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Reposted by Yves Van de Peer

Plant Systems Biology @psb-vib.bsky.social · 11d

PAPER from @yvdp.bsky.social
www.science.org/doi/10.1126/...

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...

www.science.org

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Reposted by Yves Van de Peer

Plant Systems Biology @psb-vib.bsky.social · Jul 13

PAPER from @yvdp.bsky.social
advanced.onlinelibrary.wiley.com/doi/10.1002/...

Subgenome Partitioning and Polyploid Genome Evolution in the Loach Family Botiidae (Order Cypriniformes)

This study investigates subgenome evolution and polyploidy in Cypriniformes fish, revealing complex phylogenetic relationships and genomic dynamics. By applying advanced subgenome partitioning method...

advanced.onlinelibrary.wiley.com

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Reposted by Yves Van de Peer

Plant Systems Biology @psb-vib.bsky.social · Jul 13

PAPER from @yvdp.bsky.social in @journalofecology.bsky.social
besjournals.onlinelibrary.wiley.com/doi/abs/10.1...

Polyploid—Diploid coexistence in the greater duckweed Spirodela polyrhiza

Mortier and colleagues demonstrate the crucial role of competition and frequency dependency on neopolyploid establishment. They, therefore, caution against inferring neopolyploid success based solely...

besjournals.onlinelibrary.wiley.com

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Reposted by Yves Van de Peer

Fabrício Almeida-Silva @almeidasilvaf.bsky.social · May 28

Happy to share #ourlatest.

You may have seen studies investigating how duplicated genes diverge in expression across multiple tissues. Here, we zoomed in in tissues (using #spatial transcriptomic data) to investigate how genes diverge in expression across tissue compartments.

w/ @yvdp.bsky.social

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · May 28

Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes https://www.biorxiv.org/content/10.1101/2025.05.27.656262v1

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Reposted by Yves Van de Peer

Plant Systems Biology @psb-vib.bsky.social · May 5

PAPER from @yvdp.bsky.social in @natplants.nature.com
www.nature.com/articles/s41...

Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls - Nature Plants

New fern transcriptomes reveal repeated whole-genome duplications, unique gene families and distinct lignocellulosic evolution, providing a comprehensive database that underscores the ancient divergen...

www.nature.com

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Reposted by Yves Van de Peer

Plant Systems Biology @psb-vib.bsky.social · Apr 25

PAPER from @yvdp.bsky.social in @narjournal.bsky.social
academic.oup.com/nar/article/...

SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics

Abstract. With the explosive growth of whole-genome datasets, accurate detection of orthologous synteny has become crucial for reconstructing evolutionary

academic.oup.com

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Jonathan Wendel @jonathanfwendel.bsky.social · Mar 24

Polyploidy Conference! Registration deadline is May 5th
cjm.sb-roscoff.fr/en/conferenc...

Evolutionary and ecological genomics of polyploidy in plants: temporal dynamics across scales of biological organization from molecules to ecosystems | CNRS - Conférences Jacques Monod (CJM)

cjm.sb-roscoff.fr

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Reposted by Yves Van de Peer

Plant Systems Biology @psb-vib.bsky.social · Mar 24

PAPER from @yvdp.bsky.social in @newphyt.bsky.social
nph.onlinelibrary.wiley.com/doi/full/10....

Expanding the toolkit for ploidy manipulation in Chlamydomonas reinhardtii

Whole-genome duplications, widely observed in plant lineages, have significant evolutionary and ecological impacts. Yet, our current understanding of the direct implications of ploidy shifts on shor...

nph.onlinelibrary.wiley.com

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Will Ratcliff @wcratcliff.bsky.social · Mar 5

6/46 WGD, like multicellularity, evolved many times in history (see www.nature.com/articles/nrg... by @yvdp.bsky.social et al.), driving species radiations and innovations (like at the roots of vertebrates and angiosperms). In fact, most species either are polyploids or bear signs of ancient WGDs.

The evolutionary significance of polyploidy - Nature Reviews Genetics

Polyploidy occurs frequently but is usually detrimental to survival; thus, few polyploids survive in the long term. Here, evidence linking the short-term evolutionary success of polyploids to environm...

www.nature.com

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Reposted by Yves Van de Peer

pdhsu.bsky.social @pdhsu.bsky.social · Feb 19

This was an insane team effort between Arc and Nvidia that convened machine learning and computational biology researchers across Stanford, UC Berkeley, and UCSF. Especially grateful to Jensen Huang for his belief and support of this vision and labor of love, and the entire Evo 2 team below

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pdhsu.bsky.social @pdhsu.bsky.social · Feb 19

Evo 2 is trained on 9.3T tokens of DNA with single-base resolution at 1M token context length 🥳

We release two models with 7B and 40B parameters along with weights, training and inference code, and pretraining data—making this one of the largest fully open AI models available

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Yves Van de Peer @yvdp.bsky.social · Jan 26

doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome du… pubmed.ncbi.nlm.nih.gov/39862387/

doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications - PubMed

Supplementary data are available at Bioinformatics online and at https://github.com/almeidasilvaf/doubletrouble_paper.

pubmed.ncbi.nlm.nih.gov

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Reposted by Yves Van de Peer

Moritz K. Nowack @moritznowack.bsky.social · Jan 15

In just 5 month’s time we’ll be raising the curtain @debijloke in Ghent www.bijloke.be for Arabidopsis and much much more #ICAR2025 ! Registration is now OPEN, submit abstracts for oral presentations until March 17th, early bird registration runs until April 20th. More info on
www.icar2025.com !

