Ksenia Krasileva

Fig. 4. Sweetpotato genotypes and wild relatives harbor a compact NRC-H subclade. Maximum likelihood (ML) phylogeny of complete coiled-coil nucleotide-binding and leucine-rich repeat immune receptor (CNL) proteins identified across all 35 sweetpotato and wild relative genotypes, using NB-ARC domain sequences as predicted by NLRtracker. Branches predicted to correspond to major nucleotide-binding and leucine-rich repeat receptor (NLR) required for cell death (NRC) helper and sensor clades (NRC-H, NRC-S) were highlighted based on phylogenetic placement of NRC0/1 (helpers, purple) and Hero-A, Rpi-amr3i, and Bs2 (sensors, green), respectively. Tips linked to CNLs containing integrated domains are labeled with yellow dots. The purple phylogenetic tree (right) includes only sequences from the indicated NRC-H lineage (left), underlining the Ipomoea batatas, I. trifida, I. triloba, and I. littoralis sequences phylogenetically predicted as helper NLRs.

C. H. Parada-Rojas et al. present a reference-quality NLRome for the hexaploid sweetpotato and diploid wild relatives. Learn more: https://doi.org/10.1094/MPMI-03-25-0034-R

The annotated blueprint: integrated functional genomic resources for a model tetraploid wheat Triticum turgidum cv Kronos Triticum turgidum cv Kronos is a tetraploid wheat cultivar that underpins one of the most widely used community platforms for functional genomics. Over the past decade, researchers have generated c. ...

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

Davis Summer Population Genomics Program Want to learn population genetics? Please fill out this form to indicate your potential interest in a 2-week intensive online summer population genetics course taught by Jeffrey Ross-Ibarra and Graham...

Fun news! @gcbias.bsky.social and I are teaching a 2-week online population genetics workshop this summer to raise money for the Center for Population Biology at UC Davis. We're trying to gauge interest -- please fill this out if you might be interested! And please share broadly!

If you are interested in using AI to predict and test microbial (bacterial, archaeal) cultivation requirements, please reach out. We are ~waist deep in this already.

The Plant Cell welcomes 2026 Assistant Features Editors The Plant Cell is pleased to announce our Assistant Features Editors (AFEs) for 2026 (Fig. 1). The Plant Cell AFE program provides AFEs with experience in

Super excited to share that I’ve joined @theplantcell.bsky.social as an Assistant Feature Editor! I’ll be writing “In Brief” highlights, receiving editor and peer-review training, and helping share amazing plant science with a wider audience, all with a fantastic community of editors and authors 🌱🦠🔬

Full professor for plant ecology in Regensburg. #plantscience #plantscijobs

jobs.zeit.de/jobs/w3-prof...

Fungi can become drug-resistant without changing their DNA. They just... turn off the gene. And turn it back on when the drug's gone. This is wild and concerning for treating infections like mucormycosis (50-90% mortality). From Joe Heitman's group at @duke-university.bsky.social.

Duckweeds are an important plant research model but have been challenging to modify genetically. A study published in @newphyt.bsky.social by the Marí-Ordóñez group at the GMI, presents a new and highly reproducible method for genetic transformation in the duckweed species Spirodela polyrhiza.

📣 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

Red flower and dark green leaves with rocks in the background

Red bush monkeyflower #BloomScrolling

Killing of Alex Pretti - Wikipedia

en.wikipedia.org/wiki/Killing...

A multi-plant transcriptomic atlas reveals conserved and lineage specific defense architectures in response to Botrytis cinerea Generalist pathogens pose a challenge to plant immunity by infecting diverse hosts while harboring extensive intraspecific genetic variation. Whether evolutionary distant plant lineages rely on a shar...

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

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My "Friends don't let friends make bad graphs" repo is approaching 7k stars on GitHub. As of this moment, 6962, to be exact. 38 more to go to 7000.

github.com/cxli233/Frie...

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

🎉 New year, NEW PREPRINT!

Bacteria exhibit astonishing genetic diversity, but where do new genes come from?

My best friend Arya Kaul (/labmate in the @baym lab) investigates how advantageous deletions can spawn new genes - "deletion-born fusions." 🧵:

Reupping this perennial #MPMI question, has an apoplastic Superoxide dismutase been cloned and proven to take RBOHD O2-• into H2O2? Or are all the models still assuming?

An energy-based model of protein conformational space can be used to predict structure from sequence, sample from the conformational landscape, rank structures, and predict mutation effects.

@sokrypton.org

www.biorxiv.org/content/10.6...

The Sudmant Lab & Wilsterman Lab are hiring a postdoc! Come work on the genetics and evolution of the placenta and dissecting genetic adaptations to altitude in deer mice!

Check out more details here: evol.mcmaster.ca/brian/evoldi...

www.sudmantlab.org
www.thewilstermanlab.com

Please Share!

