We are often asked whether pangenomes are worth the hassle. The files can be large and methods to explore them are much more challenging than linear references. Earlier this week, we preprinted a clear example of how and why pan-genome graphs are so important for trait discovery.

bioRxiv Genomics@biorxiv-genomic.bsky.social · 3mo ago

Dissecting the regulatory and genomic drivers of the dichogamy determining G-locus in pecan https://www.biorxiv.org/content/10.64898/2026.05.14.725045v1

Revision of the Angiosperm Phylogeny Group (APG) classification has been underway! The group is requesting community feedback until April 22nd. Here is a link to a survey to gather feedback, which includes links to the manuscript and the new classification: docs.google.com/forms/d/e/1F...

APG V Survey - Extended Deadline

Dear Colleagues: We are soliciting community input on a draft of APG V, which is available at https://docs.google.com/document/d/1M8ZWZoJTj1mFYUe_bRKrP-NCwwEzoGuC/edit?usp=sharing&ouid=11366933678134...

docs.google.com

‪ 🌳 Do you want to contribute to research on how humans perceive forests? Take this quick, anonymous 10-min survey 🌲 👉 www.biodiful.org#/forest This will help us explore how people experience forest biodiversity! Please share on 🦋 & tag @biodiful.bsky.social to reach more participants 🙏💚 🌐🌍🦤🦑🪴🍁🧪

Introgression fuelling reproductive isolation? 👀 Impressive work & fascinating story ✨

Jenn Coughlan@jenncoughlan.bsky.social · 5mo ago

I am SO THRILLED to share our first fully-lab lab paper!!!!!! Led by @hybridzones.bsky.social & @hagarsoliman.bsky.social, w/ a major assist from @pfschwarz.bsky.social!!!!!!!!!!!!! Read more below, if you're curious (you should be- it's AWESOME!!!!!!!) link: www.sciencedirect.com/science/arti...

I am SO THRILLED to share our first fully-lab lab paper!!!!!! Led by @hybridzones.bsky.social & @hagarsoliman.bsky.social, w/ a major assist from @pfschwarz.bsky.social!!!!!!!!!!!!! Read more below, if you're curious (you should be- it's AWESOME!!!!!!!) link: www.sciencedirect.com/science/arti...

Introgression and parental conflict shape repeated occurrences of postzygotic isolation in Mimulus

Postzygotic reproductive isolation is often thought to accumulate as a byproduct of neutral divergence. Yet it frequently evolves rapidly, in line wit…

sciencedirect.com

Awesome to see @cfcollins.bsky.social first paper out from her PhD - a huge amount of work!! Regulatory features determine the evolutionary fate of laterally acquired genes in plants url: academic.oup.com/mbe/article/...

Regulatory features determine the evolutionary fate of laterally acquired genes in plants

Abstract. Lateral gene transfer (LGT) is widespread in eukaryotes, including in animals and plants where it can fuel adaptive evolution and innovation. How

academic.oup.com

Collins et al. combined expression, methylation, and genomic data to investigate long-term persistence of laterally acquired genes in the grass Alloteropsis, showing that those capable of regulating their own expression are more likely to persist. 🔗 doi.org/10.1093/molbev/msag042 #evobio #molbio

Regulatory features determine the evolutionary fate of laterally acquired genes in plants

Abstract. Lateral gene transfer (LGT) is widespread in eukaryotes, including in animals and plants where it can fuel adaptive evolution and innovation. How

doi.org

So cool. Multiple cell lineages contribute to the germline in maize -- and differences between apical and lateral branches! www.biorxiv.org/content/10.6...

🏵 Check out the latest #AJB Synthesis article, by Haley Branch! 🏵 The sleeping giant needs coffee: Overlooked areas for integrating plant #ecophysiology & evolutionary biology doi.org/10.1002/ajb2... #botany #plantscience #ecology #evolution

Updated tutorials for nQuack today. Want to predict ploidy level of sequence data? See this new tutorial on how to process and model data faster: mlgaynor.com/nQuack/artic...

a little boy is driving a red toy car on the street .

Alt: a little kid is driving a red toy car on the street.

media.tenor.com

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

Really excited to share our latest paper led by @simonaube.bsky.social. Fascinating results examining whether regulatory mutations can lead to adaptation as fast as coding mutations do. #mevosky #evobio #evoSky www.biorxiv.org/content/10.1...

Adaptation is less accessible through mutations in promoters than in coding sequences when large effect sizes are needed

Mutations within promoters and coding sequences are both involved in adaptation, but their relative contributions remain to be compared directly. Using the fungal enzyme cytosine deaminase, we examine...

biorxiv.org

📣 The Call for Symposia for the Society for Molecular Biology and Evolution (SMBE) 2026 Annual Meeting is now open. 🌍 The meeting will be in Copenhagen June 28th to July 2nd 🖊️ We invite you to submit a symposium proposal and help shape the scientific content of SMBE 2026 Best the organisers

Symposia - SMBE 2026 - Copenhagen Denmark

SMBE 2026 Symposia Check deadlines and important dates below.  Days Hours Minutes Seconds Conference Symposia We are now accepting proposals for symposium for the 2026 Annual meeting taking place in C...

smbe2026.org

Environmental conditions drive variation in C4 photosynthetic capacity more than species traits Fan, et al. 📖 nph.onlinelibrary.wiley.com/doi/10.1111/... #PlantScience @yuzhenfan.bsky.social

I've set off to Bougainville,PNG, for another #NoFly journey. I want to complete my research there. Travelling the ~25,000km distance from Italy by🚢,🚅,&🚌,I'll emit ~10 times less than✈️ (computations to come).Here the long read on my motivations: gianlu777.substack.c... 1/🧵

So excited to see our review on how to detect horizontal gene transfers and their impact on plant functional evolution finally published in @theplantcell.bsky.social! Great teamwork between @lrsv-toulouse.bsky.social and LGDP-Perpignan 😎🥳🌱 academic.oup.com/plcell/advan...

