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

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

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  • Agulhas Current properties shape microbial community diversity and potential functionality 
    Phoma, Sandra; Vikram, Surendra; Jansson, Janet K.; Ansorge, Isabelle J.; Cowan, Don A.; Van de Peer, Yves; Makhalanyane, Thulani Peter (Nature Publising Group, 2018-07-12)
    Understanding the impact of oceanographic features on marine microbial ecosystems remains a major ecological endeavour. Here we assess microbial diversity, community structure and functional capacity along the Agulhas ...
  • A chromosome-level Amaranthus cruentus genome assembly highlights gene family evolution and biosynthetic gene clusters that may underpin the nutritional value of this traditional crop 
    Ma, Xiao; Vaistij, Fabian E.; Li, Yi; Jansen van Rensburg, Willem S.; Harvey, Sarah; Bairu, Michael W.; Venter, Sonja L.; Mavengahama, Sydney; Ning, Zemin; Graham, Ian A.; Van Deynze, Allen; Van de Peer, Yves; Denby, Katherine J. (Wiley, 2021-05)
    Traditional crops have historically provided accessible and affordable nutrition to millions of rural dwellers but have been neglected, with most modern agricultural systems over-reliant on a small number of internation ...
  • Chromosome-level genome assembly of a parent species of widely cultivated azaleas 
    Yang, Fu-Sheng; Nie, Shuai; Liu, Hui; Shi, Tian-Le; Tian, Xue-Chan; Zhou, Shan-Shan; Bao, Yu-Tao; Jia, Kai-Hua; Guo, Jing-Fang; Zhao, Wei; An, Na; Zhang, Ren-Gang; Yun, Quan-Zheng; Wang, Xin-Zhu; Mannapperuma, Chanaka; Porth, Ilga; El-Kassaby, Yousry Aly; Street, Nathaniel Robert; Wang, Xiao-Ru; Van de Peer, Yves; Mao, Jian-Feng (Nature Publising Group, 2020-10-19)
    Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for Rhododendron simsii, the primary ancestor of ...
  • Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plants 
    Shi, Tao; Rahmani, Razgar Seyed; Gugger, Paul F.; Wang, Muhua H.; Li, Hui; Zhang, Yue; Li, Zhizhong; Wang, Qingfeng; Van de Peer, Yves; Marchal, Kathleen; Chen, Jinming (Oxford University Press, 2020-08)
    For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or ...
  • Draft genome assembly of the false spider mite Brevipalpus yothersi 
    Navia, Denise; Novelli, Valdenice M.; Rombauts, Stephane; Freitas-Astua, Juliana; Santos de Mendonca, Renata; Nunes, Maria Andreia; Machado, Marcos A.; Lin, Yao-Cheng; Le, Phuong; Zhang, Zaichao; Grbic, Miodrag; Wybouw, Nicky; Breeuwer, Johannes A. J.; Van Leeuwen, Thomas; Van de Peer, Yves (American Society for Microbiology, 2019-02-07)
    The false spider mite Brevipalpus yothersi infests a broad host plant range and has become one of the most economically important species within the genus Brevipalpus. This phytophagous mite inflicts damage by both feeding ...
  • Draft genome assembly of the poultry red mite, Dermanyssus gallinae 
    Burgess, Stewart T.G.; Bartley, Kathryn; Nunn, Francesca; Wright, Harry W.; Hughes, Margaret; Gemmell, Matthew; Haldenby, Sam; Paterson, Steve; Rombauts, Stephane; Tomley, Fiona M.; Blake, Damer P.; Pritchard, James; Schicht, Sabine; Strube, Christina; Oines, Oines; Van Leeuwen, Thomas; Van de Peer, Yves; Nisbet, Alasdair J. (American Society for Microbiology, 2018-11-08)
    The poultry red mite, Dermanyssus gallinae, is a major worldwide concern in the egg-laying industry. Here, we report the first draft genome assembly and gene prediction of Dermanyssus gallinae, based on combined PacBio ...
  • Draft genome of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens and Ophiostoma ips 
    Wingfield, Brenda D.; Berger, David Kenneth; Steenkamp, Emma Theodora; Lim, Hye-Jin; Duong, Tuan A.; Bluhm, Burton H.; De Beer, Z. Wilhelm; De Vos, Lieschen; Fourie, Gerda; Naidoo, Kershney; Olivier, Nicholas Abraham; Lin, Yao-Cheng; Van de Peer, Yves; Joubert, Fourie; Crampton, Bridget Genevieve; Swart, Velushka; Soal, Nicole Christine; Tatham, Catherine; Van der Nest, Magrieta Aletta; Van der Merwe, Nicolaas Albertus (Albie); Van Wyk, Stephanie; Wilken, Pieter Markus; Wingfield, Michael J. (International Mycological Association, 2017-11-21)
    The genomes of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens, and Ophiostoma ips are presented in this genome announcement. Three of these genomes are from plant pathogens and ...
