Someone in the Arabidopsis/clock community seems to deeply dislike my work on research culture. Just want to say: whoever you are, please write & debate me directly instead of cowering behind anonymous grant reviews that threaten my students’ work. (2nd year in a row)
Back in the field: Eneza @enezer.bsky.social, Maria, and this year’s students are on Spiekeroog again in 2026, continuing to phenotype wild Arabidopsis in 2026. The dataset grows, and the story continues: Watching climate shape plants - in real time, in real environments.
Resequencing hundreds or thousands of individuals from the same species has become routine... but processing all those genomes efficiently? Still a headache!
Here's my solution that used to be lab-internal but that I am happy to share:
crolllab.github.io/genomepanel_...
1/11 🔥 New preprint alert 🔥
We wanted to know what plants in the wild really care about. So we asked them 🎤.
Here is what we learned: “Biotic-response networks are an important organizer of the transcriptome in wild Arabidopsis thaliana populations”
www.biorxiv.org/content/10.6...
This work would not have been possible without the help of:
@albertoglezdelgado.bsky.social
@wabniklab.bsky.social
@cbgpmadrid.bsky.social
@csic.es
@upm.es
@ijpb-versaillescly.bsky.social
@spsplantsciences.bsky.social
📄 Read it here: www.biorxiv.org/content/10.6...
Our observations fit a model in which evening-phased genes sense photoperiod through coincidence mechanisms and change transcription dynamics of morning-phased genes.
All this, brought to you by the incredible @albertoglezdelgado.bsky.social
@wabniklab.bsky.social
Let us know if you like it!!
We studied the characteristics of cycling transcripts separated by their phase (dawn vs. dusk). We see that they differ in expression levels, and in how their waveform is modulated by photoperiod.
Conclusion in next post...
🌱 New preprint out on bioRxiv!
How do plants sense seasonal changes in day length?
In our new study, we profiled high resolution (2h) RNA seq time courses in tomato across three photoperiods to uncover how light duration shapes gene expression dynamics.
Summary in next post...
Preprint!!!! This is the result of an ongoing collaboration between us and the genomics core to make genetics cheap and easy. A synergy between library prep and analytical approaches. This one hinges on recognizing 1. that DNA molecules are shaped by evolution and 2. we have friends everywhere.
Did you know that most knockouts in Arabidopsis actually do have phenotypes and aren't some redundancy situation? All you have to do is measure in multiple tissues in multiple environments and then the phenotypes show up. Redundancy was an assumption never tested.
Malate matters! Especially in tomato fruit, where malate reaches levels that would shut down “normal” metabolism. Tomato solves this with BTPC, part of a malate-insensitive Class-2 PEPC complex.
Chromosome-scale Solanum pennellii and Solanum cheesmaniae genome assemblies reveal structural variants, repeat content and recombination barriers of the tomato clade www.biorxiv.org/content/10.64898/2025.12...
Congrats to RootResponse lab members (CBGP) for this review in JXB
DOI: 10.1093/jxb/eraf520
how root traits, microbiome interactions, and epigenetic regulation play a role in plant heat stress resilience, stressing the need for lab approaches that closely reflect field-conditions
We (Nordborg & Weigel labs) need input on the next generation of genome browsers & data download modes for the #Arabidopsis #1001GenomesPlus project. We have now a curated collection of over 500 long read genomes.
Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...
New preprint from the lab on @biorxivpreprint.bsky.social! We show how SEPALLATA MADS-box genes in tomato functionally diverged to regulate inflorescence and floral organ development while maintaining redundant functions in conferring floral meristem identity.
www.biorxiv.org/content/10.1...
🗣️ Today, José Jiménez Gómez from @cbgpmadrid.bsky.social came to visit us in Málaga to share his research with a great talk entitled “Metabolic adaptations towards salt tolerance in Arabidopsis plants from the Cape Verde Islands” as part of our #IHSMLaMayoraSeminars series
Amazing talk by @jimenezgomez.bsky.social at @ihsmumacsic.bsky.social
PhD advert
I recently moved my lab to Purdue University and am looking for graduate students. We are working at the interface of population genomics, quantitative genetics and functional genomics to understand how plants adapt to extreme environments. Reach out if you would like to discuss potential projects.
There are lots of answers out there that are beautiful because the truth of the system is beautiful. If I find one of these beautiful facts, it doesn’t make me brilliant. Just right place and right time. True scientific heroes acknowledge that fact.
📋 Join us on Friday 14th for a fascinating seminar with the researcher José Jiménez Gómez (@cbgpmadrid.bsky.social, Centro de Biotecnología y Genómica de Plantas). Don't miss it!
🕓 9:30 AM
📍 IHSM La Mayora Auditorium
More information here! ⬇️
I’m very pleased to share our latest work, led by the talented @cbuckley.bsky.social as part of his PhD. It’s our first attempt at studying #circadian rhythms in wheat with the help of some great collaborators @jesshyles.bsky.social @adaevo.bsky.social et al. #plantsci 🌾⏰ 1/7
doi.org/10.1111/nph....
Save the date, 1-3 July 2026, for the XVIII Plant Molecular Biology Meeting #RBMP2026 in Bilbao. Check out the website for updates rbmp2026.com/RBMP/en/info
Out after peer review, collaborative study from Nordborg & Weigel labs with help from many others. Not the largest collection of new Arabidopsis thaliana genomes, but we hopefully put forward some good ideas for how to think about pangenomes and their analysis!
www.nature.com/articles/s41...
Like I mentioned last week I like it when plants find a way against all odds. It is not just the perseverance and adaption. But also, that we can learn something from how those pioneering plants manage to survive against all odds. 🧵1/3
🧪 #PlantScience
Congratulation to all authors!
(only @laskotillean.bsky.social in #bluesky?)
Institutions
@cbgpmadrid.bsky.social
@ijpb-versaillescly.bsky.social
@lipme-toulouse.bsky.social
@inrae-france.bsky.social
#GAFL
@csic.es
and funding agencies
@agencerecherche.bsky.social
@ageinves.bsky.social
Parallel evolution in this case could be indicative of positive selection to produce the metabolite in this environment.
Indeed, plants carrying different alleles of GH38cv present different accumulation of the metabolite, and germinate, grow and reproduce better under high salt concentrations.
Looking at genome sequences from a global set of Arabidopsis plants (~1600), only two populations have non-functional aleles of GH38cv, and both come from the Cape Verde archipelago, but each population comes from a different island!
This is a case of parallel evolution!
We performed metabolite QTL analysis in a plant population derived from Cape Verde Islands (Cvi-0) and central Europe (Col-0).
The strongest QTL is in an unidentified metabolite.
We characterize the metabolite as glucuronyl-mannose, and we map the gene to a glycoside hydrolase family 38 (GH38cv).
graphical abstract from the article: Parallel evolution of salinity tolerance in Arabidopsis thaliana accessions from Cape Verde Islands
We just published our work in #ScienceAdvances
"Parallel evolution of salinity tolerance in Arabidopsis thaliana accessions from Cape Verde Islands"
www.science.org/doi/10.1126/...
Short summary and credits follow: