Rowena Hill
@rowenahill.bsky.social
๐ค 151
๐ฅ 79
๐ 16
Researching fungi
@earlhaminst.bsky.social
๐ Norwich, UK ๐
https://rowena-h.github.io/
reposted by
Rowena Hill
Alexis Stamatakis
22 days ago
Our raxtax tool for taxonomic classification is published: it is 2.7โ100 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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reposted by
Rowena Hill
Dan Udwary
24 days 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! ๐งช๐งฌ๐ฆ ๐ฅ๏ธ
#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
about 1 month ago
โฐ Closing soon! We're looking for a Research Scientist to work on novel platforms for sustainable myco-food production and precision fermentation. ๐ท ยฃ37,500 to ยฃ40,240 ๐๏ธ Apply by 30 November 2025 โก๏ธ
buff.ly/WDsrbgl
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reposted by
Rowena Hill
Francis M. Martin
about 2 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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reposted by
Rowena Hill
about 2 months ago
๐จ PhD project offer linked to Fungarium Sequencing Project! Do you like bioinformatics? fungal genomics? historical DNA? check this out ๐
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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reposted by
Rowena Hill
Saloni
about 2 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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reposted by
Rowena Hill
Aaron Vogan
about 2 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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reposted by
Rowena Hill
Megan McDonald
about 2 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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reposted by
Rowena Hill
British Mycological Society
about 2 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 plantโfungus associations. ๐
www.sciencedirect.com/science/arti...
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reposted by
Rowena Hill
Richard Leggett
about 2 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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reposted by
Rowena Hill
Stephanie Watts-Fawkes
2 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 Salomonโs workโฆ 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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reposted by
Rowena Hill
Katie Field
2 months ago
๐ฟ๐โ๐ซ๐ฑ๐Weโre recruiting!!๐ฟ๐โ๐ซ๐ฑ๐ Iโm 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 ๐ค๐
#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
2 months ago
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reposted by
Rowena Hill
Earlham Institute
2 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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reposted by
Rowena Hill
Toby Baril
2 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
2 months ago
๐ฃ Now announcing the journal publication ๐ of our work in
@newphyt.bsky.social
on how Verticillium undermines the plant's ๐ฑ "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 toย undermine host recruitment of antagonistic Pseudomonas bacteria
During pathogen attack, plants recruit beneficial microbes in a โcry for helpโ 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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reposted by
Rowena Hill
Richard Leggett
2 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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reposted by
Rowena Hill
Earlham Institute
3 months ago
PHD: What does an โoptimalโ 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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reposted by
Rowena Hill
PLOS Biology
3 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
๐งช
plos.io/4hcC5tx
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reposted by
Rowena Hill
Mark McMullan
3 months ago
PhD studentship Come help us understand the wheat rhizosphere at the Earlham Institute ๐ฆ 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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reposted by
Rowena Hill
Michael Habig
3 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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reposted by
Rowena Hill
Earlham Institute
3 months ago
๐ 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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reposted by
Rowena Hill
Benjamin Wolfe
4 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! ๐งต
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
๐
doi.org/10.1111/nph.70472
add a skeleton here at some point
4 months ago
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reposted by
Rowena Hill
4 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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reposted by
Rowena Hill
The British Lichen Society
4 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! ๐๐งฌ๐ณ
@neilhall.bsky.social
@norwichmicro.bsky.social
4 months ago
0
6
4
reposted by
Rowena Hill
John Lovell
5 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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reposted by
Rowena Hill
Fantin Mesny
5 months ago
๐ฃ NEW PREPRINT ๐ 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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reposted by
Rowena Hill
Jason Stajich
5 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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reposted by
Rowena Hill
Laura van Galen
5 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 โ fungi need their own conservation focus
@spun.earth
@ethz.ch
doi.org/10.1038/s414...
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13
reposted by
Rowena Hill
Team Thomma
6 months ago
๐ฃ Happy to see the journal publication ๐ of our work on Starships ๐ 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 โStarshipsโ, 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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reposted by
Rowena Hill
Laurie Belcher
6 months ago
OrthoFinder just dropped a major update Itโs faster, more accurate, and ready for thousands of genomes Letโs break it down (1/10)
github.com/OrthoFinder/...
www.biorxiv.org/content/10.1...
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reposted by
Rowena Hill
Earlham Institute
6 months ago
๐ฌ โWe are taking genome
#annotations
from disparate methods and harnessing the information contained in them to produce a more unified set of annotations.โ Comparing
#genomes
at scale with pan-annotation tools.
buff.ly/TMOWcG8
@rowenahill.bsky.social
๐งฌ ๐ฅ๏ธ
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Pangenome annotation opens up a multiverse of genes
Gaining deeper insights into genetic diversity with pangenome annotation.
https://www.earlham.ac.uk/articles/pangenome-annotation-opens-multiverse-genes
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3
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reposted by
Rowena Hill
Michael Cunliffe ๐ณ๏ธโ๐
7 months ago
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 worldโs biggest challenges ๐๐=๐๐ฅ๐ชฒ
@uk.theconversation.com
@plymbiomarsci.bsky.social
@erc.europa.eu
๐
theconversation.com/marine-fungi...
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reposted by
Rowena Hill
7 months ago
๐จ 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
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reposted by
Rowena Hill
Michael Cunliffe ๐ณ๏ธโ๐
7 months ago
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 ๐
www.bbc.co.uk/programmes/p...
@thembauk.bsky.social
@plymbiomarsci.bsky.social
0
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reposted by
Rowena Hill
Emily Josephs
7 months ago
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...