  • The draft genomes of five agriculturally important African orphan crops 
    Chang, Yue; Liu, Huan; Liu, Min; Liao, Xuezhu; Sahu, Sunil Kumar; Fu, Yuan; Song, Bo; Cheng, Shifeng; Kariba, Robert; Muthemba, Samuel; Hendre, Prasad S.; Mayes, Sean; Ho, Wai Kuan; Yssel, A.E.J. (Anna); Kendabie, Presidor; Wang, Sibo; Li, Linzhou; Muchugi, Alice; Jamnadass, Ramni; Lu, Haorong; Peng, Shufeng; Van Deynze, Allen; Simons, Anthony; Yana-Shapiro, Howard; Van de Peer, Yves; Xu, Xun; Yang, Huanming; Wang, Jian; Liu, Xin (Oxford University Press, 2019)
    BACKGROUND : The expanding world population is expected to double the worldwide demand for food by 2050. Eighty-eight percent of countries currently face a serious burden of malnutrition, especially in Africa and south ...
  • Draft genomes of two artocarpus plants, jackfruit (A. heterophyllus) and breadfruit (A. altilis) 
    Sahu, Sunil Kumar; Liu, Min; Yssel, A.E.J. (Anna); Kariba, Robert; Muthemba, Samuel; Jiang, Sanjie; Song, Bo; Hendre, Prasad S.; Muchugi, Alice; Jamnadass, Ramni; Kao, Shu-Min; Featherston, Jonathan; Zerega, Nyree J. C.; Xu, Xun; Yang, Huanming; Van Deynze, Allen; Van de Peer, Yves; Liu, Xin; Liu, Huan (MDPI, 2020)
    Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for ...
  • Dual RNA sequencing of Vitis vinifera during Lasiodiplodia theobromae infection unveils host-pathogen interactions 
    Gonçalves, Micael F.M.; Nunes, Rui B.; Tilleman, Laurentijn; Van de Peer, Yves; Deforce, Dieter; Van Nieuwerburgh, Filip; Esteves, Ana C.; Alves, Artur (MDPI Publishing, 2019-12-03)
    Lasiodiplodia theobromae is one of the most aggressive agents of the grapevine trunk disease Botryosphaeria dieback. Through a dual RNA-sequencing approach, this study aimed to give a broader perspective on the infection ...
  • The evolution of gene duplicates in angiosperms and the impact of protein–protein interactions and the mechanism of duplication 
    Defoort, Jonas; Van de Peer, Yves; Carretero-Paulet, Lorenzo (Oxford University Press, 2019-08)
    Gene duplicates, generated through either whole genome duplication (WGD) or small-scale duplication (SSD), are prominent in angiosperms and are believed to play an important role in adaptation and in generating evolutionary ...
  • The evolutionary conundrum of whole‐genome duplication 
    Carretero‐Paulet, Lorenzo; Van de Peer, Yves (Wiley, 2020-08)
    Whole‐genome duplication (WGD) is a dramatic, common event in plants. Because of the detrimental effects arising from doubling the entire chromosome set, such as minority cytotype exclusion, genomic instability, mitotic ...
  • Fern genomes elucidate land plant evolution and cyanobacterial symbioses 
    Li, Fay-Wei; Brouwer, Paul; Carretero-Paulet, Lorenzo; Cheng, Shifeng; De Vries, Jan; Delaux, Pierre-Marc; Eily, Ariana; Koppers, Nils; Kuo, Li-Yaung; Li, Zheng; Simenc, Mathew; Small, Ian; Wafula, Eric; Angarita, Stephany; Barker, Michael S.; Brautigam, Andrea; DePamphilis, Claude; Gould, Sven; Hosmani, Prashant S.; Huang, Yao-Moan; Huettel, Bruno; Kato, Yoichiro; Liu, Xin; Maere, Steven; McDowell, Rose; Mueller, Lukas A.; Nierop, Klaas G.J.; Rensing, Stefan A.; Robison, Tanner; Rothfels, Carl J.; Sigel, Erin M.; Song, Yue; Timilsena, Prakash R.; Van de Peer, Yves; Wang, Hongli; Wilhelmsson, Per K.I.; Wolf, Paul G.; Xu, Xun; Der, Joshua P.; Schluepmann, Henriette; Wong, Gane K.-S.; Pryer, Kathleen M. (Nature Publishing Group, 2018-07-02)
    Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata ...
