A quick tutorial blog on a method I haven't seen before to plot gene gain/loss from e.g. CAFE5 across a phylogeny - and clearly shows I always have fungi on the mind 🤓🍄 #rstats #ggplot2 rowena-h.github.io/data-visuali...

@tobybarilbio.bsky.social and I are very excited to release MycoMobilome! A very extensive effort to discover, QC and annotate TEs across the fungal kingdom. 👉 Ready-to-use for your own genome with a simple tutorial! 👉 Metadata about TEs discovered in your genome! 👉 Contribute and get recognition!

Super excited to see our bioRxiv paper out! It furthers our understanding of an FHB resistance locus in timopheevii with some DON resistance too!

PHD: What does an ‘optimal’ community of #bacteria and #fungi look like for #pathogen suppression? That's a key question to explore in this fully-funded #PhDproject with @neilhall.bsky.social, @mcmullan0.bsky.social and @rowenahill.bsky.social at the Earlham Institute.

PHD: Are you interested in gene regulation, #immune function, or tech development? We have a fully-funded 4-year #PhDproject with @whatchamacaulay.bsky.social at the Earlham Institute and @tiagocluis.bsky.social at Imperial looking at niche cell–cell communication. ➡️ buff.ly/M7u6thJ

📣 New @biorxiv-microbiol.bsky.social preprint, another joint-venture of @wolki95.bsky.social & @antonkraege.bsky.social, co-directed by @nicksnelders.bsky.social. Here’s a 🧵

We are advertising a PhD project investigating a cellular mechanism that ensures protein quality control during mRNA translation in plants. Please get in touch on here or via email if you are interested and I can provide further details! Lab website: sites.google.com/site/danielg...

Great new postdoc fellowship for foundational plant research. If you’re into genetics and genomics of plant reproductive evolution or adaptive convergence (incl in the cool and charismatic nightshades!) I’d be happy to talk about possible projects! www.simonsfoundation.org/grant/simons...

PhD studentship Come help us understand the wheat rhizosphere at the Earlham Institute 🦠 Working at the interface of fungal antagonists & pathogens (@rowenahill.bsky.social @neilhall.bsky.social ), host genetic diversity (Simon Griffiths -JIC) and bacterial community diversity (Jacob Malone -JIC)

Professorship in plant genetics. The Botanical Institute at Kiel University is advertising a W2 professorship. Great opportunity to do plant research in the north of Germany. See: www.berufungen.uni-kiel.de/de/dateien/o...

A genetic map of human metabolism across the allele frequency spectrum https://www.europesays.com/uk/474140/ Study design The UKB is a prospective cohort study from the UK that contains more than 500,000 volunteers…#uk #news #uknews

🍄 Today marks #UKFungusDay where we get to celebrate the weird and wonderful kingdom of Fungi. As well as being fundamental to a healthy ecosystem, and often fascinating to spot, #Fungi can be devastating to plant and animal populations.

Was a pleasure to contribute a small part to this massive WGS effort of Kew's fungarium! @estergaya.bsky.social @rbgkew.bsky.social Check out the paper @newphyt.bsky.social 👉 doi.org/10.1111/nph.70472

New OA Article: "Enhancing local meiotic crossovers in Arabidopsis and maize through juxtaposition of heterozygous and homozygous regions" rdcu.be/eDWJI With News & Views: "Diversity favoured: heterozygosity attracts crossovers" rdcu.be/eDWKQ

It was a delight to have Guillaume Delhaye and Torda Varga (@rbgkew.bsky.social) at @earlhaminst.bsky.social last week, talking to a packed Norwich Research Park audience about mushroom-forming and mycorrhizal fungi from molecule to ecosystem! 🍄🧬🌳 @neilhall.bsky.social @norwichmicro.bsky.social

Our editors write: - Wheat immunity: "Unlocking yellow rust resistance" rdcu.be/eBbSJ about rdcu.be/eBbT0 - Auxin signalling: "A rack for the hook" rdcu.be/eBbTg about www.pnas.org/doi/10.1073/...