Mechanisms, Detection, and Impact of Horizontal Gene Transfer in Plant Functional Evolution

Abstract. Horizontal gene transfers (HGT) have been observed across the tree of life. While their adaptive importance in bacteria is conspicuous, the occur

academic.oup.com

Excited / nervous to share the “magnum opus” of my postdoc in Andreas Wagner’s lab! "De-novo promoters emerge more readily from random DNA than from genomic DNA" This project is the accumulation of 4 years of work, and lays the foundation for my future group. In short, we… (1/4)

De-novo promoters emerge more readily from random DNA than from genomic DNA

Promoters are DNA sequences that help to initiate transcription. Point mutations can create de-novo promoters, which can consequently transcribe inactive genes or create novel transcripts. We know lit...

biorxiv.org

Happy to see our latest work out in @molbioevol.bsky.social. We revisit the evolution of 5-methylcytosine across neglected eukaryotic supergroups, establishing an ancestral repressive role silencing genome invaders, both transposons and viral elements👾: academic.oup.com/mbe/advance-... 🧵 1/7

Repressive cytosine methylation is a marker of viral gene transfer across divergent eukaryotes

Abstract. Cytosine DNA methylation patterns vary widely across eukaryotes, with its ancestral roles being understood to have included both transposable ele

academic.oup.com

Our #research on #drought #recovery, now published with @springernature.com in @natcomms.nature.com: Drought recovery in plants triggers a cell-state-specific immune activation. doi.org/10.1038/s414... Read thread below 👇

Drought recovery in plants triggers a cell-state-specific immune activation - Nature Communications

Post-drought rehydration triggers a preventive immune response in plants, revealing targets to enhance crop resilience by linking drought stress recovery with improved pathogen resistance.

doi.org

Bourne et al. analyzed immune receptor gene repertoires of 15 domesticated crop species, showing that grapes, mandarins, rice, barley, and yellow sarson exhibit reduced immune receptor gene repertoires compared to wild counterparts. 🔗 doi.org/10.1093/gbe/evaf147 #genome #evolution #PlantSky

Domestication Reduces Plant Immune Receptor Gene Repertoires Across Lineages

Abstract. Plant domestication is sometimes associated with a reduction in the diversity of immune receptor genes, critical for pathogen recognition and def

doi.org

The European Reference Genome Atlas (ERGA) is a pan-European community initiative to coordinate the generation of reference genomes representing European eukaryotic biodiversity @ergabiodiv.bsky.social #eseb2025

Out after peer review, collaborative study from Nordborg & Weigel labs with help from many others. Not the largest collection of new Arabidopsis thaliana genomes, but we hopefully put forward some good ideas for how to think about pangenomes and their analysis! www.nature.com/articles/s41...

Today also, @thorstenreusch.bsky.social presented the fascinating work conducted on somatic mutations in the clonal seagrass Zostera! ✨ #ESEB2025

Inspiring talk from @marcrr.bsky.social presenting student Christabel Bucao’s work. Expression variability predicts retention and functional divergence of genes after WGD! « variability creates » #ESEB2025

Unfortunately, I couldn't join in person #eseb2025, but the organizers kindly accommodated a video. Posted here in case you missed it! youtu.be/n9Ls9-8p8x0?...

Zenil-Ferguson. The importance of quantifying rate uncertainty

YouTube video by Rosana Z-F

youtu.be

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...

Excited to be in Barcelona for #ESEB2025 So many great talks, familiar faces and cool posters already!

This collaboration was so much fun!! I’m excited to see it online! www.cell.com/trends/genet...

The molecular evolutionary basis of species formation revisited

How do new species arise? This is among the most fundamental questions in evolutionary biology. The first genetic model for how reproductive barriers lead to the origin of new species was proposed nea...

cell.com

Jenn Coughlan@jenncoughlan.bsky.social · 12mo ago

Oh hey, we did a thing!!! Fun collab between the Coughlan and @mollyschumer.bsky.social labs!!! www.cell.com/trends/genet... Lead by the absolutely ✨STELLAR✨ @hybridzones.bsky.social, @nemovrobles.bsky.social, and @majorodriguezb.bsky.social.

Paper led by @movillome.bsky.social on unbiased detection of (somatic) #TE insertions in #Arabidopsis with @pacbio.bsky.social long reads out after peer review. Thanks to academic editor Leandro Quadrana for shepherding it through the review process. #plantscience link.springer.com/article/10.1...?

Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals - Genome Biology

Background Because transposable elements (TEs) can cause heritable genetic changes, past work on TE mobility in Arabidopsis thaliana has mostly focused on new TE insertions in the germline of hypometh...

link.springer.com

Please RT! I'm hiring a postdoc to work in my new lab at UCSB (!) on an NSF-funded project investigating the phenotypic consequences of WGD for photosynthesis and respiration. Check out the full posting here: recruit.ap.ucsb.edu/JPF02986 And more info about the lab here: sharbroughlab.com