Our new experimental evolution study across 30+ locations using the plant Arabidopsis thaliana —— we direct "see" adaptation and extinction to different climates at the genetic as it happens!

Read it in Science
dx.doi.org/10.1126/scie...

@ucberkeleyofficial.bsky.social
@hhmi-science.bsky.social

Imputation integrates single-cell and spatial gene expression data to resolve transcriptional networks in barley shoot meristem development - Nature Plants Spatially resolved gene expression during barley development was done by integrating an scRNA-seq dataset from cells with unknown position with spatial transcriptomics. This dataset is publicly availa...

We recently published a first story on combining spatial and single cell transcriptomics in barley (see here: www.nature.com/articles/s41...)

Lets go for the next level now, i.e. understanding gene networks and barley meristem development in 4D!

The Bart Lab at UC Berkeley is looking for a postdoc. Please share!

Congrats Mat! 174(!) sections are truly impressive, excited to look into the data!

New collaborative preprint out in which we use @10xgenomics.bsky.social Xenium to do some (a lot!) of plant spatial transcriptomics, led by Jim Whelan's team: "Mitochondrial Retrograde Signaling in Arabidopsis thaliana: heterogenous, spatial and polarised aspects" www.biorxiv.org/content/10.6...

New preprint! The same TFs can drive distinct regulatory programs depending on where they bind.

TSS → rapid stress responses

Intronic & upstream → cell-type programs

Enhancer-like CRMs → embryo/meristem programs

Coding-sequence binding → repression
www.biorxiv.org/content/10.6...

Integrative phylogenomics positions sponges at the root of the animal tree Determining whether sponges or ctenophores root the animal tree has important implications for understanding early animal evolution. Here, we examined support for these competing hypotheses by constru...

Who lived in a pineapple under the sea?

All of our ancestors

www.science.org/doi/10.1126/...

We like to introduce map3C, developed by Joseph Galasso, that drastically improves the mapping and contact calling performance of snm3C-seq and now enables accurate 3D genome modeling. map3C was developed in collaboration with
Jason Ernst and Frank Alber. www.biorxiv.org/content/10.1...

New pre-print from the team!

The manuscript is @emma-raven.bsky.social's PhD work showing that whether a leaf is a carbon sink or a carbon source influences how they execute immune responses.

Have a read!

#PlantScience
@johninnescentre.bsky.social

Congrats, Joe Ecker @salkinstitute.bsky.social, to receiving the McClintock Prize! Joe has been a visionary leader of the field of genetics and genomics – not only for plants – for decades
www.salk.edu/news-release...

Coming to you live from #ISPLORE2025JP Fresh preprint from my lab showing that leaves progressively oxygenate and how this is important for their morphogenesis.Thanks to our collaborators from @Fra_LicO2si lab. #plantscience
www.biorxiv.org/content/10.1...

New OA Article: "A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution" rdcu.be/eHce3

Chromatin accessibility in rice & related grasses: how regulatory DNA elements evolve across cell types & species; identifying potential silencers.

Multiple overlapping binding sites determine transcription factor occupancy - Nature A new method enables comprehensive screening and identification of low-affinity DNA binding sites for transcription factors, and reveals that nucleotides flanking high-affinity binding sites create ov...

A timely article as several recent conference discussions have led to similar thoughts

www.nature.com/articles/s41...

Thank you Rashmi!

Drought recovery in plants triggers a cell-state-specific immune activation - Nature Communications Post-drought rehydration triggers a preventive immune response in plants, revealing targets to enhance crop resilience by linking drought stress recovery with improved pathogen resistance.

Our #research on #drought #recovery, now published with @springernature.com in @natcomms.nature.com:
Drought recovery in plants triggers a cell-state-specific immune activation.
doi.org/10.1038/s414...

Read thread below 👇

Our new Nature Plants paper is out (and we’re on the cover 😁)!👉 bit.ly/4lS8sOB
By combining scRNA-seq with conserved TF binding (multiDAP) we define gene regulatory networks for 65 cell types across 4 tissues in a wide range of flowering plants!

Plant cells at the organ surface use mechanical cues to activate a specific growth control programme During morphogenesis of multicellular organs, cells acquire distinct identities that meet specific functional requirements. Epidermal identity is widely considered essential for plant morphogenesis du...

Thrilled to share our latest work: how plants control growth through activation of a surface-specific growth programme. Thanks @zoenv.bsky.social, @nathan-german.bsky.social and the other coauthors for all the hard work! www.biorxiv.org/content/10.1...

Ethylene signal integration through epigenetic mechanisms in plants Ethylene is an essential phytohormone that controls a plethora of plant developmental and stress responses. Accordingly, ethylene signal generation an…

Happy to see our latest #plantscience review by @aidamaric.bsky.social, @advaitagashe.bsky.social and Johanna onlinr! We describe how epigenetic mechanisms control ethylene signal generation and progression, and how ethylene in turn modulates chromatin.

www.sciencedirect.com/science/arti...

#Kpopdemonhuntersquad

Equity, Diversity and Inclusion: Making conferences in the plant sciences more inclusive through community recommendations The ROOT & SHOOT project in the plant sciences has produced guidelines to help scientific societies organize conferences that are more inclusive and offer more supportive environments to all attendees...

Plz share! (I am a co-author from NAASC) “An unwelcoming climate & culture at scientific conferences is an obstacle to retaining scientists w/marginalized identities. Here we describe..a professional plant science societies..collaboration to make conferences more inclusive.”
doi.org/10.7554/eLif...

Thanks for the enthusiasm in using our online web browser! Due to the high traffic, we have allocated additional resources for user access, so if anyone encountered a bug with accessing the data, please give it a try again and reach out if additional errors are encountered!

It may arrive sooner than you think, the resources and equipment are there!

a little secret- the actual amount of data produced and filtered using the Drosophila cell atlas standards was >800k but we more stringently filtered it to ~430k for all downstream analyses. We plan to make this additional 400k data availability in NCBI GEO and here arabidopsisdevatlas.salk.edu

Tremendous work by the extremely talented postdocs @TrALEE_Sci @NatanellaE @nobolly .Thank you for putting in a major effort on this “side project” to develop a powerful community resource arabidopsisdevatlas.salk.edu

A single-cell, spatial transcriptomic atlas of the Arabidopsis life cycle - Nature Plants This study presents an extensive single-nucleus and spatial transcriptomic atlas of the Arabidopsis life cycle that represents ten distinct developmental time points inclusive of six diverse organs.

From a gene’s single cell expression–through spatial localization–to novel function, and beyond!
Now out @natplants.nature.com
We built a comprehensive spatial-transcriptomic atlas of Arabidopsis, revealing cell-type identities across organs in unprecedented detail
www.nature.com/articles/s41...

All datasets should be back online as we experienced a surge of traffic, thank you for your patience!

Thanks Alex!

New OA Resource: "A single-cell, spatial transcriptomic atlas of the Arabidopsis life cycle" rdcu.be/eBmkU

An extensive single-nucleus and spatial transcriptomic atlas of the Arabidopsis life cycle that represents 10 developmental time points in 6 diverse organs.

Thank you Laurence!
It looks like our server may have been overloaded with activity, I will ensure that all of the starts are up and running shortly. One challenge with our manuscript releasing at 2am local time!

Thanks Sagar!