Rowena Hill
@rowenahill.bsky.social
π€ 155
π₯ 81
π 17
Researching fungi
@earlhaminst.bsky.social
π Norwich, UK π
https://rowena-h.github.io/
reposted by
Rowena Hill
Natalie Cooper
about 7 hours ago
Hi all. I am very excited that after 6 years I finally got my phylogenetic comparative methods book and online exercises online. Feel free to use and share. The book is here:
nhcooper123.github.io/pcm-primer/
. Note that it is not finished, we had to abandon it before the sunk costs fallacy broke us
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Phylogenetic Comparative Methods
Phylogenetic Comparative Methods
https://nhcooper123.github.io/pcm-primer/
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Sally Warring
1 day ago
So nice to see this out in print, and thanks to
@microbiologysociety.org
for the smooth publish process! Single-cell sequencing reveals unexpected genetic diversity among Bodo spp. flagellates and their bacterial endosymbionts -
www.microbiologyresearch.org/content/jour...
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Single-cell sequencing reveals unexpected genetic diversity among Bodo spp. flagellates and their bacterial endosymbionts
Bodo is a cosmopolitan genus of free-living bacterivorous single-celled flagellates in the class Kinetoplastea. Genus Bodo is considered the closest free-living lineage to the parasitic lineages Trypa...
https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001642
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Rowena Hill
Mark McMullan
8 days ago
How does root invasion differ between endophyte & pathogen? We are interested in this dichotomy of expression in the most important root disease of wheat, take-all: Stealth vs SEVs Exceptional tenacity from Stella (looking for a PhD) and the team
@earlhaminst.bsky.social
@rothamsted.bsky.social
π
add a skeleton here at some point
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Year in industry student Poppy Leslie is presenting her great work on the evolution of wheat-infecting root fungi, check it out at poster 47! πΎπ
#CMINorwich26
@earlhaminst.bsky.social
@norwichmicro.bsky.social
@dsw-isp.bsky.social
@mcmullan0.bsky.social
add a skeleton here at some point
20 days ago
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Rowena Hill
Andrew Rambaut (ππ)
25 days ago
So I pleased to announce the conceptual spawn of FigTree: PearTree (acronym still to be finalised). If you want to dive right in it is hosted as a web app here:
artic-network.github.io/peartree
(click the βExample...β button for immediate candy and then click every button you can find).
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PearTree β Phylogenetic Tree Viewer
http://artic-network.github.io/peartree
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Rowena Hill
Carlos Aguilar-Trigueros
about 1 month ago
Disperal ecology meets fungi! It is more than just spores people! Check this paper led by ECR
@sarahcuprewich.bsky.social
and Kristin Barbour! Fun collab supported
@cu-esiil.bsky.social
One hundred unanswered questions on the dispersal ecology of fungi url:
academic.oup.com/ismej/articl...
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One hundred unanswered questions on the dispersal ecology of fungi
Abstract. Fungi comprise millions of species that play numerous varied roles in Earthβs natural and managed ecosystems, engaging in a multitude of positive
https://academic.oup.com/ismej/article/doi/10.1093/ismejo/wrag018/8490299
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Rowena Hill
Santa Walker
about 1 month ago
Article out about our work on
#protists
at the Earlham Instituteπ¦ π§¬
#protistsonsky
@earlhaminst.bsky.social
@nrpdtp.bsky.social
@norwichmicro.bsky.social
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Rowena Hill
Alice Laigle
about 2 months ago
Hi everyone! The talk I had the chance to give with
@fnucleosome.bsky.social
last October is now out on Youtube! If you like evolution, 3D genomics, biodiversity and/or fungi, I think you might like it! π§¬π§ͺπ The submission of this paper has never been that close!
www.youtube.com/watch?v=Plez...
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Rowena Hill
Laurie Belcher
about 2 months ago
Calling all OrthoFinder users! Weβve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny. GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
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https://www.biorxiv.org/content/10.64898/2026.01.27.702036v1
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Rowena Hill
John Lovell
about 2 months ago
This article is now published!
academic.oup.com/nargab/artic...
Weβve 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.
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Rowena Hill
Eva Stukenbrock
about 2 months ago
What enables a fungus to invade a mammal host?
