New review out in Current Biology with colleagues in the Plant Cell Atlas (@plantcellatlas.bsky.social)! We discuss how single-cell genomics is reshaping our understanding of plant cell-type identity and evolution across the Green Lineage.
bit.ly/4eAip2Q
Big congrats to my former lab bench neighbor Carly whose PhD work on building a snRNA-seq atlas of young Arabidopsis seed development was just published @natplants.nature.com
Matt Stata
Check out this cool new preprint by @willshaw.bsky.social from the Gehring and Khalil labs about the optimization of T-DNA vector backbones to achieve predictable and stable (over)expression in Arabidopsis
Roman Podolec
Roman Podolec
Genes for genetic painting in flowers now available on Addgene!: addgene.org/browse/artic...
New preprint out 🌱
We present a new T-DNA vector system for Arabidopsis that supports clean, genomically mapped, single-copy T-DNA insertion with predictable cell-type/conditional gene expression.
@mokhalil.bsky.social + Gehring labs
biorxiv.org/content/10.6...
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Not sure which scRNA-seq platform to use for 🪴 plant samples? How well do doublet detection algorithms really work in 🌱? How can I optimise sample prep ? Find out in our benchmark study! Led by @carogro.bsky.social and @thomaseekhout.bsky.social. Open access at EMBO Journal: doi.org/10.1038/s443...
The last paper of my PhD work in Argentina. We dig deeper into the Marchantia MpC1HDZ transcription factor. Many experiments, but my favourite: in addition to its role in oil body cell differentiation, it is also important for another cell type! #PlantScience academic.oup.com/plphys/advan...
The isolation of single plant cells from complex tissues is prone to selective enrichment and sampling biases, which complicates accurate profiling of the large diversity in cell types. Optimizing methodologies for cell enrichment and single-cell transcriptomics is therefore critical for single-cell studies addressing plant cell heterogeneity. Here, we systematically compared protoplast enrichment technologies (including conventional and image-based flow cytometry, as well as magnetic cell sorting) and single-cell RNA sequencing (scRNA-seq) platforms (10X Genomics Chromium, BD Rhapsody) using Arabidopsis roots. Image-based flow cytometry offered increased precision due to customizable gating strategies, while magnetic sorting provided faster processing and enhanced representation of cell size heterogeneity. Both scRNA-seq platforms captured root cell heterogeneity and yielded reproducible gene expression profiles, but showed platform-associated differences in cell type composition. Notably, single-nucleotide polymorphism analysis of a mixed ecotype sample revealed that, among cells identified as doublets by computational algorithms, two-thirds were likely to have been misclassified. These insights identify key biases in plant cell purification and scRNA-seq workflows and provide practical guidance for improving data quality across plant species.
New OA Resource: "A transcriptional atlas of early Arabidopsis seed development suggests mechanisms for inter-tissue coordination" rdcu.be/fj8H2
Single-nucleus RNAseq profiling of early Arabidopsis seed development. #PlantScience
Rational design of T-DNA vectors enables predictable, single-copy integration in Arabidopsis thaliana https://www.biorxiv.org/content/10.64898/2026.06.08.730999v1
