AmirAli Toghani

2.1 Reading Trees Chapter contents: Systematics — 1. Taxonomy — 2. Phylogenetics —— 2.1 Reading trees ← —— 2.2 Building trees —— 2.3 Character mapping —— 2.4 Phylogenetic trees and classificationParts of a tree A phylo...

If you're a #teacher interested in a great #openaccess write up on reading #phylogenetic trees, check out www.digitalatlasofancientlife.org/learn/system... created by @jonhendricks.bsky.social and Elizabeth Hermsen.

the top half shows two panels with microscopy images. Left is a light-microscopy image of a group of algal cells. The cells are round with different sizes. Two arrows point at sporangia: one looks as if someone stuffed 8 footballs in a thin elastic bag. The other is perfectly round and contains many small spores within. The right panel shows the same group of cells, but in fluorescent microscopy, where green color shows chloroplasts. In each cell the chloroplasts are globular with small lobes sticking out. The bottom half shows a photo of Xanthoria lichen - bright yellow and leafy growing on a tree branch

Our paper on the #genome of the Trebouxia #photobiont from Xanthoria is now out in @newphyt.bsky.social! Check below for a near-chromosome level assembly, secretome analysis, evidence of ancient HGT, and transcriptomic comparison of the alga in symbiosis and in pure culture
doi.org/10.1111/nph.70728

New paper led by @metalichen.bsky.social from our group presenting a chromosome-level assembly of the Trebouxia photobiont alga from the lichen Xanthoria parietina - a resource we hope will enable significant new insight into the symbiosis @newphyt.bsky.social doi.org/10.1111/nph....

My new Emmy Noether Group is recruiting!

🔬 Two PhD positions in plant pathogen evolution

🧬 Start: April 2026 (flexible)

📍 Dept. of Phytopathology & Plant Protection @rstam.bsky.social @uni-kiel.de

⏰ Apply by 15 Dec 2025

🔗 More info: www.uni-kiel.de/personal/de/...

Do get in touch or share 😊

The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine The strain of Phytophthora infestans that caused the Great Famine in the late 1840s was caused by a single genotype that is distinct from, but closely related to, the most prevalent modern genotype.

We sequenced the genome of the Phytophthora infestans from that particular historical sample back in 2013 to characterize the genetic makeup of the strain that cause the pandemic outbreak of potato late blight. elifesciences.org/articles/00731 @kamounlab.bsky.social

Undermining the cry for help: the phytopathogenic fungus Verticillium dahliae secretes an antimicrobial effector protein to undermine host recruitment of antagonistic Pseudomonas bacteria During pathogen attack, plants recruit beneficial microbes in a ‘cry for help’ to mitigate disease development. Simultaneously, pathogens secrete effectors to promote host colonisation through vario...

📣 Now announcing the journal publication 📄 of our work in @newphyt.bsky.social on how Verticillium undermines the plant's 🌱 "cry for help": terrific work by @antonkraege.bsky.social & @wolki95.bsky.social doi.org/10.1111/nph....

5!

Spooky season has arrived! 👻
We held our annual Pumpkin Carving Competition at @thesainsburylab.bsky.social —vote for your favourite carve! 🎃🕯️

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

Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes After gene and genome duplications, expression divergence across cell types is not random, and it can be explained by a combination of gene age, gene funct

Our paper on the evolution (duplicated) gene expression divergence in spatially resolved plant transcriptomes is now out @theplantcell.bsky.social

w/ @yvdp.bsky.social

#PlantSci #Evolution

academic.oup.com/plcell/advan...

Sophien Kamoun, the Google DeepMind team and Nick Desnoyer are pictured inside one of The Sainsbury Laboratory’s growth chambers, surrounded by growing plants.

Nick Desnoyer is pictured showing the Google DeepMind team growing plants inside one of The Sainsbury Laboratory’s growth chambers.

The Google DeepMind team alongside The Sainsbury Laboratory group leaders, GetGenome lead James Canham and members of the Kamoun group.

Fantastic hosting the @GoogleDeepMind team at TSL with @kamounlab.bsky.social 🌱

From AI in plant health to building scientific capacity, our missions clearly resonate!

Tools like AlphaFold can accelerate scientific breakthroughs in our field -holding real promise for global food security 🌍

Beyond Immunity: Uncovering the Hidden Diversity of Bacterial NLRs (SCHLIMPERT_J26DTP) | Doctoral Training Partnership Join us in exploring the hidden functions of ancient immune proteins in bacteria. Bacteria, like plants and animals, have evolved sophisticated systems to detect and respond to threats.

We have a PhD opportunity available in our group @johninnescentre.bsky.social through the NRP Doctoral Training Partnership. Help us uncover the Hidden Diversity of Bacterial NLRs.

Start date: October 2026. For more information and how to apply👉 biodtp.norwichresearchpark.ac.uk/projects/bey...

Vanishing Virulence: Investigating pathogenicity loss in a plant pathogenic fungus (TALBOT_T26DTP) | Doctoral Training Partnership What makes a plant killer lose its edge? This project will investigate why fungal pathogens lose virulence when they are grown in laboratory culture away from their host plant. Use cutting-edge…

New PhD opportunity in my group @thesainsburylab.bsky.social through the BBSRC NRP DTP Programme - see details of host to apply below

biodtp.norwichresearchpark.ac.uk/projects/van...

How do cells communicate when it’s hot? (FAULKNER_J26DTP) | Doctoral Training Partnership Plant cells are connected to their neighbours via ‘tubes’ called plasmodesmata, creating an interconnected cytoplasm that joins cells within and between tissues and organs.

We have a project available for 2026 NRP Doctoral Training Partnership entry (i.e. PhD studentship opportunity!)