@marco-guerreiro.bsky.social
unravels signatures of translation adaptation among pathogenic and non-pathogenic species of Trichosporonales. See more:
www.nature.com/articles/s41...
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Genomic and physiological signatures of adaptation in pathogenic fungi - Nature Communications
Emerging fungal pathogens have detrimental impacts on crops, animals, and humans, however little is known about their transition to a pathogenic lifestyle. This study demonstrates that the transition ...
https://www.nature.com/articles/s41467-026-68330-6
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Rowena Hill
Francis M. Martin
about 2 months ago
I'm delighted to inform you that our paper "Ecological genomics of saprotrophy to biotrophy transitions in the genus Clitopilus" was published in IMA Fungus. A long standing collaboration with Zhilin Yuan at RISF, Chinese Academy of Forestry, Hangzhou:
imafungus.pensoft.net/articles.php...
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Ecological genomics of saprotrophy to biotrophy transitions in the genus Clitopilus (Fr. ex Rabenh.) P. Kumm. (Agaricales, Entolomataceae)
Transitions between saprotrophic and biotrophic lifestyles represent pivotal evolutionary events in fungal ecology; however, the genomic and physiological mechanisms underlying such shifts remain poor...
https://imafungus.pensoft.net/articles.php?id=179417
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Rowena Hill
Fungal Ecology π
2 months ago
In this review in Fungal Ecology, HΓ₯vard Kauserud (
@drhyfe.bsky.social
) argues that while the ITS region is by far the best DNA (meta)barcoding marker for fungi, we should not use it naively or simplistically
doi.org/10.1016/j.fu...
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Rowena Hill
British Mycological Society
2 months ago
Open for applications: Massee Arts Grant: up to Β£5000 to support novel arts projects focused on fungi. For artists from all disciplines & all geographic locations who can help us encourage engagement and learning about mycology. Find out more & apply here:
www.britmycolsoc.org.uk/massee-arts-...
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Rowena Hill
bioRxiv Evolutionary Biology
2 months ago
Mutualistic microbes drive niche expansion yet constrain diversification
https://www.biorxiv.org/content/10.64898/2026.01.14.699472v1
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Rowena Hill
Frances Pitsillides
3 months ago
Very excited to share this article written with my PhD advisor
@hassansalem.bsky.social
, highlighting the amazing work on organ remodeling for symbiosis by Nishino et al
@fkttkm.bsky.social
. A fascinating system to think about!
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Rowena Hill
bioRxiv Ecology
3 months ago
Why Ambrosia Beetles Keep Only One Fungus: Competitive Asymmetry, Bottleneck Drift, and Eco-Evolutionary Fixation
https://www.biorxiv.org/content/10.64898/2025.12.18.694882v1
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Rowena Hill
Alexis Stamatakis
3 months ago
Our raxtax tool for taxonomic classification is published: it is 2.7β100 times faster than competing tools but equally accurate - raxtax has increasing speedups with growing query and reference sequence numbers compared to existing tools:
academic.oup.com/bioinformati...
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Rowena Hill
Dan Udwary
3 months ago
DOE's Office of Science is making a big push into AI, and that includes our work at the
@jgi.doe.gov
. We want to hear your thoughts (+ and -) on AI-enabled biological data. Consider joining one of our interviews or focus groups by filling out this form! π§ͺπ§¬π¦ π₯οΈ
#secmet
jointgeno.me/PortalStorie...
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Tell Us Your JGI Portal Stories
The JGI Portal teams (IMG, Mycocosm, Phycocosm, Phytozome, and SMC) would love to sit with you (over Zoom) to hear your stories relating to your usage of the portals, your unsupported use cases, and p...
https://jointgeno.me/PortalStoriesForm
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Rowena Hill
Quadram Institute
4 months ago
β° Closing soon! We're looking for a Research Scientist to work on novel platforms for sustainable myco-food production and precision fermentation. π· Β£37,500 to Β£40,240 ποΈ Apply by 30 November 2025 β‘οΈ
buff.ly/WDsrbgl
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Rowena Hill
Francis M. Martin
4 months ago
Another fine outcome of my long-standing collaboration with Zhilin Yuan and Long Peng at RISF in Hangzhou: Endophytes with mycorrhizal potentials: biological and ecological implications - New Phytologist
nph.onlinelibrary.wiley.com/doi/10.1111/...
