S. Lorena Ament

rambaut/figtree Automatically exported from code.google.com/p/figtree - rambaut/figtree

The first version of FigTree was released nearly 20 years ago and it is still widely used (including by me). But there are currently 85 issues on the GitHub repo (github.com/rambaut/figt...) and some of them I don’t really like the look of.

"TAIR 12 is here!"

Read more here: https://arabidopsis.org/news/breaking-news#307

#News

Mathematical modeling predicts that CRISPR-Cas has a greater potential to benefit its plasmid in defence than in offense. Structure of the mathematical model when a CRISPR-Cas plasmid is the resident (left) or the invader plasmid (right). The authors consider seven distinct cell types: C (CRISPR-Cas bearing) and T (TA-bearing) plasmids reside in host cells; CT denotes a C cell that has been invaded by a T plasmid and vice versa; Cr* and Ci* cells have undergone segregational loss of a T plasmid, and the fate of PSK is not yet resolved; PSK cells are dead cells after post-segregational killing. When the plasmids co-reside, they are subject to basic biological parameter s (segregational loss). CRISPR-Cas and TA alter parameter s by their own modes of action x and y, respectively. Parameter f describes the positive effect PSK cells have on growth of nearby cells, where fr describes the benefit to cells containing the previously resident plasmid. All parameters adopt distinct values when their respective plasmids are resident (r) or invasive (i).

Plasmids use immune systems like #CRISPR-Cas to compete with other #plasmids, but do these systems confer an advantage? @davvi36.bsky.social &co show that CRISPR-Cas benefits resident plasmids but is constrained by toxin-antitoxin systems after horizontal transfer @plosbiology.org 🧪 plos.io/4qNbdDt

🐟💃

So I did something a bit different :). Thrilled to see this fun project out! 🐟 #genomics

"Female-biased sex ratios despite stable genetic sex determination across a climatic gradient in a marine fish"

www.biorxiv.org/content/10.6...

I submitted this ms to a journal about a 1.5 months ago, and the status remains "Awaiting Referee Assignment". The editor says they are struggling to find a second reviewer... Are these waiting times normal? Should I offer a fresh list of potential reviewers or is that inappropriate? 💔 #postdoclife

Pangenomics transforms evolutionary biology | Royal Society This Theo Murphy meeting organised by Dr Joana Meier, Dr Henry North and Dr Charlotte Wright, will showcase cutting-edge pangenome tools, applied uses of pangenomes which are transforming health and a...

Are you excited about pangenomics? If so, join us in Edinburgh on 8-9th June to discuss the latest methods & insights from using these approaches across biodiversity! More details here:

royalsociety.org/science-even...

Organised together with @henrylnorth.bsky.social & @joanameier.bsky.social!

Would you say that Neurospora crassa is declining as a model organism for fungal biology?

💛 No way, that orange fun-guy is alive and well!
🔴 Yeah, not so many people work with it nowadays ...
🔵 Neuro-who?

📅 Ends: December 31, 2025, 10:03 PM UTC

📊 Show results

Whoop! New preprint has dropped - led by the amazing @trevormugoya.bsky.social. We developed a SV-calling and benchmarking platform called SaVor and test it on 1,165 Arabidopsis thaliana short read whole genomes. Do check out the paper, and try SaVor on your own data: github.com/ChabbyTMD/Sa...

A recent shift in centromere size and DNA content in Podospora pseudocomata co-occurs with the loss of a fungal genome defense system https://www.biorxiv.org/content/10.64898/2025.12.02.690432v1

Three-dimensional genome architecture connects chromatin structure and function in a major wheat pathogen - BMC Biology Background Genome spatial organization plays a fundamental role in biological function across all domains of life. While the principles of nuclear architecture have been well-characterized in animals ...

Our paper on Zymoseptoria tritici 3D genome organization is officially out! @iglavincheska.bsky.social
link.springer.com/article/10.1...

What if we could autocomplete DNA based on function?

Today in @Nature, we share semantic design—a strategy for function-guided design with genomic language models that leverages genomic context to create de novo genes and systems with desired functions. 🧵

www.nature.com/articles/s41...

Defensive fungal symbiosis on insect hindlegs Dinidorid stinkbugs were reported to possess a conspicuous tympanal organ on female hindlegs. In this study, we show that this organ is specialized to retain microbial symbionts rather than to perceiv...

"When the female bugs lay their eggs, they rub the cultivated hyphae across the egg mass. The hyphae grow to envelope the eggs and physically exclude attentive parasitoid wasps until the bugs hatch."

