Browsing Workspace (UPSpace) by UP Author "Van de Peer, Yves"

Browsing Workspace (UPSpace) by UP Author "Van de Peer, Yves"

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  • Chromosome-scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication 
    Chang, Jiyang; Marczuk-Rojas, Juan Pablo; Waterman, Carrie; Garcia-Llanos, Armando; Chen, Shiyu; Ma, Xiao; Hulse-Kemp, Amanda; Van Deynze, Allen; Van de Peer, Yves; Carretero-Paulet, Lorenzo (Wiley Open Access, 2022-09)
    The African Orphan Crops Consortium (AOCC) selected the highly nutritious, fast growing and drought tolerant tree crop moringa (Moringa oleifera Lam.) as one of the first of 101 plant species to have its genome sequenced ...
  • Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe) 
    Zhang, Ticao; Qiao, Qin; Du, Xiao; Zhang, Xiao; Hou, Yali; Wei, Xin; Sun, Chao; Zhang, Rengang; Yun, Quanzheng; Crabbe, M. James C.; Van de Peer, Yves; Dong, Wenxuan (Wiley, 2022-08)
    Cultivated hawthorn (Crataegus pinnatifida var. major) is an important medicinal and edible plant with a long history of use for health protection in China. Herein, we provide a de novo chromosomelevel genome sequence ...
  • The Cycas genome and the early evolution of seed plants 
    Liu, Yang; Wang, Sibu; Li, Linzhou; Yang, Ting; Dong, Shanshan; Wei, Tong; Wu, Shengdan; Liu, Yongbo; Gong, Yiqing; Feng, Xiuyan; Ma, Jianchao; Chang, Guanxiao; Huang, Jinling; Yang, Yong; Wang, Hongli; Liu, Min; Xu, Yan; Liang, Hongping; Yu, Jin; Cai, Yuqing; Zhang, Zhaowu; Fan, Yannan; Mu, Weixue; Sahu, Sunil Kumar; Liu, Shuchun; Lang, Xiaoan; Yang, Leilei; Li, Na; Habib, Sadaf; Yang, Yongqiong; Lindstrom, Anders J.; Liang, Pei; Goffinet, Bernard; Zaman, Sumaira; Wegrzyn, Jill; Li, Dexiang; Liu, Jian; Cui, Jie; Sonnenschein, Eva C.; Wang, Xiaobo; Ruan, Jue; Xue, Jia-Yu; Shao, Zhu-Qing; Song, Chi; Fan, Guangyi; Li, Zhen; Zhang, Liangsheng; Liu, Jianquan; Liu, Zhong-Jian; Jiao, Yuannian; Wang, Xiao-Quan; Wu, Hong; Wang, Ertao; Lisby, Michael; Yang, Huanming; Wang, Jian; Liu, Xin; Xu, Xun; Li, Nan; Soltis, Pamela S.; Van de Peer, Yves; Soltis, Douglas E.; Gong, Xun; Liu, Huan; Zhang, Shouzhou (Nature Research, 2022-04-18)
    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 ...
  • The Cymbidium genome reveals the evolution of unique morphological traits 
    Ai, Ye; Li, Zhen; Sun, Wei-Hong; Chen, Juan; Zhang, Diyang; Ma, Liang; Zhang, Qing-Hua; Chen, Ming-Kun; Zheng, Qing-Dong; Liu, Jiang-Feng; Jiang, Yu-Ting; Li, Bai-Jun; Liu, Xuedie; Xu, Xin-Yu; Yu, Xia; Zheng, Yu; Liao, Xing-Yu; Zhou, Zhuang; Wang, Jie-Yu; Wang, Zhi-Wen; Xie, Tai-Xiang; Ma, Shan-Hu; Zhou, Jie; Ke, Yu-Jie; Zhou, Yu-Zhen; Lu, Hsiang-Chia; Liu, Ke-Wei; Yang, Feng-Xi; Zhu, Gen-Fa; Huang, Laiqiang; Peng, Dong-Hui; Chen, Shi-Pin; Lan, Siren; Van de Peer, Yves; Liu, Zhong-Jian (Springer Nature, 2021-12-01)
    The marvelously diverse Orchidaceae constitutes the largest family of angiosperms. The genus Cymbidium in Orchidaceae is well known for its unique vegetation, floral morphology, and flower scent traits. Here, a ...
