Rowena Hill

1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start?

We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!

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

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....

Our MARTi @nanoporetech.com paper is now out in @genomeresearch.bsky.social after several years of development (particularly Ned Peel and Sam Martin). We'd love to hear from users about how you're using it, or suggestions for new features. @earlhaminst.bsky.social

genome.cshlp.org/content/earl...

Combatting wheat take-all disease with in-field and synthetic microbial communities 4-year Norwich Research Park Biosciences Doctoral Training Partnership (NRPDTP) PhD

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.

Widespread shifts in genome architecture and trophism across fungi. Phylogenetic positions of the shifts identified for genome size. Negative values denote an identified decrease in the genomic trait value while positive values denote an increase in the genomic trait value.

Fungal #GenomeSize variation is largely driven by TEs & lineage-specific genome defenses. @tbadet.bsky.social & @danielcroll.bsky.social show that presence/absence of RIP mutation systems influences #genome architecture, identifying a likely novel defense mechanism @plosbiology.org 🧪 plos.io/4hcC5tx

Combatting wheat take-all disease with in-field and synthetic microbial communities

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)

Open Positions ERC-funded project on the mechanism of horizontal transfer of entire fungal chromosomes PhD PostDoc

Want to understand how entire fungal chromosomes can be horizontally transferred?
Join us to unravel the mechanism/consequences of horizontal chromosome transfer in a fungal pathogen as part of an ERC-funded project. Postdoc/PhD positions available.
fungal-evolutionary-genetics.de/open-positio...

A common bracket fungus on the side of a tree

Xylaria fungus growing out of a tree stump

Small cap mushrooms surrounded by fallen leaves and grass in a woodland

🍄 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.

Long-term monitoring of a North American cheese cave reveals mechanisms and consequences of fungal adaptation Using a unique longitudinal sampling approach, Louw et al. demonstrate how a cheese-associated Penicillium population has adapted in an artisan cheese production facility in Vermont, USA. Adaptation i...

Such a delight to share our work on the evolution of a cheese rind fungus in @currentbiology.bsky.social.

This is the fantastic PhD work of @nicolasleonlouw.bsky.social and resulted from amazing collaborations, a wedding proposal(!), an undergrad course, & more!

🧵

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

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

THIS WEEK HAS SAUCE 4

Stunning fossils in sedimentary rocks reveal a new and co-oldest Early Cretaceous gilled mushroom-forming fungus

Edaphagaricites conicus gen. nov. et sp. nov.

academic.oup.com/botlinnean/a...

An opportunity of a lifetime for budding lichenologists. The National Trust and the Royal Botanics, Edinburgh are offering a PAID lichen traineeship in #Scotland! The work programme looks fascinating and a great opportunity to develop skills. Deadline: 3/10/2025. www.asva.co.uk/jobs/trainee...

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

pangenome 'expansion' curves for cotton and soybean

Determining presence-absence variation (PAV) across reference genomes is a major goal of pangenome analysis. It turns out that A LOT of gene PAV is due to methodological artifacts.

We explore the causes of this in soybean and cotton datasets in our recent preprint: www.biorxiv.org/content/10.1...

Plant-associated fungi co-opt ancient antimicrobials for host manipulation Evolutionary histories of effector proteins secreted by fungal pathogens to mediate plant colonization remain largely elusive. While most functionally characterized effectors modulate plant immunity, ...

📣 NEW PREPRINT 📝

We identified evolutionary origins of many fungal effectors!
We show that fungi secrete lots of antimicrobial proteins, and that some of them were repurposed by plant pathogens for host immune suppression.
www.biorxiv.org/content/10.1...

cc @teamthomma.bsky.social

Phyling: phylogenetic inference from annotated genomes Phyling is a fast, scalable, and user-friendly tool supporting phylogenomic reconstruction of species phylogenies directly from protein-encoded genomic data. It identifies orthologous genes by searchi...

New #preprint from talented graduate student for a workflow we have been using for a while into a formal usage www.biorxiv.org/content/10.1...