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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
https://academic.oup.com/evlett/advance-article/doi/10.1093/evlett/qraf011/8161170
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99
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reposted by
Rowena Hill
Current Biology
7 months ago
Our newest special issue is now live! Check it out to discover more about diverse and beautiful Fungi๐๐โ๐ซ๐ On the cover: the fly agaric, Amanita muscaria, releasing its spores in the early morning light.
www.cell.com/current-biol...
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reposted by
Rowena Hill
Genetics Society of America
7 months ago
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. 1/2๐งต
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8
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Our paper on phylogenetics of fungal Starship TEs is now on the cover of the June issue of Genetics
@genetics-gsa.bsky.social
๐
academic.oup.com/genetics/iss...
@mcmullan0.bsky.social
@earlhaminst.bsky.social
@rothamsted.bsky.social
add a skeleton here at some point
7 months ago
0
11
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reposted by
Rowena Hill
Kew Gardens
8 months ago
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
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reposted by
Rowena Hill
Lucy Crouch
8 months ago
๐The Last of Us - NIHR HPRU PhD opportunity๐ 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...
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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
https://www.findaphd.com/phds/project/the-last-of-us-developing-a-genomic-epidemiology-toolkit-for-fungal-outbreaks/?p185331
0
2
4
reposted by
Rowena Hill
Kew Gardens
8 months ago
๐ข JOB: Lead a landmark project to sequence 20,000 fungi & lichens from one of the worldโs largest fungarium collections. Shape science, support biodiversity, and help safeguard our fungal future ๐๐งช ๐
careers.kew.org/vacancy/seni...
๐๏ธ Apply by 25 May
#PlantSciJobs
#fungi
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reposted by
Rowena Hill
Kenichi Tsuda
8 months ago
This is wild. Chromosome distributions into different nuclei! Distribution of haploid chromosomes into separate nuclei in two pathogenic fungi
www.science.org/doi/10.1126/...
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Distribution of haploid chromosomes into separate nuclei in two pathogenic fungi
Nuclei define eukaryotes, enabling macromolecular compartmentalization and cellular regulation. Each nucleus is believed to contain one or more haploid sets of chromosomes (1N). However, we discovered...
https://www.science.org/doi/10.1126/science.abn7811
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42
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reposted by
Rowena Hill
Alexis Stamatakis
8 months ago
RAxML-NG v2.0 beta is here
github.com/amkozlov/rax...
Features 1. Difficulty prediction
academic.oup.com/mbe/article/...
2. Adaptive search
academic.oup.com/mbe/article/...
3. Early Stop
www.biorxiv.org/content/10.1...
4. Model selection 5. Rapid bootstrapping
academic.oup.com/mbe/article/...
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Release RAxML-NG v2.0-beta2 ยท amkozlov/raxml-ng
Main new features Adaptive tree search heuristic (Togkousidis 2023) , (Togkousidis 2024) Multiple fast branch support measures Integrated model testing Full Changelog: 1.2.2...2.0-beta2
https://github.com/amkozlov/raxml-ng/releases/tag/2.0-beta2
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Our recent paper is out where we propose kmer-based phylogenetics for fungal Starship TEs (which are unalignable as highly variable). We think it could help with spotting bonafide HGT events (and suggest direction of transfer?)
doi.org/10.1093/g3jo...
@mcmullan0.bsky.social
@norwichmicro.bsky.social
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Starship giant transposable elements cluster by host taxonomy using k-mer-based phylogenetics
Abstract. Starships are a recently established superfamily of giant cargo-mobilizing transposable elements in the fungal subphylum Pezizomyotina (phylum As
https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkaf082/8110972
8 months ago
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37
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reposted by
Rowena Hill
The Guardian
8 months ago
The ancient psychedelics myth: โPeople tell tourists the stories they think are interesting for themโ
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The ancient psychedelics myth: โPeople tell tourists the stories they think are interesting for themโ
The narrative of ancient tribes around the world regularly using ayahuasca and magic mushrooms in healing practices is a popular one. Is it true?
https://www.theguardian.com/science/2025/may/01/the-ancient-psychedelics-myth-people-tell-tourists-the-stories-they-think-are-interesting-for-them?utm_term=Autofeed&CMP=bsky_gu&utm_medium=&utm_source=Bluesky#Echobox=1746102802
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reposted by
Rowena Hill
Earlham Institute
8 months ago
๐ A new publication from
@mcmullan0.bsky.social
and the Hall Group studies pathogen genetic diversity to uncover how
#crop
#pathogens
may be evolving in wild reservoirs. ๐ฑ
buff.ly/I17w6p8
@neilhall.bsky.social
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Developing a crop- wild-reservoir pathogen system to understand pathogen evolution and emergence
Evidence for those pathogen genes selected specifically for success on crops.
https://buff.ly/I17w6p8
0
3
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reposted by
Rowena Hill
Joe Edwards
9 months ago
Fungal endophytes may not be a reliable way to improve plant resilience to global change. Warmer temperatures disrupt symbiosis between plants and fungal endophytes by reducing fungal colonization and diversity in plant tissues, with stronger effects in leaves than roots.
dx.doi.org/10.1111/gcb....
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Warming Disrupts PlantโFungal Endophyte Symbiosis More Severely in Leaves Than Roots
Warmer temperatures associated with climate change disrupt relationships between plants and the fungi living in their leaves and roots by reducing the abundance and diversity of these fungiโespeciall...
http://dx.doi.org/10.1111/gcb.70207
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