Yves Van de Peer
@yvdp.bsky.social
Scientific Director of the VIB-UGent Centre for Plant Systems Biology, Professor at Ghent University, the University of Pretoria (SA), and Nanjing Agricultural University (China). Hate migraines and loves Alfie.
A study of 470 angiosperms identified 132 ancient WGD events, revealing non-random clustering during environmental upheaval, highlighting polyploidy’s key evolutionary role. PMID:42105759, Cell 2026, @Cell https://www.cell.com/cell/fulltext/S0092-8674(26)00397-1 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
https://www.cell.com/cell/fulltext/S0092-8674(26)00397-1
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cell.com
PAPER from @yvdp.bsky.social in @currentbiology.bsky.social #PlantScience www.sciencedirect.com/science/arti...
A three-step model for the establishment of polyploid plants
Polyploidy, the result of whole genome duplication, is widespread in plants. Over long timescales, polyploids seem to go extinct more often than diplo…
sciencedirect.com
PAPER from @yvdp.bsky.social in @newphyt.bsky.social nph.onlinelibrary.wiley.com/doi/10.1111/...
Repeatability of phenotypic consequences due to whole‐genome duplication in Spirodela polyrhiza
Heterogeneity in growth rate and morphology in artificial tetraploid Spirodela polyrhiza populations is affected by the deterministic component of the ploidy effect but also a stochastic component of...
nph.onlinelibrary.wiley.com
PAPER from @stevenmaere.bsky.social and @yvdp.bsky.social in @cellpress.bsky.social www.cell.com/cell/abstrac...
The rise of polyploids during environmental upheaval
From the dating of 132 ancient whole-genome duplication events across 470 angiosperms, paleopolyploidization events cluster around pivotal periods of environmental upheaval and extinction, notably the...
cell.com
PAPER from @yvdp.bsky.social in @newphyt.bsky.social nph.onlinelibrary.wiley.com/doi/epdf/10....
An inter‐specific Amaranthus pangenome captures genetic variation potentially underlying key leafy vegetable traits in this underutilised crop
Amaranthus species (particularly Amaranthus cruentus, Amaranthus hypochondriacus, Amaranthus tricolor and Amaranthus caudatus) are traditional underutilised crops with the potential to contribute to ...
nph.onlinelibrary.wiley.com
Could duplicate genomes (polyploidy) have helped saved some flowering plants from the dinosaur-killing asteroid? Read more in Cell: spkl.io/63320AA0h2 @heche.bsky.social, @yvdp.bsky.social & colleagues @cp-cell.bsky.social
The rise of polyploids during environmental upheaval: Cell www.cell.com/cell/fulltex...
The rise of polyploids during environmental upheaval
From the dating of 132 ancient whole-genome duplication events across 470 angiosperms, paleopolyploidization events cluster around pivotal periods of environmental upheaval and extinction, notably the...
cell.com
Evolution of protein domains and protein domain combinations provides insights into the origin and diversification of land plants www.cell.com/cell-genomic...
PAPER from @yvdp.bsky.social @viblifesciences.bsky.social www.sciencedirect.com/science/arti...
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…
sciencedirect.com
PAPER from @yvdp.bsky.social @viblifesciences.bsky.social academic.oup.com/mbe/article/...
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
academic.oup.com
Polyploidization in diatoms accelerates adaptation to warming www.nature.com/articles/s41... #jcampubs 🌊
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...
nature.com
📢 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
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.
doi.org
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...
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
academic.oup.com
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...
science.org
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
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
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 · last yr.Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes https://www.biorxiv.org/content/10.1101/2025.05.27.656262v1
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...
nature.com
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
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
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...
nature.com
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 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
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 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
