Browsing Research Articles (Biochemistry) by Author "Van de Peer, Yves"

Browsing Research Articles (Biochemistry) by Author "Van de Peer, Yves"

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  • Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis) 
    Wang, Xuewen; Chen, Shiyu; Chen, Shiyu; Yssel, A.E.J. (Anna); Chaluvadi, Srinivasa R.; Johnson, Matthew S.; Gangashetty, Prakash; Hamidou, Falalou; Sanogo, Moussa D.; Zwaenepoel, Arthur; Wallace, Jason; Van de Peer, Yves; Bennetzen, Jeffrey L.; Van Deynze, Allen (Oxford University Press, 2021-03)
    Background: 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 ...
  • Genome sequence of Malania oleifera, a tree with great value for nervonic acid production 
    Xu, Chao-Qun; Liu, Hui; Zhou, Shan-Shan; Zhang, Dong-Xu; Zhao, Wei; Wang, Sihai; Chen, Fu; Sun, Yan-Qiang; Nie, Shuai; Jia, Kai-Hua; Jiao, Si-Qian; Zhang, Ren-Gang; Yun, Quan-Zheng; Guan, Wenbin; Wang, Xuewen; Gao, Qiong; Bennetzen, Jeffrey L.; Maghuly, Fatemeh; Porth, Ilga; Van de Peer, Yves; Wang, Xiao-Ru; Ma, Yongpeng; Mao, Jian-Feng (Oxford University Press, 2019-01-24)
    BACKGROUND : Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree’s seed is valued for its high content of precious fatty ...
  • Genome streamlining in a minute herbivore that manipulates its host plant 
    Greenhalgh, Robert; Dermauw, Wannes; Glas, Joris J.; Rombauts, Stephane; Wybouw, Nicky; Thomas, Jainy; Alba, Juan M.; Pritham, Ellen J.; Legarrea, Saioa; Feyereisen, Rene; Van de Peer, Yves; Van Leeuwen, Thomas; Clark, Richard M.; Kant, Merijn R. (eLife Sciences Publications, 2020-10)
    The tomato russet mite, Aculops lycopersici, is among the smallest animals on earth. It is a worldwide pest on tomato and can potently suppress the host’s natural resistance. We sequenced its genome, the first of an ...
  • Genomes of early-diverging streptophyte algae shed light on plant terrestrialization 
    Wang, Sibo; Li, Linzhou; Li, Haoyuan; Sahu, Sunil Kumar; Wang, Hongli; Xu, Yan; Xian, Wenfei; Song, Bo; Liang, Hongping; Cheng, Shifeng; Chang, Yue; Song, Yue; Cebi, Zehra; Wittek, Sebastian; Reder, Tanja; Peterson, Morten; Yang, Huanming; Wang, Jian; Melkonian, Barbara; Van de Peer, Yves; Xu, Xun; Wong, Gane Ka-Shu; Melkonian, Michael; Liu, Huan; Liu, Xin (Nature Research, 2020-02)
    Mounting evidence suggests that terrestrialization of plants started in streptophyte green algae, favoured by their dual existence in freshwater and subaerial/terrestrial environments. Here, we present the genomes of ...
  • A genomic analysis and transcriptomic atlas of gene expression in Psoroptes ovis reveals feeding- and stage-specific patterns of allergen expression 
    Burgess, Stewart T.G.; Marr, Edward J.; Bartley, Kathryn; Nunn, Francesca G.; Down, Rachel E.; Weaver, Robert J.; Prickett, Jessica C.; Dunn, Jackie; Rombauts, Stephane; Van Leeuwen, Thomas; Van de Peer, Yves; Nisbet, Alasdair J. (BioMed Central, 2019)
    BACKGROUND : Psoroptic mange, caused by infestation with the ectoparasitic mite, Psoroptes ovis, is highly contagious, resulting in intense pruritus and represents a major welfare and economic concern for the livestock industry ...