  • The Euscaphis japonica genome and the evolution of malvids 
    Sun, Wei-Hong; Li, Zhen; Xiang, Shuang; Ni, Lin; Zhang, Diyang; Chen, De-Qiang; Qiu, Meng-Yuan; Zhang, Qi-Gong; Xiao, Lin; Din, Le; Li, Yifan; Liao, Xing-Yu; Liu, Xue-Die; Jiang, Yu-Ting; Zhang, Pei-Lan; Ni, Hui; Wang, Yifan; Yue, Yi-Xun; Wu, Xi; Din, Xiang-Qing; Huang, Wei; Wang, Zhi-Wen; Ma, Xiaokai; Liu, Bobin; Zou, Xiao-Xing; Van de Peer, Yves; Liu, Zhong-Jian; Zou, Shuang-Quan (Wiley, 2021-12)
    Malvids is one of the largest clades of rosids, includes 58 families and exhibits remarkable morphological and ecological diversity. Here, we report a high-quality chromosome-level genome assembly for Euscaphis japonica, ...
  • Evolution of NLR resistance genes in magnoliids : dramatic expansions of CNLs and multiple losses of TNLs 
    Wu, Jia-Yi; Xue, Jia-Yu; Van de Peer, Yves (Frontiers Research Foundation, 2021-11-21)
    Magnoliids are the third-largest group of angiosperms and occupy a critical position in angiosperm evolution. In the past years, due to the lack of sequenced genomes, the disease resistance gene (R gene) profile of ...
  • Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.) 
    Qiao, Qin; Edger, Patrick P.; Xue, Li; Qiong, La; Lu, Jie; Zhang, Yichen; Cao, Qiang; Yocca, Alan E.; Platts, Adrian E.; Knapp, Steven J.; Van Montagu, Marc; Van de Peer, Yves; Lei, Jiajun; Zhang, Ticao (National Academy of Sciences, 2021-10)
    Strawberry (Fragaria spp.) has emerged as a model system for various fundamental and applied research in recent years. In total, the genomes of five different species have been sequenced over the past 10 y. Here, we report ...
  • Genome and metabolome ms-based mining of a marine strain of Aspergillus affinis 
    Gonçalves, Micael F. M.; Hilario, Sandra; Tacao, Marta; Van de Peer, Yves; Alves, Artur; Esteves, Ana C. (MDPI, 2021-12)
    Aspergillus section Circumdati encompasses several species that express both beneficial (e.g., biochemical transformation of steroids and alkaloids, enzymes and metabolites) and harmful compounds (e.g., production of ...
  • The genome of Corydalis reveals the evolution of benzylisoquinoline alkaloid biosynthesis in Ranunculales 
    Xu, Zhichao; Li, Zhen; Ren, Fengming; Gao, Ranran; Wang, Zhengfan; Zhang, Jinlan; Zhao, Tao; Ma, Xiao; Pu, Xiangdong; Xin, Tianyi; Rombauts, Stephane; Sun, Wei; Van de Peer, Yves; Chen, Shilin; Song, Jingyuan (Wiley, 2022-07)
    Species belonging to the order Ranunculales have attracted much attention because of their phylogenetic position as a sister group to all other eudicot lineages and their ability to produce unique yet diverse benzylisoquinoline ...
  • The genome of hibiscus hamabo reveals its adaptation to saline and waterlogged habitat 
    Wang, Zhiquan; Xue, Jia-Yu; Hu, Shuai-Ya; Zhang, Fengjiao; Yu, Ranran; Chen, Dijun; Van de Peer, Yves; Jiang, Jiafu; Song, Aiping; Ni, Longjie; Hua, Jianfeng; Lu, Zhiguo; Yu, Chaoguang; Yin, Yunlong; Gu, Chunsun (Oxford University Press, 2022-03-23)
    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 ...
  • The genome of homosporous maidenhair fern sheds light on the euphyllophyte evolution and defences 
    Fang, Yuhan; Qin, Xing; Liao, Qinggang; Du, Ran; Luo, Xizhi; Zhou, Qian; Li, Zhen; Chen, Hengchi; Jin, Wanting; Yuan, Yaning; Sun, Pengbo; Zhang, Rui; Zhang, Jiao; Wang, Li; Cheng, Shifeng; Yang, Xueyong; Yan, Yuehong; Zhang, Xingtan; Zhang, Zhonghua; Bai, Shunong; Van de Peer, Yves; Lucas, William John; Huang, Sanwen; Yan, Jianbin (Nature Research, 2022-09)
    Euphyllophytes encompass almost all extant plants, including two sister clades, ferns and seed plants. Decoding genomes of ferns is the key to deep insight into the origin of euphyllophytes and the evolution of seed plants. ...
  • Genome-wide analysis of butterfly bush (Buddleja alternifolia) in three uplands provides insights into biogeography, demography and speciation 
    Ma, Yong-Peng; Liao, Rong-Li; Zhang, Ren-Gang; Yun, Quan-Zheng; Olmstead, Richard G.; Chau, John H.; Milne, Richard I.; Van de Peer, Yves; Sun, Wei-Bang (Wiley, 2021-11)
    Understanding processes that generate and maintain large disjunctions within plant species can provide valuable insights into plant diversity and speciation. The butterfly bush Buddleja alternifolia has an unusual disjunct ...