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https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.70772
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Rowena Hill
4 months ago
π¨ PhD project offer linked to Fungarium Sequencing Project! Do you like bioinformatics? fungal genomics? historical DNA? check this out π
www.trees-dla.ac.uk/projects/imp...
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Improving methodologies of whole genome assembly and data processing of historical fungal collections to accelerate species discovery | TREES DLA
Fungi are essential components of ecosystems, driving nutrient cycling, carbon sequestration, and countless symbiotic interactions. Yet, fewer than 10% of the estimated three million fungal species ha...
https://www.trees-dla.ac.uk/projects/improving-methodologies-whole-genome-assembly-and-data-processing-historical-fungal
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Rowena Hill
Saloni
4 months ago
I'm surprised I only came across it now, but this review on improving communication in data visualization is excellent.
journals.sagepub.com/doi/10.1177/...
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The Science of Visual Data Communication: What Works - Steven L. Franconeri, Lace M. Padilla, Priti Shah, Jeffrey M. Zacks, Jessica Hullman, 2021
Effectively designed data visualizations allow viewers to use their powerful visual systems to understand patterns in data across science, education, health, an...
https://journals.sagepub.com/doi/10.1177/15291006211051956
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Rowena Hill
Aaron Vogan
4 months ago
We're looking for a PhD student! If you're interested in
#fungal
#genomics
&
#TEs
, meiotic drive, or pathogens, please consider applying. The project is about toxin/antidote genes in the human fungal pathogen A. fumigatus.
uu.varbi.com/en/what:job/...
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Rowena Hill
Megan McDonald
4 months ago
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...
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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...
https://www.biorxiv.org/content/10.1101/2025.11.13.688278v1
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Rowena Hill
British Mycological Society
4 months ago
Fungal fossils tell a story of resilience: research by Worobiec et al. published in
#FungalBiology
(Aug 2025) traces dark septate endophytic (DSE) microsclerotia from the Eocene to today, revealing long-term plantβfungus associations. π
www.sciencedirect.com/science/arti...
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Rowena Hill
Richard Leggett
4 months ago
Know metagenomics and could spare 2 mins? I'm applying for funding to build a visual repository for metagenomic classification data (not sequence data). To support the application, I have a short 2 minute survey and it would be a big help if you could fill it in:
docs.google.com/forms/d/e/1F...
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Rowena Hill
Stephanie Watts-Fawkes
5 months ago
New study from
@mvanderheijden.bsky.social
lab, showing that many commercial mycorrhizal inoculants are snake oil. So important for this data to be published! Between this,
@lizkoziol.bsky.social
and Matt Salomonβs workβ¦ well I think we make a strong point.
onlinelibrary.wiley.com/doi/10.1002/...
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Poor Quality of Commercial Arbuscular Mycorrhizal Inoculants Used for Agriculture and Home Gardening
There is an urgent need to develop microbial inoculants that can consistently improve crop performance as part of efforts to implement sustainable agricultural practices and reduce the environmental ...
https://onlinelibrary.wiley.com/doi/10.1002/sae2.70107
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Rowena Hill
Katie Field
5 months ago
πΏπβπ«π±πWeβre recruiting!!πΏπβπ«π±π Iβm looking for two postdocs and a technician to join my group
@sheffielduni.bsky.social
@sheffieldpps.bsky.social
to work with me on my exciting
@royalsociety.org
Faraday Discovery Fellowship project, details for each post as follows:
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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 π€π
#rstats
#ggplot2
rowena-h.github.io/data-visuali...
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Mushroom plots to visualise gain and loss on a phylogenetic tree
A tutorial on how to visualise gene gain and loss on a phylogenetic tree
https://rowena-h.github.io/data-visualisation/bioinformatics/tutorial/2025/11/07/gene-gainloss-on-tree.html
5 months ago
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Rowena Hill
Earlham Institute
5 months ago
PHD: Based at the Earlham Institute with
@neilhall.bsky.social
and
@rowenahill.bsky.social
, and in collaboration with
@rbgkew.bsky.social
, we're seeking a
#PhDstudent
interested in
#fungal
#ecology
and evolution to study functional diversity in root
#symbiotic
fungi.
