Yves Van de Peer (YVdP) obtained his PhD in 1996 at the University of Antwerp, Belgium. After a postdoctoral fellowship with Axel Meyer at the University of Konstanz, Germany, he was hired at Ghent University (BE) as Group Leader of VIB (Department of Plant Systems Biology) in 2000 and as an Associate Professor at Ghent University in 2001, and promoted to Full Professor in 2008. YVdP’s research group is considered a genome analysis powerhouse specialized in the study of the structure and evolution of (plant) genomes. Because of their unique expertise and experience in gene prediction, genome annotation, and genome analysis, his research group has been, and still is, involved in many international genome projects.
YVdP is particularly interested in the study of gene and genome duplications as well as in the evolution of novel gene functions after duplication. YVdP published more than 450 papers, many of which in high-profile journals such as Nature, Nature Genetics, Nature Reviews Genetics, Science, PNAS, Genome Research, and The Plant Cell. YVdP has an H-index > 100 and his work has been cited more than 60,000 times. For many consecutive years, YVdP has been a Highly Cited Researcher. In 2013, YVdP received an ERC Advanced Grant entitled “DOUBLE-UP: The evolutionary significance of genome duplications for natural and artificial organism populations”, and in 2018 another one entitled “DOUBLE-TROUBLE: Replaying the ‘genome duplication’ tape of life: the adaptive potential of polyploidy in a stressful or changing environment”. YVdP is Organizer and Chair of the bi-annual international Current Opinion Conference on Plant Genome Evolution. This meeting was held in 2011, 2013, 2015, 2017, and 2019. In 2019, YVdP also organized the triannual International Conference on Polyploidy, Ghent, Belgium. YVdP is a member of the Royal Flemish Academy of Belgium for Science and the Arts (KVAB; since 2012) and serves on the Editorial Boards of five international journals (The Plant Journal, PeerJ, Genome Biology and Evolution, Current Plant Biology, Frontiers in Genetics). YVdP is also part-time professor at the Department of Biochemistry, Genetics and Microbiology, at the University of Pretoria, South Africa, and at the College of Horticulture at Nanjing Agricultural University, China.
The genus Emericellopsis is found in terrestrial, but mainly in marine, environments with a worldwide distribution. Although Emericellopsis has been recognized as an important source of bioactive compounds, the range of metabolites expressed by the species of this genus, as well as the genes involved in their production are still poorly known. Untargeted metabolomics, using UPLC- QToF–MS/MS, and genome sequencing (Illumina HiSeq) was performed to unlock E. cladophorae MUM 19.33 chemical diversity. The genome of E. cladophorae is 26.9 Mb and encodes 8572 genes. A large set of genes encoding carbohydrate-active enzymes (CAZymes), secreted proteins, transporters, and secondary metabolite biosynthetic gene clusters were identified. Our analysis also revealed genomic signatures that may reflect a certain fungal adaptability to the marine environment, such as genes encoding for (1) the high-osmolarity glycerol pathway; (2) osmolytes’ biosynthetic processes; (3) ion transport systems, and (4) CAZymes classes allowing the utilization of marine polysaccharides. The fungal crude extract library constructed revealed a promising source of antifungal (e.g., 9,12,13-Trihydroxyoctadec-10-enoic acid, hymeglusin), antibacterial (e.g., NovobiocinA), anticancer (e.g., daunomycinone, isoreserpin, flavopiridol), and anti-inflammatory (e.g., 2’-O-Galloylhyperin) metabolites. We also detected unknown compounds with no structural match in the databases used. The metabolites’ profiles of E. cladophorae MUM 19.33 fermentations were salt dependent. The results of this study contribute to unravel aspects of the biology and ecology of this marine fungus. The genome and metabolome data are relevant for future biotechnological exploitation of the species.
Hibiscus hamabo is a semi-mangrove species with strong tolerance to salt and waterlogging stress. However, the molecular basis and mechanisms that underlie this strong adaptability to harsh environments remain poorly understood. Here, we assembled a high-quality, chromosome-level genome of this semi-mangrove plant and analyzed its transcriptome under different stress treatments to reveal regulatory responses and mechanisms. Our analyses suggested that H. hamabo has undergone two recent successive polyploidy events, a whole-genome duplication followed by a whole-genome triplication, resulting in an unusually large gene number (107,309 genes). Comparison of the H. hamabo genome with that of its close relative Hibiscus cannabinus, which has not experienced a recent WGT, indicated that genes associated with high stress resistance have been preferentially preserved in the H. hamabo genome, suggesting an underlying association between polyploidy and stronger stress resistance. Transcriptomic data indicated that genes in the roots and leaves responded differently to stress. In roots, genes that regulate ion channels involved in biosynthetic and metabolic processes responded quickly to adjust the ion concentration and provide metabolic products to protect root cells, whereas no such rapid response was observed from genes in leaves. Using co-expression networks, potential stress resistance genes were identified for use in future functional investigations. The genome sequence, along with several transcriptome datasets, provide insights into genome evolution and the mechanism of salt and waterlogging tolerance in H. hamabo, suggesting the importance of polyploidization for environmental adaptation.
Cycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. Here, we report the 10.5-Gb reference genome of
To improve our understanding of the origin and evolution of mycoheterotrophic plants, we here present the chromosome-scale genome assemblies of two sibling orchid species: partially mycoheterotrophic
All extant core-eudicot plants share a common ancestral genome that has experienced cyclic polyploidizations and (re)diploidizations. Reshuffling of the ancestral core-eudicot genome generates abundant genomic diversity, but the role of this diversity in shaping the hierarchical genome architecture, such as chromatin topology and gene expression, remains poorly understood. Here, we assemble chromosome-level genomes of one diploid and three tetraploid
Pinewood nematode (PWN, Bursaphelenchus xylophilus) is the causal agent of pine wilt disease (PWD), which severely affects Pinus pinaster stands in southwestern Europe. Despite the high susceptibility of P. pinaster, individuals of selected half-sib families have shown genetic variability in survival after PWN inoculation, indicating that breeding for resistance can be a valuable strategy to control PWD. In this work, RNA-seq data from susceptible and resistant plants inoculated with PWN were used for SNP discovery and analysis. A total of 186,506 SNPs were identified, of which 31 were highly differentiated between resistant and susceptible plants, including SNPs in genes involved in cell wall lignification, a process previously linked to PWN resistance. Fifteen of these SNPs were selected for validation through Sanger sequencing and 14 were validated. To evaluate SNP-phenotype associations, 40 half-sib plants were genotyped for six validated SNPs. Associations with phenotype after PWN inoculation were found for two SNPs in two different genes (MEE12 and PCMP-E91), as well as two haplotypes of HIPP41, although significance was not maintained following Bonferroni correction. SNPs here detected may be useful for the development of molecular markers for PWD resistance and should be further investigated in future association studies.