  • Genomic resources to guide improvement of the shea tree 
    Hale, Iago; Ma, Xiao; Melo, Arthur T.O.; Padi, Francis Kwame; Hendre, Prasad S.; Kingan, Sarah B.; Sullivan, Shawn T.; Chen, Shiyu; Boffa, Jean-Marc; Muchugi, Alice; Danquaah, Agyemang; Danquah, Agyemang; Barnor, Michael Teye; Jamnadass, Ramni; Van de Peer, Yves; Van Deynze, Allen (Frontiers Research Foundation, 2021-09-09)
    A defining component of agroforestry parklands across Sahelo-Sudanian Africa (SSA), the shea tree (Vitellaria paradoxa) is central to sustaining local livelihoods and the farming environments of rural communities. Despite ...
  • Insights into the mechanisms implicated in Pinus pinaster resistance to pinewood nematode 
    Modesto, Ines; Sterck, Lieven; Arbona, Vicent; Gomez-Cadenas, Aurelio; Carrasquinho, Isabel; Van de Peer, Yves; Miguel, Celia M. (Frontiers Media, 2021-06-10)
    Pine wilt disease (PWD), caused by the plant–parasitic nematode Bursaphelenchus xylophilus, has become a severe environmental problem in the Iberian Peninsula with devastating effects in Pinus pinaster forests. Despite ...
  • The Litsea genome and the evolution of the laurel family 
    Chen, Yi-Cun; Li, Zhen; Zhao, Yun-Xiao; Gao, Ming; Wang, Jie-Yu; Liu, Ke-Wei; Wang, Xue; Wu, Li-Wen; Jiao, Yu-Lian; Xu, Zi-Long; He, Wen-Guang; Zhang, Qi-Yan; Liang, Chieh-Kai; Hsiao, Yu-Yun; Zhang, Di-Yang; Lan, Si-Ren; Huang, Laiqiang; Xu, Wei; Tsai, Wen-Chieh; Liu, Zhong-Jian; Van de Peer, Yves; Wang, Yang-Dong (Nature Publishing Group, 2020-04-03)
    The laurel family within the Magnoliids has attracted attentions owing to its scents, variable inflorescences, and controversial phylogenetic position. Here, we present a chromosomelevel assembly of the Litsea cubeba ...
  • Loss of wood formation genes in monocot genomes 
    Roodt, Danielle; Li, Zhen; Van de Peer, Yves; Mizrachi, Eshchar (Oxford University Press, 2019-07)
    Woodiness (secondary xylemderived from vascular cambium) has been gained and lostmultiple times in the angiosperms, but has been lost ancestrally in all monocots. Here, we investigate the conservation of genes involved ...
  • Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants 
    Xue, Jia-Yu; Dong, Shan-Shan; Wang, Ming-Qiang; Song, Tian-Qiang; Zhou, Guang-Can; Li, Zhen; Van de Peer, Yves; Shao, Zhu-Qing; Wang, Wei; Chen, Min; Zhang, Yan-Mei; Sun, Xiao-Qin; Chen, Hong-Feng; Zhang, Yong-Xia; Zhang, Shou-Zhou; Chen, Fei; Zhang, Liang-Sheng; Cox, Cymon; Liu, Yang; Wang, Qiang; Hang, Yue-Yu (Wiley, 2022-07)
    The early diversification of angiosperms is thought to have been a rapid process, which may complicate phylogenetic analyses of early angiosperm relationships. Plastid and nuclear phylogenomic studies have raised several ...
  • Model-based detection of whole-genome duplications in a phylogeny 
    Zwaenepoel, Arthur; Van de Peer, Yves (Oxford University Press, 2020-09)
    Ancient whole-genome duplications (WGDs) leave signatures in comparative genomic data sets that can be harnessed to detect these events of presumed evolutionary importance. Current statistical approaches for the detection ...
  • Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution 
    Roelofs, Dick; Zwaenepoel, Arthur; Sistermans, Tom; Nap, Joey; Kampfraath, Andries A.; Van de Peer, Yves; Ellers, Jacintha; Kraaijeveld, Ken (BioMed Central, 2020-05)
    BACKGROUND: Gene duplication events play an important role in the evolution and adaptation of organisms. Duplicated genes can arise through different mechanisms, including whole-genome duplications (WGDs). Recently, WGD ...
