Yves Van de Peer

The paper investigates the origin of Chloranthales by analyzing subgenome phylogenies and finds evidence of an ancient allopolyploidization event involving monocot and eudicot lineages.

This study presents chromosome-scale genomes for three Greyia species, revealing that regulatory divergence after a whole-genome triplication drives morphological variation in trichome and floral traits.

This paper shows that ecological drift and dispersal limitation, not adaptive advantages, can enable polyploid populations to establish and diverge from diploids, leading to niche divergence.

This study identifies 132 ancient whole-genome duplication events in angiosperms, showing they cluster around periods of environmental upheaval and extinction.

This study shows that whole genome duplication in Spirodela polyrhiza leads to highly repeatable and deterministic phenotypic outcomes, with ploidy explaining more phenotypic variation than genetic background.

In spatial transcriptomes from five plant species, segmental (including whole-genome) duplicates show higher, broader, spatially variable expression and redundancy, while small-scale duplicates diverge asymmetrically.

The paper finds that genetic exchange is more frequent between animal species than plant species at the same level of genetic divergence, suggesting faster establishment of species barriers in plants.

The paper examines polyploid-diploid competition in Spirodela polyrhiza under stress and shows negative frequency-dependent growth fails to overcome competitive disadvantages.

This study presents a chromosome-level genome assembly of Pinus massoniana Minlin WY36, revealing insights into conifer evolution and resin synthesis.

The paper presents chromosome-level genomes for two orchids, revealing insights into their evolutionary relationships and genome size variation.

The paper generates transcriptomic data for 22 fern species to study their evolutionary genetics and cell wall composition, revealing unique gene families and divergent cell wall biochemistry.

This paper introduces the Orthology Index (OI) to robustly identify orthologous synteny, demonstrating its scalability and reliability across diverse polyploidization events and applications in plant evolutionary genomics.

This paper develops a method to engineer ploidy levels in Chlamydomonas reinhardtii using antibiotic markers and demonstrates the creation of diploids, triploids, and tetraploids.

doubletrouble identifies and classifies gene and genome duplications across 822 eukaryotic genomes, offering tools for analysis and visualization.

This study investigates gene expression changes in Chlamydomonas triploids resulting from asymmetric genome merging, finding expression dominance, proteostasis restoration, and enhanced fitness.

This study identifies GFA1 as a key photoperiodic switch regulating long-day flowering by affecting pre-mRNA splicing and photoreceptor signaling.

This study sequenced the Draparnaldia genome and transcriptomes, revealing expanded gene families linked to multicellularity and terrestrial adaptations, and its ability to synthesize phytohormones used by land plants.

The paper develops a mechanistic model to explore how metabolic efficiency influences polyploid invasion and coexistence with diploid ancestors in plants.

HybridExpress is an R/Bioconductor package for analyzing gene expression in hybrid triplets, providing tools for normalization, clustering, classification, and functional analysis.

This study models how polyploidy facilitates gene flow between diploid species by acting as a bridge, showing that increased recombination can enhance allele sorting and overcome species barriers.

The paper introduces cogeqc, an R/Bioconductor package to assess genome assembly, annotation, orthogroup inference, and synteny detection quality in comparative genomics.

The paper improves the resolution of the CMD2 locus in cassava by using BAC-guided haplotype assembly, revealing new stress resistance proteins.

The paper analyzes the genome and population genomics of Coffea arabica to reveal its diversification history and breeding-related genetic changes.

The paper constructs gene co-expression networks and non-coding RNA interactions in microTom tomato using its genome and RNA-seq data, and establishes a database for research.

syntenet infers and analyzes synteny networks from whole-genome protein sequences to identify taxon-specific gene clusters and resolve phylogenetic relationships.

The paper presents the genome of Chinese fir, revealing evolutionary insights into gymnosperms and seed plant origins through phylogenomic and genomic analyses.

The paper infers a novel angiosperm phylogeny using whole-genome microsynteny analysis, revealing new relationships among key clades.

The paper presents high-quality draft genomes for jackfruit and breadfruit, revealing expanded gene families and insights into starch and sugar metabolism.

The paper presents an improved genome assembly of the European pear using long-read sequencing and other techniques, resulting in a more accurate gene count.

This study presents a genomic analysis and transcriptomic atlas of Psoroptes ovis, identifying stage- and feeding-specific gene expression patterns, including allergens and novel multigene families.