Extensive horizontal transfer of transposable elements shapes fungal mobilomes Romeijn et al. reveal that horizontal transposon transfer is widespread in fungi, contributing up to 70% of transposon content in some taxa. The authors uncover thousands of events across diverse line...

Extensive horizontal transfer of transposable elements shapes fungal mobilomes

@currentbiology.bsky.social by @jromeijn.bsky.social et al from @mfseidl.bsky.social

www.cell.com/current-biol...

The unique architecture of umbrella toxins permits a two-tiered molecular bet-hedging strategy for interbacterial antagonism Umbrella toxin particles produced by Actinobacteria contain five spokes tipped with variable lectin domains. Here, Zhao et al. show that these lectins mediate species-specific binding to a previously ...

www.cell.com/cell/fulltex...

Your periodic reminder that science is not done by a few selected "stars scientists". Science is done by hundred of thousands. Siloed money mean a few flashy discoveries and a lot of waste. Want to change things? Make funding accessible and stop funding calls with less than 2% success rate.

Undergrads in the UK, Ireland, Canada, and the US!

One week left to apply for a funded internship in my lab!

📌 Details below
🔁 Please repost to spread the word!

Large-scale culturing of the tree microbiome enables targeted disease suppression The tree microbiome is essential for host health and pathogen suppression. Synthetic microbial communities (SynComs) are emerging as important tools to understand microbiome dynamics and engineer micr...

🧵 1/ New preprint alert! From the FUTURE OAK project, led by the super talented @alejandra1909.bsky.social

Large-scale culturing of the tree microbiome enables targeted disease suppression

Here's what we found... 👇

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

CIFAR signs San Francisco Declaration on Research Assessment - CIFAR In an effort to promote responsible research assessment, CIFAR has signed the San Francisco Declaration on Research Assessment (DORA).

CIFAR signs San Francisco Declaration on Research Assessment cifar.ca/cifarnews/20...

The virulence gene ToxB is both amplified and disrupted by transposons in the wheat pathogen Pyrenophora tritici-repentis ### Competing Interest Statement The authors have declared no competing interest. Agriculture and Agri-Food Canada, https://ror.org/051dzs374 Alberta Grain Saskatchewan Wheat Development Commissio...

Our latest pre-print on TE-mediated tandem duplication of the ToxB effector is now online...still a puzzle for us but we think it is in a Helitron! Together with amazing collaborators, Reem Aboukhaddour and Ryan Gourlie #TE #fungi
www.biorxiv.org/content/10.1...

Symbiotic diversification relies on an ancestral gene network in plants | bioRxiv Symbioses have been fundamental to colonization of terrestrial ecosystems by plants and their evolution. Emergence of the ancient arbuscular mycorrhizal symbiosis was followed by the diversification of alternative intracellular symbioses, such as the ericoid mycorrhizae (ErM). We aimed at understanding how these diversifications occurred. We sequenced the genomes of ErM-forming liverworts, and reconstituted symbiosis under laboratory conditions. We demonstrated the existence of a nutrient-regulated symbiotic state that enables ErM and underlies intracellular colonization of plant tissues. Comparative transcriptomic analyses identified an ancestral gene module associated with intracellular symbiosis beyond ErM. Genetic manipulations in the liverwort Marchantia paleacea, phylogenetics and transactivation assays demonstrated its essential function for intracellular symbiosis. We conclude that plant have maintained, and convergently recruited, an ancestral gene module for intracellular symbioses.

Outstanding preprint from @leocastanedo.bsky.social, @katharinamel1.bsky.social, @pierremarcdelaux.bsky.social and coll. on an evolutionary conserved module for intracellular symbiosis. - > Symbiotic diversification relies on an ancestral gene network in plants | bioRxiv

Thanks! K-PROB GitHub link now in the preprint!
Try our k-mer–based tool for causal element discovery for pan-genomes 🌱🧬

The work is led by @weiweibio.bsky.social, a talented postdoc looking for faculty positions now and conceptualized both computational prediction and in lab validation. Computational implementation is a collaboration with Xing Wu, postdoc with @mexpositoalonso.bsky.social
Qs - contact us 💻🌱🧬

Natural variation in regulatory code revealed through Bayesian analysis of plant pan-genomes and pan-transcriptomes Understanding the genetic code of cis-regulatory elements (CREs) is essential for engineering gene expression and modulating agronomic traits in crops. In plants, CREs underlying rapid evolution of ge...

🚀 New preprint!
We introduce K-PROB, a k-mer–based Bayesian framework that mines pangenomic promoter and expression diversity to predict cis-regulatory elements driving gene expression variation in crops 🌽🌱
🔗 biorxiv.org/content/10.1101/2025.10.27.684862v1
#Genomics #GeneRegulation #Maize #Soybean

The Department of Biology at UNC-Chapel Hill is searching for an organismal biologist whose research is focused on resilience.

unc.peopleadmin.com/postings/307...