Mark McMullan

📣 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 🧵

Daniel Gibbs Lab Welcome to the lab website of Professor Daniel Gibbs @ University of Birmingham

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...

Simons Postdoctoral Fellowships in Plant Biology Simons Postdoctoral Fellowships in Plant Biology on Simons Foundation

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...

Working alongside colleagues at @earlhaminst.bsky.social , @johninnescentre.bsky.social , @dsw-isp.bsky.social , @norwichmicro.bsky.social , and @rothamsted.bsky.social.

Do get in touch to find out more

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)

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 - United Kingdom Study design

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

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.

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/...

Figure showing the experimental overview as a graphic. Remaining alt text taken from the figure caption in the paper: (A) we sampled flies from six wild orchard populations ranging from Homestead, FL, to Lancaster, MA, and established isofemale lines in the laboratory. (B) We returned to a focal orchard in Media, PA, at early- and late-season timepoints and collected flies to capture evolutionary patterns following winter and summer conditions. (C) We then seeded outdoor mesocosms (N = 9) with an outbred population originating from early-season collections in Media, PA, and sampled flies at the end of summer (mid-season) and fall (late-season) to determine if seasonal patterns are recapitulated in experimental populations controlled for migration, drift, and cryptic population structure. (D) Across each wild or experimental context, we sampled flies, established lines in the lab, completed common garden treatment to remove environmental effects, and scored females for abdominal pigmentation. We also conducted pooled DNA sequencing on additional flies sampled from each population to map genomic patterns for candidate pigmentation SNPs.

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

Phylogenetic networks empower biodiversity research | PNAS Reticulate evolution has long been recognized as a key mechanism that contributes to genetic and trait diversity. With the widespread availability ...

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/...

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 crucial for infection in a plant pathogeni...

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.

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...

John Innes Foundation Internship in Plant Science

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

Unlocking genetic secrets of the world's most vital fungi collection Fungi underpin all life on Earth, yet it is estimated that more than 95 per cent of fungal species remain undiscovered. Holding over 1.25 million dried specimens, the Fungarium at Royal Botanic Garden...

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/

YouTube video by International Wheat Genome Sequencing Consortium Breeding: Why we need to start all over again

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...

A consequence of this reduction in the signal of HGT is that we recover the expected signal of the species phylogeny. This has important implications for Starship family classifications based on captain genes and how those captain relationships differ from the starships they are found within.

Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution Starships form a recently discovered superfamily of giant transposons in Pezizomycotina fungi, implicated in mediating horizontal transfer of diverse cargo genes between fungal genomes. Their elusive nature has long obscured their significance, and their impact on genome evolution remains poorly understood. Here, we reveal a surprising abundance and diversity of Starships in the phytopathogenic fungus Verticillium dahliae . Remarkably, Starships dominate the plastic genomic compartments involved in host colonization, are enriched in virulence-associated genes, and exhibit genetic and epigenetic characteristics associated with adaptive genome evolution. We further uncover extensive horizontal transfer of Starships between Verticillium species and, strikingly, from distantly related Fusarium fungi. Finally, we demonstrate how Starship activity facilitated the de novo formation of a novel virulence gene. Our findings illuminate the profound influence of Starship dynamics on fungal genome evolution and the development of virulence. ### Competing Interest Statement The authors have declared no competing interest.

Interestingly this method drastically reduces the signal of horizontal gene transfer across t ascomycetes. We consider aggravating factors for misidentification of HGT. Importantly, the remaining HGT evidence is now stark. Making identifying HGT directionality easier

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

Starting point of DNA replication mystery solved The question of where DNA replication starts in the human genome has finally been addressed, with the conclusion it is largely random.

💬 “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.

Starship discovery reveals new frontiers of fungal genome evolution New insights into large mobile fungal genome elements, called Starships, have revealed more about how they jump between fungal species and influence their evolution.

💬 "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 🚀 🧬 🌱

Starship discovery reveals new frontiers of fungal genome evolution The discovery, from scientists at the Earlham Institute and Rothamsted Research, allows researchers to better study how similar species of Pezizomycotina fungus have evolved to adopt radically different lifestyles.

📃 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