to obtain AA seqs 3)Try to align in FRAST and using info in paper above from additional file 3.

[CuzickA]

FVEG_09254 https://www.ncbi.nlm.nih.gov/nuccore/XM_018898235.1 FPRN_07779 https://www.ncbi.nlm.nih.gov/nuccore/XM_031234126.1

[CuzickA]

FVEG_09254 https://www.ncbi.nlm.nih.gov/nuccore/XM_018898235.1 Very bad / non-alignment in FRAST with beta-tubulin (alignment (?) not saved in FRAST). Unable to find AA sequence match of FASTA file with Additional file seq above.

Not sure how to proceed.

Actually looking at beta-tubulin archetype sequence at position 134 there is 'Q' which matches the Q134 in Fusarium verticillioides /moniliformis strain SJ51 (also Fusarium fujikuroi / proliferatum strains HC30 and HC30M) above.

Perhaps we could use this AE for βtub-Q134L(aaQ134L)[Not assayed] 'Q134L; β-tubulin; ASPEND'

[CuzickA]

FPRN_07779 https://www.ncbi.nlm.nih.gov/nuccore/XM_031234126.1

Similar poor alignment issue as above.

looking at beta-tubulin archetype sequence at position 351 there is 'S' which matches the S351 in Fusarium verticillioides /moniliformis strain SJ51 and SJ51M above.

However Fusarium fujikuroi / proliferatum strain HC30 has T351and HC30M has I351. Therefore Ff/Fp beta-tubulin differs from the archetype beta-tubulin sequence at position 351.

Perhaps we could use this AE for βtub-Q134L(aaQ134L)[Not assayed] '351I; β-tubulin; ASPEND' We would leave the first AA blank as this differed from the archetype.

To check this with Nichola.

[CuzickA]

Next steps 1) check AE with Nichola

Then session will be ready for approval.

[CuzickA]

Discussed poor alignment with Nichola. I have given her the sequence ids and she will look into this one.