  • Genomic and metabolomic analyses of the marine fungus Emericellopsis cladophorae: insights into saltwater adaptability mechanisms and its biosynthetic potential 
    Goncalves, Micael; Hilario, Sandra; Van de Peer, Yves; Esteves, Ana; Alves, Artur (MDPI, 2022-01)
    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 ...
  • Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger 
    Cheng, Shi-Ping; Jia, Kai-Hua; Liu, Hui; Zhang, Ren-Gang; Li, Zhi-Chao; Zhou, Shan-Shan; Shi, Tian-Le; Ma, Ai-Chu; Yu, Cong-Wen; Gao, Chan; Cao, Guang-Lei; Zhao, Wei; Nie, Shuai; Guo, Jing-Fang; Jiao, Si-Qian; Tian, Xue-Chan; Yan, Xue-Mei; Bao, Yu-Tao; Yun, Quan-Zheng; Wang, Xin-Zhu; Porth, Ilga; El-Kassaby, Yousry A.; Wang, Xiao-Ru; Li, Zhen; Van de Peer, Yves; Mao, Jian-Feng (Springer Nature, 2021-08)
    Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a ...
  • Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass) 
    Ma, Xiao; Olsen, Jeanine L.; Reusch, Thorsten B.H.; Procaccini, Gabriele; Kudrna, Dave; Williams, Melissa; Grimwood, Jane; Rajasekar, Shanmugam; Jenkins, Jerry; Schmutz, Jeremy; Van de Peer, Yves (F1000Research, 2021-09-19)
    BACKGROUND : Seagrasses (Alismatales) are the only fully marine angiosperms. Zostera marina (eelgrass) plays a crucial role in the functioning of coastal marine ecosystems and global carbon sequestration. It is the most ...
  • MicroRNA-mediated post-transcriptional regulation of Pinus pinaster response and resistance to pinewood nematode 
    Modesto, Ines; Inacio, Vera; Van de Peer, Yves; Miguel, Celia (Nature Research, 2022-03-25)
    Pine wilt disease (PWD), caused by the parasitic nematode Bursaphelenchus xylophilus, or pinewood nematode (PWN), is a serious threat to pine forests in Europe. Pinus pinaster is highly susceptible to the disease and it ...
  • Nearby transposable elements impact plant stress gene regulatory networks : a meta-analysis in A. thaliana and S. lycopersicum 
    Deneweth, Jan; Van de Peer, Yves; Vermeirssen, Vanessa (BMC, 2022-01)
    BACKGROUND: Transposable elements (TE) make up a large portion of many plant genomes and are playing innovative roles in genome evolution. Several TEs can contribute to gene regulation by influencing expression of nearby ...
  • The neighborhood of the spike gene Is a hotspot for modular intertypic homologous and nonhomologous recombination in coronavirus genomes 
    Nikolaidis, Marios; Markoulatos, Panayotis; Van de Peer, Yves; Oliver, Stephen G.; Amoutzias, Grigorios D. (Oxford University Press, 2022-01)
    Coronaviruses (CoVs) have very large RNA viral genomes with a distinct genomic architecture of core and accessory open reading frames (ORFs). It is of utmost importance to understand their patterns and limits of homologous ...
  • Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp 
    Farhat, Sarah; Le, Phuong; Kayal, Ehsan; Noel, Benjamin; Bigeard, Estelle; Corre, Erwan; Maumus, Florian; Florent, Isabelle; Alberti, Adriana; Aury, Jean-Marc; Barbeyron, Tristan; Cai, Ruibo; Da Silva, Corinne; Istace, Benjamin; Labadie, Karine; Marie, Dominique; Mercier, Jonathan; Rukwavu, Tsinda; Szymczak, Jeremy; Tonon, Thierry; Alves-de-Souza, Catharina; Rouze, Pierre; Van de Peer, Yves; Wincker, Patrick; Rombauts, Stephane; Porcel, Betina M.; Guillou, Laure (BioMed Central, 2021-01-06)
    BACKGROUND : Dinoflagellates are aquatic protists particularly widespread in the oceans worldwide. Some are responsible for toxic blooms while others live in symbiotic relationships, either as mutualistic symbionts in ...
  • SNP detection in Pinus pinaster transcriptome and association with resistance to pinewood nematode 
    Modesto, Ines; Inacio, Vera; Novikova, Polina; Carrasquinho, Isabel; Van de Peer, Yves; Miguel, Celia (MDPI, 2022-06-17)
    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, ...