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.
Digitaria exilis, white fonio, is a minor but vital crop of West Africa that is valued for its resilience in hot, dry, and low-fertility environments and for the exceptional quality of its grain for human nutrition. Its success is hindered, however, by a low degree of plant breeding and improvement.
We sequenced the fonio genome with long-read SMRT-cell technology, yielding a ∼761 Mb assembly in 3,329 contigs (N50, 1.73 Mb; L50, 126). The assembly approaches a high level of completion, with a BUSCO score of >99%. The fonio genome was found to be a tetraploid, with most of the genome retained as homoeologous duplications that differ overall by ∼4.3%, neglecting indels. The 2 genomes within fonio were found to have begun their independent divergence ∼3.1 million years ago. The repeat content (>49%) is fairly standard for a grass genome of this size, but the ratio of Gypsy to Copia long terminal repeat retrotransposons (∼6.7) was found to be exceptionally high. Several genes related to future improvement of the crop were identified including shattering, plant height, and grain size. Analysis of fonio population genetics, primarily in Mali, indicated that the crop has extensive genetic diversity that is largely partitioned across a north-south gradient coinciding with the Sahel and Sudan grassland domains.
We provide a high-quality assembly, annotation, and diversity analysis for a vital African crop. The availability of this information should empower future research into further domestication and improvement of fonio.