S. Lorena Ament

S. Lorena Ament

@loreament.bsky.social

Bioinformatician at NBIS, SciLifeLab, Sweden. ---------------------------------------------- Interested in genomics, speciation, reproductive strategies, fungi, and biodiversity. And cats! She/her Views are my own.

562 followers394 following69 posts

Pinned

S. Lorena Ament
@loreament.bsky.social

It's out!! Using population and comparative genomics of Podospora fungi, we show that a class of genes called #NLRs display evolutionary signatures that are consistent with an immune function, much like in plants and animals! 1/n 🍄 #popgen #balancingselection #introgression doi.org/10.1093/gbe/...

doi.orgNOD-Like Receptor Genes Undergo Diversity-Enhancing Evolution in a Fungal Species ComplexAbstract. Fungi harbor diverse arrays of genes encoding NOD-like receptors (NLRs), key intracellular immune proteins found in plants, animals, and bacteria

S. Lorena Ament reposted

PLOS Biology
@plosbiology.org

The ratio of nonsynonymous to synonymous DNA substitutions (dN/dS) encodes information about selection pressures. This study develops a model of dN/dS in recombining bacterial populations, offering insights on how horizontal gene transfer shapes the genome. 🧪 #AcademicSky #evolution plos.io/3Wcy9lT

S. Lorena Ament reposted

Will Ratcliff
@wcratcliff.bsky.social

1/ How do cells divide when they're stuck in something squishy? Most of what we know about the cell cycle comes from yeast in liquid or on flat plates, but in nature they live in dough, mucus, soil and tissue. This new paper asks what that does to division. Love this one!

S. Lorena Ament
@loreament.bsky.social

This is a lovely study. Ferns have such interesting life history that shakes any species concept #speciation #ferns nph.onlinelibrary.wiley.com/doi/abs/10.1...

nph.onlinelibrary.wiley.comLife phases integration uncovers long‐lived gametophytes mediated reticulate evolution in <fi>Haplopteris</fi> (Pteridaceae)Accumulating evidence suggests that speciation often resembles a reticulate network rather than a bifurcating process. In ferns, which possess independent gametophyte and sporophyte phases, reticu...

S. Lorena Ament reposted

Gema Puebla
@gemapuebla.bsky.social

Starting my bluesky with this super exciting new! New preprint from Di Pietro's Lab www.biorxiv.org/content/10.6... How do fungal pathogens maintain dispensable chromosomes without losing them in clonal evolution? Here's a thread 🧵

biorxiv.orgKiller meiotic driver prevents chromosome loss and enhances fitness in a fungal pathogenFungal pathogens often carry dispensable chromosomes (DCs) that confer a selective advantage in adverse environments or during host infection but can be spontaneously lost under non-selective conditio...

S. Lorena Ament reposted

NBIS
@nbis.se

📢 Registration is now open for the course "R Programming Foundations for Data Analysis"! Beginner course, no prior experience needed. 📅 When: 9-13 November 2026 📍 Where: BMC, Uppsala ⏰ Apply by: 12 October 2026 🔗 Course webpage: training.scilifelab.se/events/r-pro...

training.scilifelab.seR Programming Foundations for Data Analysis<p>The course is addressed to individuals with little or no experience in programming but who are enthusiastic about learning how to use R for data analysis and streamline their work.</p> <p>The cour...

S. Lorena Ament reposted

Genome Biology and Evolution
@genomebiolevol.bsky.social

@loreament.bsky.social & Saupe suggest that fungal NOD-like receptors evolve under diversity-enhancing mechanisms and display selective signatures consistent with a general immune function. 🔗 doi.org/10.1093/gbe/... #societyjournal #genome #evolution

doi.orgNOD-Like Receptor Genes Undergo Diversity-Enhancing Evolution in a Fungal Species ComplexAbstract. Fungi harbor diverse arrays of genes encoding NOD-like receptors (NLRs), key intracellular immune proteins found in plants, animals, and bacteria

S. Lorena Ament reposted

Mario Vallejo-Marin
@nicrodemo.bsky.social

Last year we took a small amber with a fossil bee to the Oxford synchrotron. Little did we know that it would become a tiny window into the ecology of bees and their mites in the subtropical forests 40 million years ago. @charliezoology.bsky.social @hfspo.bsky.social www.cell.com/iscience/ful...

cell.comInsights into the ecology of early leaf-cutter bees revealed through synchrotron X-ray tomographyZoology; Entomology; Evolutionary biology; Paleobiology
S. Lorena Ament
@loreament.bsky.social

It's out!! Using population and comparative genomics of Podospora fungi, we show that a class of genes called #NLRs display evolutionary signatures that are consistent with an immune function, much like in plants and animals! 1/n 🍄 #popgen #balancingselection #introgression doi.org/10.1093/gbe/...

