Soham Mukhopadhyay

A rose by another name, the #Willow #Rose #Gall (Rhabdophaga sp) and some bonus smaller tooth like galls caused by (Euura sp) observed in Willow, AK. #midge #sawfly #nature #insects #bug #plant #ecology #botany #entomology

Link to our recent preprint describing the unusually large genome of this wasp. www.biorxiv.org/content/10.6...

If an editor can’t do this, they should not be an editor, either paid or unpaid. From my experience, “just address all reviewer comments” is prevalent.

Great to see this work finally out! This study should serve as a helpful resource in better understanding the clubroot virulence. Cheers to @asimjaved.bsky.social and @edelplopez.bsky.social for leading this global effort.

Farnesylated Ptr C-term negatively regulates the channel, and fungal effector AvrPita directly activates the channel by cleaving it off 🤯. Graphical abstract 👇

Wait, wait, what !!!!! Regulation of target gene expression by chromatin-associated protein-coding transcripts in plants 686 protein-coding transcripts that mediate cross-locus chromatin interactions in Arabidopsis www.science.org/doi/10.1126/...

As genomes become easy, there is a definite need to really teach species and gene phylogenetic analysis to all molecular biologists and biochemists. If a paper/manuscript shows 1:1 orthologues between monocots and dicots for genes unique to the Brassicaceae, I think that is a major red flag.

AlphaFold Database is expanding into pandemic preparedness. Together with NVIDIA, DeepMind, EBI et al. we exhaustively predicted ~1.7 million homo- & heterodimers across 2,812 viral proteomes, resulting in 8,028 high-confidence predictions. 📄 research.nvidia.com/labs/dbr/ass... 🌐 alphafold.ebi.ac.uk

Plants use the hormone salicylic acid (SA) to fight infection, but how it activates gene expression remained unclear. Two studies @nature show that the mechanism involves interaction between SA receptor NPR1 and a component of the transcriptional machinery. shorturl.at/7PymL & shorturl.at/Iy4oY

New paper! Amphibious plant, H. difformis, reprograms C3 to potential C4 photosynthesis underwater, highlighting its amazing plasticity of carbon assimilation machineries for aquatic environment. Congrats, Hongwei & the team🥳🌿🐸! academic.oup.com/hr/advance-article/doi/10.1093/hr/uhag230/8708086

Our latest views on deep ARF evolution are finally out in New Phytologist! nph.onlinelibrary.wiley.com/doi/10.1111/...

Plants can synthesize mimics of the insect molting hormone 20-hydroxyecdysone (20E) to defend against pests. In this preprint, we discover that two plant families independently evolved biosynthetic gene clusters to make 20E. Amazing team effort by my lab! www.biorxiv.org/content/10.6...

👏🏼👏🏼 this is how it should be done

The demonstration of a single origin for nodule evolution, with nodule engineering in a non-nodulating species https://www.biorxiv.org/content/10.64898/2026.05.31.728964v1

Researchers have identified superparamagnetic macrophages in the livers of rock pigeons to be crucial for magnetic sensing. The finding uncovers an unexpected role for immune cells in sensory perception and may fundamentally change our understanding of animal navigation. https://scim.ag/4nTQ3nq

Excited to see the structurally conserved nucleoside hydrolase like fold that we found (elifesciences.org/articles/105...) to be conserved among biotrophs now being experimentally validated to target EDS1 !! Link to the preprint - www.biorxiv.org/content/10.6...

Proud to share our new paper on how prion-like fungal effectors target plastids and modulate host metabolism during root symbiosis. Exciting collaborative work uncovering PEPSI effectors and the interaction of one of them with DXR in plants. www.biorxiv.org/content/10.6... bsky.app/profile/eell...

Check out our latest work! AlphaFold 3 revealed a transient immune receptor complex that eluded biochemical studies for almost a decade 🤯 We describe a conserved structural logic underlying sensor–helper communication in an NLR immune receptor network 🧵👇

We are excited to release the BAT!🦇🚨 We've used this phylogenetic analysis pipeline in our lab for years, and grad Ben Sheppard now presents a Github release and preprint. I run BAT analyses almost daily. It makes exploring gene families routine, customizable, and fun🧵

Hey #MPMI crowd, we are having trouble finding co-proteome papers looking into the host and pathogen proteome at the same time. I know they must exist but can’t find them. Any suggestions?

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_...

Very excited to see this work out today! Discovering viral immune antagonists directly from predicted protein structures. 🤩 www.science.org/doi/10.1126/... Huge thanks to the amazing collaborators! 🤗

@ismpmi.bsky.social

Plant weirdness. After injecting agro rhizogenes into the stem of Kalanchoe, they start sprouting roots from stem after few weeks later.

