New preprint! I always wondered: How much diversity do pathogens have within a single field? This important to assess the risk of resistance breakdown or spread of fungicide resistance . Together with colleagues from BASF we looked into this. www.biorxiv.org/content/10.1... - ThreadSky

rstam.bsky.social • 55 days ago

New preprint! I always wondered: How much diversity do pathogens have within a single field? This important to assess the risk of resistance breakdown or spread of fungicide resistance . Together with colleagues from BASF we looked into this.
https://www.biorxiv.org/content/10.1101/2025.01.03.631207v1

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ljanss.bsky.social•51 days ago

Very interesting work finding large diversity in a fungal wheat pathogen. Can be fun to build on this with some epidemiological (host) genetic modeling, and to think about implications for disease resistance breeding

rstam.bsky.social•55 days ago

We look at the major wheat pathogen Zymoseptoria tritici. We sampled 160 isolates from a field in the UK sequenced the genomes. We contrast our field with published data from single sites (US: 98 isolates & CH: 158 isolates).

rstam.bsky.social•55 days ago

Total diversity differs per field (A). More isolates = more SNPs, but in both the UK and CH field SNPs start to plateau at ~150 isolates. Looking at the PCA of all SNPs (B), we can distinguish each field, suggesting some between field differentiation.

rstam.bsky.social•55 days ago

We see that SNPs are well dispersed over all chromosomes. Only few invariable regions can be detected. As expected, also regions containing effectors are rich in SNPs. This plot shows the summary for the UK field.

rstam.bsky.social•55 days ago

The PCA for effectors (A) shows no between field structure! We find many diverse haplotypes of well-known effectors in all fields! This can be seen in the Minimum Spanning Networks for AvrStb6 (B), avr3D1 (C) and AvrStb9 (D)

rstam.bsky.social•55 days ago

Lastly we show that within the UK field, different effector haplotypes (A) can be found within isolates that by previous definitions were considered clones and that these haplotypes co-occur within a single plant and/or lesion (B): each dot represents where the isolates were collected

rstam.bsky.social•55 days ago

Concluding: within-field diversity for Zymoseptoria is huge! We should keep this in mind when designing protection strategies. I.e. R gene deployment or fungicide use.

see also: https://bsppjournals.onlinelibrary.wiley.com/doi/abs/10.1111/mpp.12636

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