How predictably does complex trait adaptation proceed over space and time in wild populations? doi.org/10.1093/evle... Now in @evolletters.bsky.social by @skylerberardi.bsky.social, @paulrschmidt.bsky.social et al. 📷: Dr. Rush Dhillon

Advances in computational methods for inferring networks from #genome-scale data and guidelines for deriving biological insights from #phylogenetic networks www.pnas.org/doi/10.1073/...

www.nature.com/articles/s41... Really nice. Especially nice RIP result linked to ancestral sex hypotheses. Which then links nicely to plastic genomic regions and adaptation in the face of asexual reproduction.

Hey, Miles' @milesroberts.bsky.social beautiful paper showing that sequence diversity missed by standard methods contributes to Lewontin's paradox is officially published in @evolletters.bsky.social. academic.oup.com/evlett/advan...

Keen to work in #PlantSciences? 🌿 Applications are open for a new John Innes Foundation Internship with Dr Carolina Grandellis at the Earlham Biofoundry. 🧬 You'll work on #bioengineering approaches for plant sciences, utilising high-throughput platforms at the Earlham Institute.

Using an alignment-free k-mer-based phylogenetic method, @rowenahill.bsky.social, @mcmullan0.bsky.social, and the team found that relationships between entire Starships differed from those inferred from captain genes. Read more about Starships fungal transposons in #G3journal: buff.ly/vxOe5oq

In case you want to know more about Kew’s Fungarium and our sequencing work! #Fungi #museomics @rbgkew.bsky.social www.newscientist.com/video/248375...

Our paper on phylogenetics of fungal Starship TEs is now on the cover of the June issue of Genetics @genetics-gsa.bsky.social 🙂 academic.oup.com/genetics/iss... @mcmullan0.bsky.social @earlhaminst.bsky.social @rothamsted.bsky.social

While helping out on a cool genomics project recently, I came to realise I’d been taught a pretty big inaccuracy about the events that occur at fertilization. I suspect that almost everyone reading this has the same misapprehension, so let’s do some learning together: 1/

If you missed the @wheatgenome.bsky.social webinar yesterday with @simongriff.bsky.social "Breeding: Why we need to start over again" watch it here: www.youtube.com/watch?v=X0kZ...

💬 “When we looked at the replication start sites we’d identified, we discovered only 20% of them had been reported previously. The majority were newly discovered with this approach." 📃 Researchers use ultra #longreads to reveal where #DNAreplication starts in the #humangenome: buff.ly/pQWGasr

Kmer based phylogenetic methods like Mashtree (@lskatz.github.io), are really powerful for difficult to align and repetitive regions including TEs, Integrative and conjugative elements & Starships etc. Really nice work from @rowenahill.bsky.social and thanks to collaborators @rothamsted.bsky.social

Thanks for posting @reviewcommons.org If you're interested you can also find the reviewed version here: doi.org/10.7554/eLif... Really keen to get people's perspectives on the population genetics of reservoirs, and what they tell us about variation associated with emergent crop pathogens.

New Paper out! apsjournals.apsnet.org/doi/epdf/10.... We wanted to know how much genetic variation exists for Zymoseptoria in a single wheat field.

💬 "Some #fungi can change their behaviour in different environments, so understanding how a changing climate might affect fungal behaviour – and what role Starships play in this – is vital.” Starships enable new frontier of fungal genome evolution 🚀 🧬 🌱

📃 A new study from the Earlham Institute and @rothamsted.bsky.social reveals insights into large mobile #fungal #genome elements - Starships - and how they jump between fungal species and influence their evolution. 🖥️ 🧬 🧪 ➡️ buff.ly/R5SF9j8 @rowenahill.bsky.social #Transposons #PlantScience

Excited to share our latest preprint 🥳 Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen @danielcroll.bsky.social #TESky www.biorxiv.org/content/10.1...

Those trying to understand the tariffs as economic policy are dangerously naive. No, the tariffs are a tool to collapse our democracy. A means to compel loyalty from every business that will need to petition Trump for relief. 1/ A 🧵 to explain his plan and how we fight back.