Our paper mapping plant and mycorrhizal fungal diversity correlations is out! Relationships are weak at the global level, but both positive and negative at smaller scales. Plants are not always proxies for fungi — fungi need their own conservation focus @spun.earth @ethz.ch
doi.org/10.1038/s414...

Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution Nature Communications - Giant transposons, known as ‘Starships’, mediate horizontal gene transfer between fungal genomes. Here, Sato et al. show that Starships occupy genome regions...

📣 Happy to see the journal publication 📄 of our work on Starships 🚀 in Verticillium fungi: terrific work led by @yukiyosato.bsky.social
rdcu.be/exBSp

OrthoFinder just dropped a major update

It’s faster, more accurate, and ready for thousands of genomes

Let’s break it down (1/10)

github.com/OrthoFinder/...
www.biorxiv.org/content/10.1...

Pangenome annotation opens up a multiverse of genes Gaining deeper insights into genetic diversity with pangenome annotation.

💬 “We are taking genome #annotations from disparate methods and harnessing the information contained in them to produce a more unified set of annotations.”

Comparing #genomes at scale with pan-annotation tools.
buff.ly/TMOWcG8

@rowenahill.bsky.social

🧬 🖥️

Marine fungi culture collections (such as the one we have at @thembauk.bsky.social) are helping unlock the possibility for finding new solutions to many of the world’s biggest challenges 🌊🍄=💊🥓🪲 @uk.theconversation.com @plymbiomarsci.bsky.social @erc.europa.eu
👉 theconversation.com/marine-fungi...

Some magnolias do perform 'remontant' (second) flowering in the summer or autumn bygl.osu.edu/index.php/no... ours does it some years🙂

🚨 Job Alert at RBG Kew! We are looking for Lab Research Assistants in genomics to join our Fungarium Sequencing Project! Do you like Fungi? Do you want to develop new -omics techniques? Interested in historical collections? Join the team! Posts to start ASAP. Apply here:https://lnkd.in/e2BpWJpA

Marine Fungi are found everywhere in the ocean. They are recyclers, a goldmine of compounds and symbiotic with other marine life. I chat about Marine Fungi in the BBC programme 'Secrets of the Sea'. Follow the link 👉 www.bbc.co.uk/programmes/p... @thembauk.bsky.social @plymbiomarsci.bsky.social

k-mer-based diversity scales with population size proxies more than nucleotide diversity in a meta-analysis of 98 plant species Abstract. A key prediction of neutral theory is that the level of genetic diversity in a population should scale with population size. However, as was note

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...

Our newest special issue is now live! Check it out to discover more about diverse and beautiful Fungi🍄🍄‍🟫🍄 On the cover: the fly agaric, Amanita muscaria, releasing its spores in the early morning light. www.cell.com/current-biol...

The #GENETICS June cover features an illustration of Starships, giant cargo-mobilising transposable elements found in fungal species of the subphylum Pezizomycotina. Starship elements are highly variable in overall length & genetic content.

1/2🧵

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

Image of the front cover of Field Mycology with the BMS logo at the top, the title "Field Mycology" in crimson below it, and a large photo of a cream-coloured cyphelloid fungus growing among glistening moist liverworts.

This #FungiFriday we want to share the latest issue of Field Mycology! This is the first issue to be edited by Kew Mycologist @clareblencowe.bsky.social and marks the publication now being #OpenAccess

Check it out at fieldmycology.org

The Last of Us: Developing a Genomic Epidemiology Toolkit for Fungal Outbreaks at University of Birmingham on FindAPhD.com PhD Project - The Last of Us: Developing a Genomic Epidemiology Toolkit for Fungal Outbreaks at University of Birmingham, listed on FindAPhD.com

🍄The Last of Us - NIHR HPRU PhD opportunity🍄 Very exciting project on developing a genomic epidemiology toolkit for fungal outbreaks with @mcdonaldmeganc.bsky.social @drjorhodes.com @scalene.bsky.social and the Mycological Reference Lab Bristol www.findaphd.com/phds/project...