#fungi #symbiosis

Wow O_o

GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.

Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....

genzplyr is dplyr, but bussin fr fr no cap.

Our paper was included in the Collection "Microbial Genomics of Eukaryotes" from the @microbiologysociety.org 🧬 😁

#genomics #longreadsequencing

www.microbiologyresearch.org/content/micr...

From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes - Nature A newly compiled atlas of species-wide structural variants and gene-based and graph pangenomes derived from highly complete assemblies of genomes from 1,086 natural isolates enable integrative genome-...

O.o
"From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes" | Nature share.google/IAaPSj5t9OvQ...

#pangenome #fungi #yeast

A timetree of Fungi dated with fossils and horizontal gene transfers - Nature Ecology & Evolution Combining fossil-based and molecular calibrations with data on horizontal gene transfer events, the authors develop a time-calibrated phylogeny of Fungi. This timescale, which integrates analytic uncertainties, suggests an older age of crown Fungi (1,401–896 million years ago), as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems (1,253–797 Ma).

A timetree of Fungi dated with fossils and horizontal gene transfers

www.nature.com/articles/s41...

Wooo!

How do species diverge? Could the relative immobility of plants increase their likelihood of speciating in the same place?🧵

Hybridization and introgression are major evolutionary processes. Since the 1940s, the prevailing view has been that they shape plants far more than animals. In our new study (www.science.org/doi/10.1126/...
), we find the opposite: animals exchange genes more, and for longer, than plants

Rapid establishment of species barriers in plants compared with that in animals Speciation, the process by which new reproductively isolated species emerge from ancestral populations, results from the gradual accumulation of barriers to gene flow within genomes. To date, the noti...

"Rapid establishment of species barriers in plants compared with that in animals" by Monnet et al
#Speciation

www.science.org/doi/10.1126/...

Hyphal editing of the conserved premature stop codon in CHE1 is stimulated by oxidative stress in Fusarium graminearum - Stress Biology Although genome-wide A-to-I editing mediated by adenosine-deaminase-acting-on-tRNA (ADAT) occurs during sexual reproduction in the presence of stage-specific cofactors, RNA editing is not known to occ...

mRNA A-to-I editing in vegetative cells of Fusarium

#fungionsky #fungi #epigenetics

link.springer.com/article/10.1...

I think their point is “they occur more in the populations where they are adaptive”, which makes me uncomfortable haha. Having said, I haven’t read the paper carefully and I didn’t understand their method on a quick scan.

De novo rates of a Trypanosoma-resistant mutation in two human populations | PNAS Mutation rates have long been measured as averages across many genomic positions. Recently, a method to measure the rates of individual mutations w...

Uhm 🤔, another "mutation is not random" paper:

#mutation #genomics

www.pnas.org/doi/10.1073/...

Population diversity declines between inoculated and exposed guinea pigs. Viral titers in nasal lavage samples are indicated by the overall height of the bar. Red lines show LOD (50 PFU/mL). Colors within the bars represent unique barcodes, and the height of each color indicates barcode frequency within the sample. Plots for individual animals are paired with those of their cage mate. Representative pairs for direct contact (top half) and aerosol (bottom half) exposure are shown from three experimental replicates. Guinea pig ID numbers are shown in the upper right corner of each plot.

What causes viral transmission bottlenecks? This study uses barcoded virions to show that in the case of #influenza A #virus, early within-host replication dynamics (rather than a reduced inoculum population) drive loss of diversity during transmission @plosbiology.org 🧪 plos.io/4ngicDK

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024...

Check out our new paper on adopting a trait-based framework for protist diversity! We make the case for a unified protist trait database, how to build it, and how it could transform research on protist ecology and evolution.
#protistsonsky

Normal meiosis in the fungus Sclerotinia sclerotiorum despite the irregular distribution of haploid chromosomes between two nuclei - Nature Communications The fungus Sclerotinia sclerotiorum distributes its 16 chromosomes irregularly between two nuclei within single ascospore cells. Here, the authors show that chromosomal segregation and genetic recombi...

Sclerotina and its weird-ass arrangement of different chromosomes in two separate nuclei still follow normal meiosis, it turns out.

#fungi #meiosis

www.nature.com/articles/s41...

I'm super bummed to be missing #ESEB2025 @eseb2025.bsky.social due to a cancelled flight! Here's a quick overview of my talk "Gene- and genome-focused perspectives on microbial pangenomes" slated to be part of The Evolution of Microbial Pangenomes -- which I recommend you attend tomorrow (Fri) !
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