Conserved effectors underpin the virulence of liverwort-isolated Pseudomonas in divergent plants Very happy to share the published version of our work on natural Marchantia-Pseudomonas interactions. Out now in Current Biology: www.cell.com/current-biol...

Happy to share that our paper "Analyses of Transposable Elements in Arbuscular Mycorrhizal Fungi Support Evolutionary Parallels With Filamentous Plant Pathogens" is out. academic.oup.com/gbe/article/...

💬 "Fungi are notoriously challenging when it comes to DNA extraction. The challenge is to extract high concentrations of DNA while preserving strand lengths and integrity" In a new blog, Research Assistant Michelle guides you through her adapted protocols for the extraction of HMW #DNA from fungi.🧪

Excited to share the first publication from my PhD!! We identify premature termination codons specific to the cheetah in genes associated with male fertility and immunity 🐆🧬 @earlhaminst.bsky.social @whaerty.bsky.social academic.oup.com/evolut/advan...

Funded #PhD with Dr Chris Quince at the Earlham Institute and @quadraminstitute.bsky.social, working on understanding the mechanisms of faecal #microbiome transplantation, with major potential impact to the treatment of IBD. buff.ly/AqvE0j5 @mmbdtp.bsky.social

The latest technical blog from scientists at the Earlham Institute comes from Research Assistant Michelle, who shares her methodology for modifying two commercial high molecular weight (HMW) DNA extraction kits. 🧪 buff.ly/fKdw2K9 #DNA #longreads

The structural basis of the arms race between a blast effector and a rice immune receptor (2018) #Immunity #Effectors #BlastOFF www.nature.com/articles/s41...

This the second in a clutch of papers that start to look at the genome biology of virulence of this important wheat pathogen (@dsw-ISP.bsky.social). Here detailing methods for extracting fungal DNA for @pacbio.bsky.social HiFi T2T genomes when melanin is an issue. Well Done.

🆕 Fully funded #PhD with @neilhall.bsky.social and @mcmullan0.bsky.social analysing genetic diversity in the genomes of potential crop invasion pathogens and plant hosts associated with resistance. 📆 Apply by: 21 April ➡️ buff.ly/RpmTSFN #plantscience #agritech

Me on the radio this morning talking about UK preparedness for #xylella, froghoppers and the BRIGIT project in the @saskiahogenhout.bsky.social lab @johninnescentre.bsky.social www.bbc.co.uk/sounds/play/...

📄 A new study from the Earlham Institute and @rothamsted.bsky.social presents 9 near-complete #genome assemblies of take-all & related fungi, using @pacbio.bsky.social #HiFi sequencing. The results present a significant resource for studying important #fungal pathogens. @rowenahill.bsky.social

The final version of our paper on genomics of understudied fungal root pathogens/endophytes of wheat is now out! The result of close ongoing collab between @earlhaminst.bsky.social (@mcmullan0.bsky.social @greymj.bsky.social @neilhall.bsky.social et al) and @rothamsted.bsky.social rdcu.be/edlB9

This is the first in a clutch of papers that start to look at the genome biology of virulence of this important wheat pathogen (@dsw-isp.bsky.social). Here dipping into RIP, gene copy number variation, biosynthetic gene clusters, and giant cargo mobilising elements (Starships). Well done.

Wheat Pathogens webinar, March 20th! Dr. Daniel Croll, University of Neuchâtel, Switzerland, will talk about “Understanding mechanisms of crop pathogen emergence using large genome panels”. Please share! buff.ly/45ttOjL @karchuntan.bsky.social @ReemWheat

Do you want to make genetic maps from sperm/pollen/gametes? Now there is an easy way, based on Hi-C sequencing. Thanks to Richard Durbin and Ed Green for the idea and a group of co-authors including @mariontalbi.bsky.social and @danielbolnick.bsky.social for contributions.

We did it! We caught Starship #transposons moving between #fungal species in the lab, including between species separated by ~100my. We think Starships are a mediator of HGT in fungi, akin to conjugative elements in bacteria. Check out the preprint. www.biorxiv.org/content/10.1...