@aries-dtp.bsky.social
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Genomic signatures underlying functional diversity in root symbiotic fungi
https://www.earlham.ac.uk/studentship/genomic-signatures-underlying-functional-diversity-root-symbiotic-fungi
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Rowena Hill
Toby Baril
5 months ago
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...
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Rowena Hill
Team Thomma
5 months ago
π£ Now announcing the journal publication π of our work in
@newphyt.bsky.social
on how Verticillium undermines the plant's π± "cry for help": terrific work by
@antonkraege.bsky.social
&
@wolki95.bsky.social
doi.org/10.1111/nph....
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Undermining the cry for help: the phytopathogenic fungus Verticillium dahliae secretes an antimicrobial effector protein toΒ undermine host recruitment of antagonistic Pseudomonas bacteria
During pathogen attack, plants recruit beneficial microbes in a βcry for helpβ to mitigate disease development. Simultaneously, pathogens secrete effectors to promote host colonisation through vario...
http://doi.org/10.1111/nph.70686
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Rowena Hill
Richard Leggett
5 months ago
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...
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Real-time analysis and visualization of nanopore metagenomic samples with MARTi
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
https://genome.cshlp.org/content/early/2025/10/13/gr.280550.125
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Rowena Hill
Earlham Institute
5 months ago
PHD: What does an βoptimalβ 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.
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Combatting wheat take-all disease with in-field and synthetic microbial communities
4-year Norwich Research Park Biosciences Doctoral Training Partnership (NRPDTP) PhD
https://buff.ly/URGX6QT
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Rowena Hill
PLOS Biology
5 months ago
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
π§ͺ
plos.io/4hcC5tx
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Rowena Hill
Mark McMullan
5 months ago
PhD studentship Come help us understand the wheat rhizosphere at the Earlham Institute π¦ 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)
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Combatting wheat take-all disease with in-field and synthetic microbial communities
https://www.earlham.ac.uk/studentship/combatting-wheat-take-all-disease-field-and-synthetic-microbial-communities
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Rowena Hill
Michael Habig
5 months ago
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...
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Open Positions
ERC-funded project on the mechanism of horizontal transfer of entire fungal chromosomes PhD PostDoc
https://fungal-evolutionary-genetics.de/open-positions/
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Rowena Hill
Earlham Institute
6 months ago
π 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.
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Rowena Hill
Benjamin Wolfe
6 months ago
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! π§΅
www.cell.com/current-biol...
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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...
https://www.cell.com/current-biology/fulltext/S0960-9822%2825%2901119-4
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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
π
doi.org/10.1111/nph.70472
add a skeleton here at some point
6 months ago
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Rowena Hill
7 months ago
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...
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Rowena Hill
The British Lichen Society
7 months ago
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...
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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! ππ§¬π³
@neilhall.bsky.social
@norwichmicro.bsky.social
7 months ago
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Rowena Hill
John Lovell
7 months ago
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...
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Rowena Hill
Fantin Mesny
7 months ago
π£ NEW PREPRINT π 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
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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, ...
https://www.biorxiv.org/content/10.1101/2024.01.04.574150v2
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Rowena Hill
Jason Stajich
8 months ago
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...
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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...
https://www.biorxiv.org/content/10.1101/2025.07.30.666921v1
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Rowena Hill
Laura van Galen
8 months ago
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 β fungi need their own conservation focus
@spun.earth
@ethz.ch
doi.org/10.1038/s414...
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Rowena Hill
Team Thomma
8 months ago
π£ Happy to see the journal publication π of our work on Starships π in Verticillium fungi: terrific work led by
@yukiyosato.bsky.social
rdcu.be/exBSp
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Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution
Nature Communications - Giant transposons, known as βStarshipsβ, mediate horizontal gene transfer between fungal genomes. Here, Sato et al. show that Starships occupy genome regions...
https://rdcu.be/exBSp
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Rowena Hill
Laurie Belcher
8 months ago
OrthoFinder just dropped a major update Itβs faster, more accurate, and ready for thousands of genomes Letβs break it down (1/10)
github.com/OrthoFinder/...
www.biorxiv.org/content/10.1...
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