Yves Van de Peer

Revisiting ancient whole-genome duplications in the seed and flowering plants through the lens of dosage-sensitive genes Dosage-sensitive genes suggest no ancestral angiosperm WGD.

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

Evolution of protein domains and protein domain combinations provides insights into the origin and diversification of land plants www.cell.com/cell-genomic...

Multi-Omics Roadmap to Plant-Derived Medicines Medicinal plants are invaluable sources of bioactive natural products or metabolites, however the discovery and sustainable utilization of these metab…

PAPER from @yvdp.bsky.social @viblifesciences.bsky.social
www.sciencedirect.com/science/arti...

Resolving the Stasis-Dynamism Paradox: Genome Evolution in Tree Ferns Abstract. The paradox of evolutionary stasis and dynamism—how morphologically static lineages persist through deep geological periods despite environmental

PAPER from @yvdp.bsky.social @viblifesciences.bsky.social
academic.oup.com/mbe/article/...

Polyploidization in diatoms accelerates adaptation to warming - Nature Climate Change The authors obtained large-volume individuals of diatom cultures under thermal stress. These polyploids (having more than two sets of chromosomes) are shown to rapidly adapt to high temperatures, high...

Polyploidization in diatoms accelerates adaptation to warming www.nature.com/articles/s41... #jcampubs 🌊

Bryophytes hold a larger gene family space than vascular plants - Nature Genetics A super-pangenome analysis incorporating 123 newly sequenced bryophyte genomes reveals that bryophytes exhibit a larger number of unique and lineage-specific gene families than vascular plants.

📢 New publication ' #Bryophytes hold a larger gene family space than vascular plants' by Shanshan Dong et al. in @natgenet.nature.com 🧬🧪

doi.org/10.1038/s415...

#evolution #pangenome

Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes After gene and genome duplications, expression divergence across cell types is not random, and it can be explained by a combination of gene age, gene funct

Our paper on the evolution (duplicated) gene expression divergence in spatially resolved plant transcriptomes is now out @theplantcell.bsky.social

w/ @yvdp.bsky.social

#PlantSci #Evolution

academic.oup.com/plcell/advan...

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...

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

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...

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

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...

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

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

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...

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

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

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

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

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...

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

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...

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.

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

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

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.

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

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 !

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...

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...

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

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

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/content/10.1...

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...

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/...

Join the Pereiralab at vib.ai 👇

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...

🚨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...

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

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