  • A multi-omics analysis of the grapevine pathogen Lasiodiplodia theobromae reveals that temperature affects the expression of virulence- and pathogenicity-related genes 
    Felix, Carina; Meneses, Rodrigo; Gonçalves, Micael F.M.; Tilleman, Laurentijn; Duarte, Ana S.; Jorrín-Novo, Jesus V.; Van de Peer, Yves; Deforce, Dieter; Nieuwerburgh, Filip; Esteves, Ana C.; Alves, Artur (Nature Publishing Group, 2019-09)
    Since the end of the Cold War, the practice of defence diplomacy has received much attention, as has the proactive prevention of conflict. However, the preventive diplomacy of defence forces – something that is implied ...
  • Multi-proxy analyses of a mid-15th century middle iron age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome 
    Rifkin, Riaan F.; Vikram, Surendra; Ramond, Jean-Baptiste; Rey-Iglesia, Alba; Brand, Tina B.; Porraz, Guillaume; Val, Aurore; Hall, Grant; Woodborne, Stephan M.; Le Bailly, Matthieu; Potgieter, Marnie; Underdown, Simon J.; Koopman, Jessica E.; Cowan, Don A.; Van de Peer, Yves; Willerslev, Eske; Hansen, Anders J. (BioMed Central, 2020-05-06)
    BACKGROUND : The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, ...
  • De novo assembly of transcriptomes from a B73 maize line introgressed with a QTL for resistance to gray leaf spot disease reveals a candidate allele of a lectin receptor-like kinase 
    Welgemoed, Tanya; Pierneef, Rian Ewald; Sterck, Lieven; Van de Peer, Yves; Swart, Velushka; Scheepers, Kevin Daniel; Berger, David Kenneth (Frontiers Media, 2020-03-13)
    Gray leaf spot (GLS) disease in maize, caused by the fungus Cercospora zeina, is a threat to maize production globally. Understanding the molecular basis for quantitative resistance to GLS is therefore important for food ...
  • Optimising orbit counting of arbitrary order by equation selection 
    Melckenbeeck, Ine; Audenaert, Pieter; Van Parys, Thomas; Van de Peer, Yves; Colle, Didier; Pickavet, Mario (BioMed Central, 2019-01-15)
    BACKGROUND : Graphlets are useful for bioinformatics network analysis. Based on the structure of Hoˇcevar and Demšar’s ORCA algorithm, we have created an orbit counting algorithm, named Jesse. This algorithm, like ORCA, ...
  • ORCAE-AOCC : a centralized portal for the annotation of African orphan crop genomes 
    Yssel, A.E.J. (Anna); Kao, Shu-Min; Van de Peer, Yves; Sterck, Lieven (MDPI, 2019-11-20)
    ORCAE (Online Resource for Community Annotation of Eukaryotes) is a public genome annotation curation resource. ORCAE-AOCC is a branch that is dedicated to the genomes published as part of the African Orphan Crops ...
  • Phages actively challenge niche communities in Antarctic soils 
    Bezuidt, Keoagile Ignatius Oliver; Lebre, Pedro H.; Pierneef, Rian Ewald; Leon-Sobrino, Carlos; Adriaenssens, Evelien M.; Cowan, Don A.; Van de Peer, Yves; Makhalanyane, Thulani Peter (American Society for Microbiology, 2020-05-05)
    By modulating the structure, diversity, and trophic outputs of microbial communities, phages play crucial roles in many biomes. In oligotrophic polar deserts, the effects of katabatic winds, constrained nutrients, and ...
  • Polyploidy : a biological force from cells to ecosystems 
    Fox, Donald T.; Soltis, Douglas E.; Soltis, Pamela S.; Ashman, Tia-Lynn; Van de Peer, Yves (Elsevier, 2020)
    Polyploidy, resulting from the duplication of the entire genome of an organism or cell, greatly affects genes and genomes, cells and tissues, organisms, and even entire ecosystems. Despite the wide-reaching importance ...
  • Polyploidy : an evolutionary and ecological force in stressful times 
    Van de Peer, Yves; Ashman, Tia-Lynn; Soltis, Pamela S.; Soltis, Douglas E. (Oxford University Press, 2021-01)
    Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for evolutionary innovation and species diversification. Although polyploid organisms, especially plants, abound, the apparent nonrandom ...