Is the lesson from this that, if ones reasoning is freed from the pull of gravity, one can still publish with MDPI?

@thaisdalsasso.bsky.social is applying new tools to address the evolution and functional diversification of secreted proteins of fungal plant pathogen. Preprint here: www.biorxiv.org/content/10.6...

Out in @NaturePlants. We discover that the fungal pathogen Fusarium graminearum secretes an apoplastic effector that disrupts the N-glycosylation of a maize immune receptor, thereby inducing its degradation via selective autophagy. Very proud of the team~ doi.org/10.1038/s414...

Out in New Phytologist! The annotated blueprint: integrated functional genomic resources for a model tetraploid wheat cv. Kronos 🌾 chromosome-scale genome, high-conf annotations, manually curated 1000+ NLRs, ~3000 remapped datasets 🔗 doi.org/10.1111/nph.... #Plants #Genomics #FunctionalGenomics

the estimated 1 billion biochemical reactions that occur every second in every cell of our bodies 🤯

🎉📣 #TAIR12, the latest reannotation of the Arabidopsis thaliana genome, is now available under accession number PRJEB100887 on ENA and NCBI! Thank you all the volunteer researchers whose hard work has made this possible! #plantscience #plantbiology 🧪 bit.ly/3ZHtneT

Out in @science.org this week, two fungal enzymes synthesise DHHA, which controls cell wall porosity and turgor in plant pathogenic fungi www.science.org/doi/10.1126/... #mycology #plantscience

📣 Our latest story just dropped on bioRxiv:: A structurally unique effector shared between Verticillium dahliae and Fusarium oxysporum is involved in cotton defoliation and virulence on other hosts www.biorxiv.org/content/10.6... 🧵

Thrilled to announce that I am joining the Editorial Board of Molecular Plant–Microbe Interactions as a Senior Editor! 🌱🦠 Grateful for the opportunity to serve this vibrant research community and help amplify impactful science 👏 🔗 apsjournals.apsnet.org/page/mpmi/ed...

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This article is now published! academic.oup.com/nargab/artic... We’ve added a few new analyses. First off, we show that, while gene presence absence variation (PAV) scales with evolutionary distance in both plants and animals, the base level and rate of accrual are both twice as high in plants.

📣 Our lab is seeking a postdoc to study mutation mechanisms in fungi using cutting-edge sequencing + computational biology. No active posting/grant right now, but we’re excited to host postdoc fellowship applicants in our comparative immunology team. Interested? Reach out DM email. krasilevalab.org

Ever wondered if diverse plant species respond similarly when infected by the same exact pathogen? Infect different asterids and rosids with the same Botrytis genotypes and teh short answer, quite differently. www.biorxiv.org/content/10.6... @annajomu.bsky.social @ccaseys.bsky.social (1/3)

Although it went online in 2025, here is our second paper of 2026! 🎉 Bravo to @jiaxuwu.bsky.social for leading this (possibly) controversial, but much-needed, analysis. Enjoy! Now out in the January 2026 issue of Trends in Genetics. 🔗 www.cell.com/trends/genet...

Towards a quantitative view of NLR evolution in genome space -- check out where we think the field of #NLR #evolution research is heading in this review led by Luzie Wingen and Aurélien Tellier. ecoevorxiv.org/repository/v... #plantscience

Comment in @nature.com: "Food will be more affordable — if we double funds for agriculture research now" www.nature.com/articles/d41... A global drop in public and private investment in agricultural science in the past four decades is partly to blame for high food prices, an analysis reveals.

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n

AI model Helixer predicts eukaryotic genes ab initio, directly from a plain text FASTA file. No RNA-seq. No protein homology. No repeats, hints, or curated evidence. Raw genome → accurate gene models. Deep learning + HMM, published in @natmethods.nature.com www.nature.com/articles/s41...

gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats

Rewriting the code of plant immunity go.nature.com/475WgV7

Just when you thought plant galls couldn't be of any more shapes! Such cool findings! "Dasineura asteriae Reprograms the Flower Gene Expressions of Vegetative Organs to Create Flower-Like Gall in Aster scaber" onlinelibrary.wiley.com/doi/10.1111/...

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...

New preprint! 🐛 Root-knot nematodes hijack root cells, turning them into feeding sites and making plants very sick. Using a cross-species scRNA-seq approach we mapped this process and show how this knowledge can be used to engineer resistant crops.🌱 A summary🧵 : www.biorxiv.org/content/10.1...

“from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.”