How do cells communicate when it's hot?

Don't know? Me either! Come work with us @johninnescentre.bsky.social and figure it out

biodtp.norwichresearchpark.ac.uk/projects/how...

Understanding Host Compatibility in the Marchantia-Phytophthora System (CARELLA_J26DTP) | Doctoral Training Partnership The fossil record demonstrates that filamentous microbes invaded ancient plant cells with intracellular hyphal structures over 450 million years ago. To this day, a rich diversity of extant land plant...

New opportunity to undertake a PhD in my group ⁦‪at the John Innes Centre - if you’re interested in plant immunity and evolution check out the link!

Huge congratulations to PhD students @lenaknorr.bsky.social, from the Ma group, and @amiralito.bsky.social, from the @kamounlab.bsky.social, for their 2025 ASM poster awards! 🎉🌱

A secreted citrus protease cleaves an outer membrane protein of the Huanglongbing pathogen Plants secrete a variety of proteases as a defense response during infection by microbial pathogens. However, the relationship between their catalytic activities and antimicrobial functions remains la...

1/13 Thankfully, both you and your plants have a lot of sophisticated ways to fight off invading pathogens.
In our new preprint, we describe a new way in which animals and plants share a common strategy to ward off harmful bacteria.
www.biorxiv.org/content/10.1...

Origin of chaperone dependence and assembly complexity in Rubisco biogenesis Molecular chaperones assist with the folding and assembly of protein clients. Consequently, they are essential to diverse cellular functions. In most aerobic photosynthetic organisms such as B-cyanoba...

A new preprint from the lab. I won't do a tweetorial until this is peer reviewed, but I think it's a banger, led by
@JedNzy. It's about Rubisco and what chaperones are really for. He's on the market, get him while you can. www.biorxiv.org/content/10.1...

A host organelle integrates stolen chloroplasts for animal photosynthesis Sea slugs steal foreign chloroplasts and store them in specialized organelles that facilitate photosynthesis and eventual digestion to mediate starvation resistance.

www.cell.com/cell/abstrac...

A host organelle (in sea slugs) integrates stolen chloroplasts for animal photosynthesis

The sequences of 91,366 NLR immune proteins from 230 superasterid genomes are now printed in 931 bound volumes #OpenScience #OpenPlantNLR

Nick Talbot, Executive Director and senior group leader at TSL, is pictured in a glasshouse surrounded by rice plants.

We are pleased to announce that @talbotlabtsl.bsky.social has been awarded the RKS Wood Prize 2026 by the @bspp.bsky.social.

“I am humbled to have been awarded the RKS Wood Prize 2026. I’d like to thank my research group and my TSL colleagues for their inspiration and support.”

buff.ly/VvoR27Q

Our latest work on how chloroplasts contribute to immunity: Membrane contact sites between chloroplasts and the pathogen interface underpin plant focal immune responses url: academic.oup.com/plcell/artic...

Systematic discovery and engineering of synthetic immune receptors in plants Plants deploy a diverse array of pattern recognition receptors (PRRs), which perceive microbe-associated molecular patterns to activate immune responses. Leucine-rich repeat receptor-like kinase subgr...

Very happy to share our latest work “Systematic discovery and engineering of synthetic immune receptors in plants” out in @science.org !

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

Thrilled to share our new bioRxiv preprint!✨ Huge credit to first author Yujin Chen and thanks to all co-authors. Extra special: my first paper as co-corresponding author (with Lieve Gheysen).
Check how nematodes uncouple FLS2–BSK signalling in 🌱👇
www.biorxiv.org/content/10.1...

First a pentamer, then a hexamer… now an octamer!

The riddle of the enigmatic CCG10-NLR immune receptor family cracked open 🔥

Congrats Guanghao @GuanghaoGuo He Zhang @mhz1989 Selva @M__Selvaraj et al.

#NLRbiology #plantsci #immunology

Carton says “eggs from plants”

Embyophytes what’s up

#iamabotanist

Genomic constraints shape the evolution of alternative routes to drug resistance in prokaryotes Background Variation within the prokaryotic pangenome is not random, and natural selection that favours particular combinations of genes appears to dominate over random drift. What is less clear is wh...

New preprint reveals bacteria can't just collect all resistance genes like Pokemon cards.
We found mutually exclusive evolutionary pathways to multidrug resistance in E. coli & P. aeruginosa - some resistance mechanisms actively prevent others from coexisting www.biorxiv.org/content/10.1...

"Little Flower"

A Cryo-SEM portrait of my micro-rose depicting the flower as a sculpture of cells, fractured and frozen in time. Full image is 10k x 10k pixels.

Climate change effects on plant immune activation The forecasted global climate changes will expose plants to challenging environmental conditions that further increase outbreak risks and threaten ecosystems and food security. The sole host defense mechanism plants possess is innate immunity. This system relies on extra- and intracellular receptors mediating pattern- and damage-triggered immunity (PTI/DTI) and effector-triggered immunity. Here, we discuss how environmental changes can alter the expression dynamics of extracellular receptors activating PTI/DTI, the so-called pattern-recognition receptors, and cell wall integrity sensors. We examine possible crosstalk between selected abiotic stress and immune signaling and briefly argue how two major abiotic stress-related transcription factor families, such as the heat stress factors and dehydration-responsive element-binding/C-repeat-binding factors, cooperate with immune signaling during acclimation responses.

Climate change effects on plant immune activation #plantscience

Thank you @newphyt.bsky.social for organizing this great meeting. Met some very cool people and had constructive discussions! I presented our most recent work, now published in New Phytologist. You can check out my poster here:
doi.org/10.5281/zeno...