doi.orgNOD-Like Receptor Genes Undergo Diversity-Enhancing Evolution in a Fungal Species ComplexAbstract. Fungi harbor diverse arrays of genes encoding NOD-like receptors (NLRs), key intracellular immune proteins found in plants, animals, and bacteria
View full thread
S. Lorena Ament
@loreament.bsky.social

So in conclusion, NLR genes might play underappreciated roles in fungal immunity, like pathogen defense or even symbiont recognition. Now it's time for molecular biologists to prove it! #immunity

S. Lorena Ament
@loreament.bsky.social

This work is the culmination of my postdoc grant and work with Sven Saupe from the University of Bordeaux, France. It's a very long and comprehensive paper 😅, very much in my style. I know it's a lot but I hope you give it a chance! /fin #postdoclife #fungi #immunity

S. Lorena Ament
@loreament.bsky.social

It's out!! Using population and comparative genomics of Podospora fungi, we show that a class of genes called #NLRs display evolutionary signatures that are consistent with an immune function, much like in plants and animals! 1/n 🍄 #popgen #balancingselection #introgression doi.org/10.1093/gbe/...

doi.orgNOD-Like Receptor Genes Undergo Diversity-Enhancing Evolution in a Fungal Species ComplexAbstract. Fungi harbor diverse arrays of genes encoding NOD-like receptors (NLRs), key intracellular immune proteins found in plants, animals, and bacteria
View full thread
S. Lorena Ament
@loreament.bsky.social

We also confirmed that HIC NLR paralogs exchange repeat units from the Cterm, increasing allelic diversity and fast evolution. This process potentially makes them sources of genetic load too, as observed in a few well-studied allorecognition NLRs that cause reproductive incompatibilities. 9/n

S. Lorena Ament
@loreament.bsky.social

Finally, we went a bit crazy and looked for HIC NLRs all across the tree of life. Different kinds of proteins can have HIC repeats, but we found that they often have an NLR configuration. Could HIC be advantageous in the context of self-nonself recognition in other taxa too? 10/n

S. Lorena Ament
@loreament.bsky.social

It's out!! Using population and comparative genomics of Podospora fungi, we show that a class of genes called #NLRs display evolutionary signatures that are consistent with an immune function, much like in plants and animals! 1/n 🍄 #popgen #balancingselection #introgression doi.org/10.1093/gbe/...

doi.orgNOD-Like Receptor Genes Undergo Diversity-Enhancing Evolution in a Fungal Species ComplexAbstract. Fungi harbor diverse arrays of genes encoding NOD-like receptors (NLRs), key intracellular immune proteins found in plants, animals, and bacteria
View full thread
S. Lorena Ament
@loreament.bsky.social

HIC NLRs are more associated with transposable elements, have a higher mutational input (probably from a process called RIP), higher piN/piS, higher dN/dS, higher Tajima's D, you name it. They are funky! 7/n #popgen #molecularevolution #transposons

S. Lorena Ament
@loreament.bsky.social

We also aimed at distinguishing balancing selection from #introgression, by contrasting patterns of differentiation, trans-species polymorphism, and by examining signatures of selective sweeps. It turns out that NLRs are preferentially introgressed between species! 8/n #hybridization

S. Lorena Ament
@loreament.bsky.social

It's out!! Using population and comparative genomics of Podospora fungi, we show that a class of genes called #NLRs display evolutionary signatures that are consistent with an immune function, much like in plants and animals! 1/n 🍄 #popgen #balancingselection #introgression doi.org/10.1093/gbe/...

doi.orgNOD-Like Receptor Genes Undergo Diversity-Enhancing Evolution in a Fungal Species ComplexAbstract. Fungi harbor diverse arrays of genes encoding NOD-like receptors (NLRs), key intracellular immune proteins found in plants, animals, and bacteria
View full thread
S. Lorena Ament
@loreament.bsky.social

We reasoned that if NLRs have a general immune function, we should observe signals in their molecular evolution, such as fast gene turnover, gene expansions and balancing selection. And that's exactly what we found! HIC NLRs are particularly crazy! 6/n #popgen #balancingselection

S. Lorena Ament
@loreament.bsky.social

It's out!! Using population and comparative genomics of Podospora fungi, we show that a class of genes called #NLRs display evolutionary signatures that are consistent with an immune function, much like in plants and animals! 1/n 🍄 #popgen #balancingselection #introgression doi.org/10.1093/gbe/...

doi.orgNOD-Like Receptor Genes Undergo Diversity-Enhancing Evolution in a Fungal Species ComplexAbstract. Fungi harbor diverse arrays of genes encoding NOD-like receptors (NLRs), key intracellular immune proteins found in plants, animals, and bacteria
View full thread
S. Lorena Ament
@loreament.bsky.social

Podosporologists have been studying vegetative fusion between different individuals (allorecognition) since the 50s! So we know there are 9 allorecognition genes in P. anserina, and 4 of those are NLRs. But there are >60 other NLR genes in #Podospora genomes. What are those doing? 3/n

