Classical problem of data driven vs hypothesis driven research.
Contrasting with other comparisons might also be a way to show that there is little/no diff in focal contrast.

Depends on the testing system, or?
If you need to expect variable background regulation (like from field samples) you should consider higher n in experimental planning.
Higher thresholds only in case the data has been collected?

#plants #plantbiology #genomics #evolution #transcriptomics #WGCNA #Solanum #QDR #phytopathology

If you dont have time to read the whole manuscript, make sure not to miss @pngsabrina.bsky.social 's commentary!
tinyurl.com/49c2wazk

I am very grateful for the trust and support of my collaborators Chris T.-Ramirez, Florent Delplace and @rstam.bsky.social
I’d also like to thank the reviewers for their time and helpful input, which really improved the manuscript and sparked valuable discussions.

Very exciting: the natural #diversity across S. pennellii accessions supports the hypothesis for a role of NAC29 in #resistance: two accessions with premature STOP codons are indeed highly susceptible to sclerotinia! So, we hypothesize that NAC29 divergence might play a role in QDR evolution!

We also observed significant regulatory plasticity of the putative QDR-TFs and their downstream networks as exemplified by #spNAC29 (OG0005445). It is central in the S. pennellii QDR network, but not in any of the other species. A first hint that #cooption might drive QDR!

By generating species-wise gene coexpression #networks ( #WGCNA) and gene regulatory networks, we compared the QDR-driving networks of S. pennellii and S. lycopersicoides. We observed some overlap between both networks, but also a considerable number of species-specific nodes.

We then observed that regulatory pattern do not resemble the degree of QDR. We could confirm this observation with a pan-species gene coexpression network. #Gene-expression pattern do not follow a gradient of QDR. This supports the hypothesis of diversified QDR-regulation.

We used #orthogroups to observe the QDR-regulation in this pan-species panel. Interestingly, we found strong evidence that resistance-associated reprogramming is species-specific! Only a few DEOGs are shared across all species!

Next, we wanted to understand how one of those QDR mechanisms (lesion doubling time) is controlled and whether conserved or divergent regulatory patterns underlie this #resistance phenotype.
We conducted a #phylotranscriptomic study on our most favourite Solanum species:

This journey started with a thorough look at infection phenotypes. Using image-based #phenotyping, we characterised distinct mechanisms that are driving QDR against #Sclerotinia and found an astonishing diversity in wild Solanum species!
Read more about this here:

📸https://tinyurl.com/3wjwxncm

🔗 More info here: https://www.uni-kiel.de/en/details/news/167-barragan-noether