  • First draft genome assembly of the Argane tree (Argania spinosa) [version 2; peer review: 2 approved] 
    Khayi, Slimane; Azza, Nour Elhouda; Gaboun, Fatima; Pirro, Stacy; Badad, Oussama; Lightfoot, David A.; Unver, Turgay; Chaouni, Bouchra; Merrouch, Redouane; Rahim, Bouchra; Essayeh, Soumaya; Ganoudi, Matika; Abdelwahd, Rabha; Diria, Ghizlane; Mdarhi, Meriem Alaoui; Labhilili, Mustapha; Iraqi, Driss; Claros, M Gonzalo; Mouhaddab, Jamila; Sedrati, Hayat; Memari, Majid; Hamamouch, Noureddine; De Dios Alche, Juan; Alche, Juan de Dios; Boukhatem, Noureddine; Mrabet, Rachid; Dahan, Rachid; Legssyer, Adelkhaleq; Khalfaoui, Mohamed; Badraoui, Mohamed; Van de Peer, Yves; Tatusova, Tatiana; El Mousadik, Abdelhamid; Mentag, Rachid; Ghazal, Hassan (F1000 Research, 2020)
    BACKGROUND : The Argane tree (Argania spinosa L. Skeels) is an endemic tree of mid-western Morocco that plays an important socioeconomic and ecologic role for a dense human population in an arid zone. Several studies ...
  • First draft genome assembly of the desert locust, Schistocerca Gregaria 
    Verlinden, Heleen; Sterck, Lieven; Li, Jia; Li, Zhen; Yssel, A.E.J. (Anna); Gansemans, Yannick; Verdonck, Rik; Holtof, Michiel; Song, Hojun; Behmer, Spencer T.; Sword, Gregory A.; Matheson, Tom; Ott, Swidbert R.; Deforce, Dieter; Van Nieuwerburgh, Filip; Van de Peer, Yves; Vanden Broeck, Jozef (F1000Research, 2020)
    BACKGROUND: At the time of publication, the most devastating desert locust crisis in decades is affecting East Africa, the Arabian Peninsula and South-West Asia. The situation is extremely alarming in East Africa, where ...
  • Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant 
    Defoort, Jonas; Van de Peer, Yves; Vermeirssen, Vanessa (Oxford University Press, 2018-06-05)
    Gene regulatory networks (GRNs) consist of different molecular interactions that closely work together to establish proper gene expression in time and space. Especially in higher eukaryotes, many questions remain on ...
  • Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen 
    Lin, Yao-Cheng; Wang, Jing; Delhomme, Nicolas; Schiffthaler, Bastian; Sundstrom, Gorel; Zuccolo, Andrea; Nystedt, Bjorn; Hvidsten, Torgeir R.; De la Torre, Amanda; Cossu, Rosa M.; Hoeppner, Marc P.; Lantz, Henrik; Scofield, Douglas G.; Zamani, Neda; Johansson, Anna; Mannapperuma, Chanaka; Robinson, Kathryn M.; Mahler, Niklas; Leitch, Ilia J.; Pellicer, Jaume; Park, Eung-Jun; Van Montagu, Marc; Van de Peer, Yves; Grabherr, Manfred; Jansson, Stefan; Ingvarsson, Par K.; Street, Nathaniel R. (National Academy of Sciences, 2018-10-29)
    The Populus genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily Populus trichocarpa (Torr. & Gray), which was the first tree with ...
  • Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude 
    Zhang, Ticao; Qiao, Qin; Novikova, Polina Yu.; Wang, Qia; Yue, Jipei; Guan, Yanlong; Ming, Shengping; Liu, Tianmeng; De, Ji; Liu, Yixuan; Al-Shehbaz, Ihsan A.; Sun, Hang; Van Montagu, Marc; Huang, Jinling; Van de Peer, Yves; Qiong, La (National Academy of Sciences, 2019-04)
    Crucihimalaya himalaica, a close relative of Arabidopsis and Capsella, grows on the Qinghai–Tibet Plateau (QTP) about 4,000 m above sea level and represents an attractive model system for studying speciation and ecological ...
  • The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants 
    Li, Linzhou; Wang, Sibo; Wang, Hongli; Sahu, Sunil Kumar; Marin, Birger; Li, Haoyuan; Xu, Yan; Liang, Hongping; Li, Zhen; Cheng, Shifeng; Reder, Tanja; Cebi, Zehra; Wittek, Sebastian; Petersen, Morten; Melkonian, Barbara; Du, Hongli; Yang, Huanming; Wang, Jian; Wong, Gane Ka-Shu; Xu, Xun; Liu, Xin; Van de Peer, Yves; Melkonian, Michael; Liu, Huan (Nature Research, 2020-09)
    Genome analysis of the pico-eukaryotic marine green alga Prasinoderma coloniale CCMP 1413 unveils the existence of a novel phylum within green plants (Viridiplantae), the Prasinodermophyta, which diverged before the split ...
  • The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments 
    De Vos, Stephanie; Rombauts, Stephane; Coussement, Louis; Dermauw, Wannes; Vuylsteke, Marnik; Sorgeloos, Patrick; Clegg, James S.; Nambu, Ziro; Van Nieuwerburgh, Filip; Norouzitallab, Parisa; Van Leeuwen, Thomas; De Meyer, Tim; Van Stappen, Gilbert; Van de Peer, Yves; Bossier, Peter (BMC, 2021-08-31)
    BACKGROUND : Brine shrimp Artemia have an unequalled ability to endure extreme salinity and complete anoxia. This study aims to elucidate its strategies to cope with these stressors. RESULTS AND DISCUSSION : Here, we ...