S. Lorena Ament
@loreament.bsky.social

NLR genes, although constructed somewhat differently, exist in other domains of life. NLRs are key components of the innate immune system in plants, animals and even bacteria. So what if fungal NLRs are also generally defense genes, rather than just #allorecognition genes? 4/n

S. Lorena Ament
@loreament.bsky.social

It's out!! Using population and comparative genomics of Podospora fungi, we show that a class of genes called #NLRs display evolutionary signatures that are consistent with an immune function, much like in plants and animals! 1/n 🍄 #popgen #balancingselection #introgression doi.org/10.1093/gbe/...

doi.orgNOD-Like Receptor Genes Undergo Diversity-Enhancing Evolution in a Fungal Species ComplexAbstract. Fungi harbor diverse arrays of genes encoding NOD-like receptors (NLRs), key intracellular immune proteins found in plants, animals, and bacteria
S. Lorena Ament
@loreament.bsky.social

Previous studies took more of a macroevolutionary perspective, or did not look at NLRs specifically. So we focused on #Podospora anserina and its relatives, model systems for studying the molecular mechanisms of self/nonself recognition. 2/n

S. Lorena Ament
@loreament.bsky.social

How do fungi distinguish conspecific self from non-self? The genetics of this fascinating topic are plagued with misunderstandings even amongst mycologists. We wrote a review/rant to address this confusion, out now! 🍄 #fungi #allorecognition #HETgenes www.sciencedirect.com/science/arti...

sciencedirect.comDrawing the line: Clarifying fungal allorecognition from HET domains to het genes to heterokaryon incompatibilityThe iconic networks of filamentous fungi are connected through hyphal fusions. While fusion is beneficial among hyphae from the same fungal individual…

S. Lorena Ament reposted

James McInerney
@jomcinerney.bsky.social

I’ve seen trees you people wouldn’t believe. Deep branches collapsing off the shoulder of a saturated site, unresolved. I watched long-branch attraction glitter in the dark near the root of the Archaea. All those topologies will be lost in time… like tips in a polytomy.

S. Lorena Ament reposted

Björn Usadel
@usadellab.bsky.social

1/8 What if the genomic features we associate with fungal pathogens were also used by mutualists? We assembled 41 scale lichen genomes across 11 Peltigera species with 30 chromosome scale and 5 T2T revealing an unexpected genomic toolkit behind lichen symbiosis. doi.org/10.64898/202... #lichen

doi.orgA chromosome-scale super-pangenome of the lichen genus Peltigera reveals genome architecture and expanded interaction repertoires shared across pathogenic and mutualistic fungiFungi engage in associations with other organisms across a continuum from pathogenic to mutualistic lifestyles. Hence, they require a compendium of molecular capacities, including partner recognition,...

S. Lorena Ament reposted

Seána Duggan
@seanaduggan.bsky.social

🗞️New Paper🗞️ We show that #Candida & #Staph cooperate via copper handling - with fungal copper uptake & bacterial copper export shaping the community. @mrccmm.bsky.social @microbiologysociety.org @universityofexeter.bsky.social www.microbiologyresearch.org/content/jour...

microbiologyresearch.orgCopper-driven mutualism of Candida albicans and Staphylococcus aureus interkingdom biofilmsAlthough fungi and bacteria commonly co-exist within polymicrobial communities, the molecular mechanisms underlying their interactions are still not well understood. Here, we show that the fungus Cand...
S. Lorena Ament
@loreament.bsky.social

"Unifying Repbase and Dfam: a new open foundation for transposable element research" #genomics #transposons link.springer.com/article/10.1...

link.springer.comUnifying Repbase and Dfam: a new open foundation for transposable element research - Mobile DNARepbase and Dfam, the two foundational resources for transposable element annotation, are being unified into a single, fully open access framework, with Repbase released under CC-0 and its core curati...

S. Lorena Ament reposted

Team Thomma
@teamthomma.bsky.social

Where do plant pathogen effectors come from? @mesny.bsky.social shows how fungi turned shield 🛡️ into sword ⚔️ to end up with dual-function molecules to disrupt host immunity & protective host microbiota. @ceplas.bsky.social @mibinet.bsky.social @madfungi.bsky.social www.science.org/doi/10.1126/...

science.orgPlant-associated fungi co-opt ancient antimicrobials for host manipulationFungal effectors may have evolved from ancient antimicrobials, shaping plant microbiota and immunity during infection.

S. Lorena Ament reposted

Danve Castroverde
@danvec.bsky.social

Incorporating genetic load contributes to predicting Arabidopsis thaliana’s response to climate change @naturecomms.bsky.social www.nature.com/articles/s41...

nature.comIncorporating genetic load contributes to predicting Arabidopsis thaliana’s response to climate change - Nature CommunicationsGenetic load is often overlooked in conservation predictions of species response to climate change. This study found that effective population size was the major determinant of genetic load and that g...