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Reposted by Yves Van de Peer

fmortier.bsky.social @fmortier.bsky.social · Jan 16

Polyploid success isn’t just about growing fast—it’s about outcompeting progenitors! 🌱
We had neopolyploid duckweed and their progenitor invade each other, testing how stress & frequency-dependent growth shape WGD success... or failure. @yvdp.bsky.social #polyploid #duckweed
doi.org/10.1101/2025...

Polyploid - diploid coexistence in the greater duckweed Spirodela polyrhiza

Polyploidy, resulting from whole-genome duplication (WGD), is widespread among plants and originates in sympatry with their lower-ploidy progenitors. New polyploids can only succeed when they overcome...

doi.org

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Yves Van de Peer @yvdp.bsky.social · Jan 16

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

Polyploid - diploid coexistence in the greater duckweed Spirodela polyrhiza

Polyploidy, resulting from whole-genome duplication (WGD), is widespread among plants and originates in sympatry with their lower-ploidy progenitors. New polyploids can only succeed when they overcome...

www.biorxiv.org

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Yves Van de Peer @yvdp.bsky.social · Dec 31

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Reposted by Yves Van de Peer

Plant Systems Biology @psb-vib.bsky.social · Dec 4

We are delighted to bring #ICAR2025 to Gent in Belgium! Abstract submission OPEN! icar2025.com
@aabiologists.bsky.social @moritznowack.bsky.social @hildenelissen.bsky.social @bertderybel.bsky.social @mehta-lab.com @kuleuvenuniversity.bsky.social @viblifesciences.bsky.social

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Yves Van de Peer @yvdp.bsky.social · Nov 24

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

The Rise of Polyploids During Environmental Catastrophes

Polyploidy, or whole-genome duplication (WGD), both a strong evolutionary and ecological force and a potential pitfall, occurs extensively across the tree of life, particularly in angiosperms. While p...

www.biorxiv.org

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Reposted by Yves Van de Peer

Plant Systems Biology @psb-vib.bsky.social · Nov 21

PAPER from @bertderybel.bsky.social about SPL13-dependent oriented cell divisions that control the onset of a juvenile to adult phase change in the root apical meristem. www.science.org/doi/10.1126/...

SPL13 controls a root apical meristem phase change by triggering oriented cell divisions

Oriented cell divisions are crucial for determining the overall morphology and size of plants, but what controls the onset and duration of this process remains largely unknown. Here, we identified a s...

www.science.org

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Reposted by Yves Van de Peer

Stein Aerts @steinaerts.bsky.social · Nov 16

Join the Pereiralab at vib.ai 👇

Joana Pereira @joanampereira.bsky.social · Nov 16

🚨The future Pereira lab is hiring!

We will start at @vibai.bsky.social in Feb 2025 and are looking for a postdoc to join our team 🤓

If you want to leverage AI and large networks to explore and understand the protein universe 🌌, check below!

*deadline: 21 Nov 2024*

jobs.vib.be/j/93314/post...

Postdoc in Protein Computational Biology / Structural Bioinformatics - VIB

Job description We are seeking a postdoc to join the Pereira Lab for an interdisciplinary project that integrates structural bioinformatics, protein evolution, complex network analysis, and deep learn...

jobs.vib.be

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Reposted by Yves Van de Peer

Joana Pereira @joanampereira.bsky.social · Nov 16

🚨The future Pereira lab is hiring!

We will start at @vibai.bsky.social in Feb 2025 and are looking for a postdoc to join our team 🤓

If you want to leverage AI and large networks to explore and understand the protein universe 🌌, check below!

*deadline: 21 Nov 2024*

jobs.vib.be/j/93314/post...

Postdoc in Protein Computational Biology / Structural Bioinformatics - VIB

Job description We are seeking a postdoc to join the Pereira Lab for an interdisciplinary project that integrates structural bioinformatics, protein evolution, complex network analysis, and deep learn...

jobs.vib.be

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Reposted by Yves Van de Peer

Alain Goossens @alaingoossenspsb.bsky.social · Nov 18

First steps on Bluesky. Let's see how much enthusiasm I can raise to send contributions to our upcoming focus issue on Metabolism in Plant Physiology @plantphys.bsky.social

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VIB.AI @vibai.bsky.social · Nov 20

Fantastic start of the #VIBAIsymposium this morning with a welcome by our scientific director @steinaerts.bsky.social and talks by Julien Gagneur and @avsecz.bsky.social

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Plant Systems Biology @psb-vib.bsky.social · Nov 20

Interested in plant research in Zambia?
Dora Shimbwambwa is working on practical, affordable ways to fight pests and help Zambian farmers thrive in a changing climate. gatesnot.es/4eAsVnt?WT.m...

She’s up at 3 a.m. to help farmers thrive

Dora Shimbwambwa is working on practical, affordable ways to fight pests and help Zambian farmers thrive in a changing climate.

gatesnot.es

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Reposted by Yves Van de Peer

Plant Systems Biology @psb-vib.bsky.social · Nov 18

To create awareness, the VIB-UGent eco teams displayed the weight-equivalent of one day of research in waste (180 kg) in their garden, representing a carbon footprint of approximately 1 ton of CO2 equivalents.

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