Mark McMullan
@mcmullan0.bsky.social
89 followers 67 following 10 posts
Evolutionary biologist -population genomics -wild-agricultural pathogen evolution, invasion and adaptation (Wheat & Beets)
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Reposted by Mark McMullan
uk-news.bsky.social
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 genetic map of human metabolism across the allele frequency spectrum - United Kingdom
Study design
www.europesays.com
Reposted by Mark McMullan
earlhaminst.bsky.social
🍄 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.
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
Reposted by Mark McMullan
rowenahill.bsky.social
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
A map of the world with countries coloured by how many accessions they have in Kew's fungarium, and pie charts for each country indicating how many accessions have had DNA extracted and their genomes sequenced
Reposted by Mark McMullan
natplants.nature.com
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
Reposted by Mark McMullan
rowenahill.bsky.social
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
Reposted by Mark McMullan
natplants.nature.com
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/...
Reposted by Mark McMullan
evolletters.bsky.social
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
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.
Reposted by Mark McMullan
earlhaminst.bsky.social
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.
John Innes Foundation Internship in Plant Science
buff.ly
Reposted by Mark McMullan
genetics-gsa.bsky.social
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
Reposted by Mark McMullan
rowenahill.bsky.social
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
Cover for the June issue of the journal Genetics, with an abstract illustration in the background showing starships flying through space trailing DNA sequences that meet in the bottom right corner to form a circular phylogenetic tree
Reposted by Mark McMullan
hanliconius.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/
mcmullan0.bsky.social
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.
mcmullan0.bsky.social
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...
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.
www.biorxiv.org
Reposted by Mark McMullan
earlhaminst.bsky.social
💬 “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
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.
buff.ly
mcmullan0.bsky.social
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
mcmullan0.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.
Reposted by Mark McMullan
Reposted by Mark McMullan
earlhaminst.bsky.social
💬 "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
New insights into large mobile fungal genome elements, called Starships, have revealed more about how they jump between fungal species and influence their evolution.
buff.ly
Reposted by Mark McMullan