Ghent University Academic Bibliography

Journal Article
A1
open access

Asymmetric genome merging leads to gene expression novelty through nucleo‐cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids

Lucas Prost (UGent) , Quinten Bafort (UGent) , Antoine Van de Vloet (UGent) , Fabricio De Almeida Silva (UGent) , Yunn Thet Paing (UGent) , Griet Casteleyn (UGent) , Sofie D'hondt (UGent) , Olivier De Clerck (UGent) and Yves Van de Peer (UGent)

(2025) NEW PHYTOLOGIST. 245(22). p.869-884

Asymmetric genome merging leads to gene expression novelty through nucleo‐cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids

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

Deciphering the biosynthetic pathway of triterpene saponins in Prunella vulgaris

Novel adaptive immune systems in pristine Antarctic soils

Flavonoids and anthocyanins in seagrasses : implications for climate change adaptation and resilience

Water lily pond : a multiomics database for water lilies

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

Expanding the toolkit for ploidy manipulation in Chlamydomonas reinhardtii

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

Untangling the gordian knot : the intertwining interactions between developmental hormone signaling and epigenetic mechanisms in insects

wgd v2 : a suite of tools to uncover and date ancient polyploidy and whole-genome duplication

Origin and evolution of the triploid cultivated banana genome

High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Interspecific transfer of genetic information through polyploid bridges

Convergent and/or parallel evolution of RNA‐binding proteins in angiosperms after polyploidization

Understanding polyploid establishment : temporary persistence or stable coexistence?

How temperature modulates the expression of pathogenesis-related molecules of the cross-kingdom pathogen Lasiodiplodia hormozganensis

Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment

Optimized tetraploidization strategies in tissue culture for Lolium, Festuca, and Festulolium

A metabolic perspective on polyploid invasion and the emergence of life histories : insights from a mechanistic model

Dosage sensitivity shapes balanced expression and gene longevity of homoeologs after whole-genome duplications in angiosperms

The immediate metabolomic effects of whole‐genome duplication in the greater duckweed, Spirodela polyrhiza

Hybridexpress : an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors

Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum

Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

The immediate effects of polyploidization of Spirodela polyrhiza change in a strain-specific way along environmental gradients

A Cas3-base editing tool for targetable in vivo mutagenesis

Diploid and tetraploid genomes of Acorus and the evolution of monocots

Whole-genome duplications and the long-term evolution of gene regulatory networks in angiosperms

The Saururus chinensis genome provides insights into the evolution of pollination strategies and herbaceousness in magnoliids

The genome of the king protea, Protea cynaroides

syntenet : an R/Bioconductor package for the inference and analysis of synteny networks

Genomic insights into adaptation to karst limestone and incipient speciation in East Asian Platycarya spp. (Juglandaceae)

A panoramic view of the genomic landscape of the genus Streptomyces

Revisiting ancient polyploidy in leptosporangiate ferns

Pigmentation enhancement techniques during ornamental fish production

Expression divergence of expansin genes drive the heteroblasty in Ceratopteris chingii

Assessing the quality of comparative genomics data and results with the cogeqc R/Bioconductor package

Comprehensive regulatory networks for tomato organ development based on the genome and RNAome of microTom tomato

The duplication of genomes and genetic networks and its potential for evolutionary adaptation and survival during environmental turmoil

Optimized tetraploidization strategies in tissue culture for Lolium and Festuca

Genome dominance in interspecific and intergeneric hybrids of Lolium, Festuca and Festulolium

Cutaneous transcriptomic profiling and candidate pigment genes in the wild discus (Symphysodon spp.)

Inference of ancient polyploidy using transcriptome data

Studying whole-genome duplication using experimental evolution of Chlamydomonas

Neutral processes underlying the macro eco-evolutionary dynamics of mixed-ploidy systems

Studying whole-genome duplication using experimental evolution of Spirodela polyrhiza

Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina)

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina) (vol 9, pg 1207, 2023)

Evolution of isoform‐level gene expression patterns across tissues during lotus species divergence

Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication

The neighborhood of the Spike gene is a hotspot for modular intertypic homologous and nonhomologous recombination in Coronavirus genomes

Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons

Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe)

The genome of homosporous maidenhair fern sheds light on the euphyllophyte evolution and defences

The genome of Corydalis reveals the evolution of benzylisoquinoline alkaloid biosynthesis in Ranunculales

The Larix kaempferi genome reveals new insights into wood properties

The Cycas genome and the early evolution of seed plants

Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy

Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax

A functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago

The genome of Hibiscus hamabo reveals its adaptation to saline and waterlogged habitat

Divergence of active site motifs among different classes of Populus glutaredoxins results in substrate switches

Application of second-generation sequencing (SGS) and third generation sequencing (TGS) in aquaculture breeding program

Genomes shed light on the evolution of Begonia, a mega‐diverse genus

Genomic and metabolomic analyses of the marine fungus Emericellopsis cladophorae : insights into saltwater adaptability mechanisms and its biosynthetic potential

Correction : divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus

Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants

Nearby transposable elements impact plant stress gene regulatory networks : a meta-analysis in A. thaliana and S. lycopersicum

MicroRNA-mediated post-transcriptional regulation of Pinus pinaster response and resistance to pinewood nematode

SNP detection in Pinus pinaster transcriptome and association with resistance to pinewood nematode

Evolution of NLR resistance genes in magnoliids : dramatic expansions of CNLs and multiple losses of TNLs

A non-duplicated magnoliid genome

The emergence and evolution of intron‐poor and intronless genes in intron‐rich plant gene families

Polyploidy : an evolutionary and ecological force in stressful times

Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts

Genome-wide analysis of butterfly bush (Buddleja alternifolia) in three uplands provides insights into biogeography, demography and speciation