A gene regulatory network built from single cell co-expression, orthology, transactivation, and overexpression. The TF IDB1 activates itself the TF IDM1. IDM1 and IDB1 together activates IDM4, which in turn activates biosynthetic genes.

New paper is online! We used single cell RNA-seq & phylogenetics to identify 2 additional cell type specific TFs that control late-stage vinca alkaloid biosynthesis. The key insights originated from Camptotheca, another species that produces alkaloids. doi.org/10.1111/nph.... #PlantScience #SecMet

Excited to see our paper online! We combined scMS and scRNA-seq from the same plant cells 🌱 — a step toward true single-cell multi-omics in plants.
Overview 👇

Congratulations @mykang.bsky.social and Hai Anh Vu 🥳

Have you tried Eurofins genomics? I think it is cheaper

Congratulations Li! 🎉

My first PhD paper is out today!
Huge thanks to Dr. Thuy Dang (UBC), Dr. Robin Buell (UGA), and @chenxinli2.bsky.social (MSU) for your guidance and support!
Special thanks to Li, for his mentorship in single-cell analysis and bioinformatics.

Discovery of iridoid cyclase completes the iridoid pathway in asterids - Nature Plants Iridoids are terpenoid metabolites found in thousands of plants. Using single-cell transcriptomics, the authors discovered an unexpected enzyme that has been neofunctionalized to catalyse the cyclization required to form the iridoid scaffold.

Very exciting to finally see our iridoid cyclase ICYC online @natplants.nature.com!
A joined effort with Robin Buell’s lab with Josh Wood generating snRNA-seq, and my student Chloée Tymen performing the initial experiment.
#natprod
#PlantScience
@mpi-ce.bsky.social
www.nature.com/articles/s41...

🤩🤩🤩

The "Florédex" ✨, a pokémon-inspired vector collection of the greatest flower designs and their science is coming along nicely 🌷🧬

All hand-drawn, digitalised, and animated.

Please share! I'm looking for a postdoc. The position is to lead one of the following projects: 1) regulation of plant specialized metabolism by cell fate, or 2) foliar embryogenesis in the succulent plant Kalanchoe.

Learn more abt projects: cxli233.github.io/cxLi_lab/res...

Large-scale single-cell profiling of stem cells identifies redundant regulators of shoot development and yield trait variation Xu et al. performed large-scale single-cell RNA-seq of maize and Arabidopsis shoot stem cells, identifying conserved regulators and candidate stem cell genes through mutant analysis. They linked stem ...

"Large-scale single-cell profiling of stem cells identifies redundant regulators of shoot development and yield trait variation"

From: www.cell.com/developmenta...

#PlantScience

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 👇

Friday Flower 001: Mimulus lewisii 🌸✨

Monkeyflowers are masterpieces of design with nectar-guide spots formed by an activator–inhibitor system of MYB transcription factors. These generate reaction–diffusion patterns across the ventral petal.

A truly enabling new approach by @taralowensohn.bsky.social Will Cody and @sattelylab.bsky.social to probe plant genetics at scale.

Single-gene-per-cell delivery coupled to an effective transcriptional selection system

www.biorxiv.org/content/10.1...

Congratulations. Hope to visit your lab one day.

Enzymatic epimerization of monoterpene indole alkaloids in kratom - Nature Chemical Biology Monoterpene indole alkaloids are formed via a 3S stereoselective condensation between secologanin and tryptamine. Here the authors uncover the mechanism of epimerization behind uncommon 3R-containing ...

Here, the authors @oconnorlab.bsky.social @mpi-ce.bsky.social uncover the mechanism of epimerization behind uncommon 3R-containing alkaloids in Mitragyna speciosa (Kratom) and study their inclusion in downstream biosynthesis #PlantScience #natprod

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

Happy to share that I’ve been awarded a grant from
@osventuresllc.bsky.social to develop a genetic toolkit for flower design! Here was my 1-minute pitch.

More details of what I'm building coming soon 🌹✨

Phylogenomics and metabolic engineering reveal a conserved gene cluster in Solanaceae plants for withanolide biosynthesis Nature Communications - Withanolides are plant steroids with potent bioactivities found in many medicinal plants including Withania somnifera, but their biosynthetic pathway is largely unknown....

Extremely happy to see our withanolide biosynthesis paper out in @natcomms.nature.com‬ rdcu.be/evHOF
Fantastic team effort with the Pucker group @bpucker.bsky.social‬ @puckerlab.bsky.social‬ at @unibonn.bsky.social and Heretsch, Herde and Witte groups at @unihannover.bsky.social. Funded by @dfg.de

Lead author @matildeflorean.bsky.social‬ et al. from the @oconnorlab.bsky.social discover a "fake" enzyme in plants that enables the formation of free indole, a key molecule for defense & attracting pollinators.
www.ice.mpg.de/496511/PR_Fl...

Next preprint out from my work @oconnorlab.bsky.social @mpi-ce.bsky.social : the discovery or iridoid cyclase in asterids!
Thread below.
#PlantScience
#natprod

www.biorxiv.org/content/10.1...

Discovery of FoTO1 and Taxol genes enables biosynthesis of baccatin III - Nature An approach that combines single-nucleus RNA sequencing and multiplexed perturbation identifies genes that enable the biosynthesis of direct precursors of the anti-cancer drug Taxol, whose curren...

Today in Nature we report a systematic strategy to activate & identify gene sets in plants. We identify 8 new genes from the yew tree's Taxol biosynthetic pathway, enabling us to engineer tobacco with 17- & 20-gene pathways to Taxol precursors baccatin III & deBz-deoxy-Taxol #SingleCell #secmet 🧬🧪🌾

Ipecac alkaloid biosynthesis in two evolutionarily distant plants - Nature Chemical Biology Ipecac alkaloids are plant-derived compounds historically used to induce vomiting. Here the authors elucidate how two evolutionary distant plant species have evolved to produce the same ipecac alkaloi...

Finally online and open access!
This revised version has a slightly different title and contains a number of additional supplementary figures, mainly in vitro enzyme assays. Kept me quite busy in the lab at the end of last year!
#PlantScience
#natprod
www.nature.com/articles/s41...

Congratulations Li

Camptotheca and Catharanthus, both produced alkaloids that are used in cancer chemotherapy, last shared a common ancestor ~115 mya. They shared an iridoid biosynthetic pathway. We found new, rare biosynthetic genes in Camptotheca that are different from those in Catharanthus.

New preprint! We used single cell sequencing & metabolomics to look at cell type specificity of specialized metabolism in Camptotheca, the source of chemotherapeutic agent camptothecin, as well as comparative analyses w/ Catharanthus, which we previously worked on. 🧵

www.biorxiv.org/content/10.1...

Our data imply that the same clades of TFs have been co-opted to regulate cell type specific biosynthesis across species. Thus, 1) cross-species analyses increase the power for finding new metabolic regulators; 2) TFs are evolutionarily older than their target biosynthetic genes. 3/n

This is my 1st paper as last author & (co-)corresponding author. It's a pleasure to mentor the 1st author @vanhungbui.bsky.social at U. British Columbia, Okanagan on single cell analysis. This study was supported by an NSF-EAGER project awarded to me (coPI) + Robin Buell at University of Georgia.

A screenshot of the long Acknowledgement section of a manuscript draft.

New manuscript has been written. An international collaboration between US, Germany, and Canada. And a long Acknowledgement section, since each lab has its own funding, services, and colleagues to acknowledge.