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

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

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  • Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus 
    Novikova, Polina Yu.; Brennan, Ian G.; Booker, William; Mahony, Michael; Doughty, Paul; Lemmon, Alan R.; Lemmon, Emily Moriarty; Roberts, J. Dale; Yant, Levi; Van de Peer, Yves; Keogh, J. Scott; Donnellan, Stephen C. (Public Library of Science, 2020-05-11)
    Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and wellstudied in plants, polyploidy ...
  • Pseudo-chromosome–length genome assembly of a double haploid “Bartlett” pear (Pyrus communis L.) 
    Linsmith, Gareth; Rombauts, Stephane; Montanari, Sara; Deng, Cecilia H.; Celton, Jean-Marc; Guerif, Philippe; Liu, Chang; Zurn, Jason D.; Cestaro, Alessandro; Bassil, Nahla V.; Bakker, Linda V.; Schijlen, Elio; Gardiner, Susan E.; Lespinasse, Yves; Durel, Charles-Eric; Velasco, Riccardo; Neale, David B.; Chagne, David; Van de Peer, Yves; Troggio, Michela; Bianco, Luca (Oxford University Press, 2019-12)
    BACKGROUND : We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII long-read sequencing, ...
  • A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils 
    Van Goethem, Marc W.; Pierneef, Rian Ewald; Bezuidt, Keoagile Ignatius Oliver; Van de Peer, Yves; Cowan, Don A.; Makhalanyane, Thulani Peter (BioMed Central, 2018-02-23)
    BACKGROUND : Soil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of ...
  • The seagrass methylome is associated with variation in photosynthetic performance among clonal shoots 
    Jueterbock, Alexander; Boström, Christoffe; Coyer, James A.; Olsen, Jeanine L.; Kopp, Martina; Dhanasiri, Anusha K.S.; Smolina, Irina; Arnaud-Haond, Sophie; Van de Peer, Yves; Hoarau, Galice (Frontiers Media, 2020-09)
    Evolutionary theory predicts that clonal organisms are more susceptible to extinction than sexually reproducing organisms, due to low genetic variation and slow rates of evolution. In agreement, conservation management ...
  • Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos 
    Rodrigues, Andreia S.; Chaves, Ines; Costa, Bruno Vasques; Lin, Yao-Cheng; Lopes, Susana; Milhinhos, Ana; Van de Peer, Yves; Migue, Celia M. (Nature Research, 2019-08)
    Regulation of seed development by small non-coding RNAs (sRNAs) is an important mechanism controlling a crucial phase of the life cycle of seed plants. In this work, sRNAs from seed tissues (zygotic embryos and megagametophytes) ...
  • syntenet : an R/Bioconductor package for the inference and analysis of synteny networks 
    Almeida-Silva, Fabricio; Zhao, Tao; Ullrich, Kristian K.; Schranz, M. Eric; Van de Peer, Yves (Oxford University Press, 2023-01)
    Interpreting and visualizing synteny relationships across several genomes is a challenging task. We previously proposed a network-based approach for better visualization and interpretation of large-scale microsynteny ...
  • Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production 
    Song, Chi; Fu, Fangfang; Yang, Lulu; Niu, Yan; Tian, Zhaoyang; He, Xiangxiang; Yang, Xiaoming; Chen, Jie; Sun, Wei; Wan, Tao; Zhang, Han; Yang, Yicheng; Xiao, Tian; Dossa, Komivi; Meng, Xiangxiao; Cao, Fuliang; Van de Peer, Yves; Wang, Guibin; Chen, Shilin (Nature Research, 2021-10-20)
    Taxol, a natural product derived from Taxus, is one of the most effective natural anticancer drugs and the biosynthetic pathway of Taxol is the basis of heterologous bio-production. Here, we report a high-quality genome ...
  • Transcriptomic analysis of the poultry red mite, Dermanyssus gallinae, across all stages of the lifecycle 
    Bartley, Kathryn; Chen, Wan; Mills, Richard I. Lloyd; Nunn, Francesca; Price, Daniel R.G.; Rombauts, Stephane; Van de Peer, Yves; Roy, Lise; Nisbet, Alasdair J.; Burgess, Stewart T.G. (BMC, 2021-04)
    BACKGROUND: The blood feeding poultry red mite (PRM), Dermanyssus gallinae, causes substantial economic damage to the egg laying industry worldwide, and is a serious welfare concern for laying hens and poultry house workers. ...
  • Using digital organisms to study the evolutionary consequences of whole genome duplication and polyploidy 
    Yao, Yao; Carretero-Paulet, Lorenzo; Van de Peer, Yves (Public Library of Science, 2019-07-31)
    The potential role of whole genome duplication (WGD) in evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary ‘dead end’, there is growing evidence that the long-term establishment of ...
  • Virus-host coexistence in phytoplankton through the genomic lens 
    Yau, Sheree; Krasovec, Marc; Benites, L. Felipe; Rombauts, Stephane; Groussin, Mathieu; Vancaester, Emmelien; Aury, Jean-Marc; Derelle, Evelyne; Desdevises, Yves; Escande, Marie-Line; Van de Peer, Yves; Vandepoele, Klaas; Gourbiere, Sebastien; Piganeau, Gwenael (American Association for the Advancement of Science:, 2020-04-01)
    Virus-microbe interactions in the ocean are commonly described by “boom and bust” dynamics, whereby a numerically dominant microorganism is lysed and replaced by a virus-resistant one. Here, we isolated a microalga strain ...
  • The water lily genome and the early evolution of flowering plants 
    Zhang, Liangsheng; Chen, Fei; Zhang, Xingtan; Li, Zhen; Zhao, Yiyong; Lohaus, Rolf; Chang, Xiaojun; Dong, Wei; Ho, Simon Y.W.; Liu, Xing; Song, Aixia; Chen, Junhao; Guo, Wenlei; Wang, Zhengjia; Zhuang, Yingyu; Wang, Haifeng; Chen, Xuequn; Hu, Juan; Liu, Yanhui; Qin, Yuan; Wang, Kai; Dong, Shanshan; Liu, Yang; Zhang, Shouzhou; Yu, Xianxian; Wu, Qian; Wang, Liangsheng; Yan, Xueqing; Jiao, Yuannian; Kong, Hongzhi; Zhou, Xiaofan; Yu, Cuiwei; Chen, Yuchu; Li, Fan; Wang, Jihua; Chen, Wei; Chen, Xinlu; Jia, Qidong; Zhang, Chi; Jiang, Yifan; Zhang, Wanbo; Liu, Guanhua; Fu, Jianyu; Chen, Feng; Ma, Hong; Van de Peer, Yves; Tang, Haibao (Nature Publishing Group, 2020-01-02)
    Water lilies belong to the angiosperm order Nymphaeales. Amborellales, Nymphaeales and Austrobaileyales together form the so-called ANA-grade of angiosperms, which are extant representatives of lineages that diverged the ...
  • The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts 
    Wan, Tao; Liu, Zhiming; Leitch, Ilia J.; Xin, Haiping; Maggs-Kolling, Gillian; Gong, Yanbing; Li, Zhen; Marais, Eugene; Liao, Yiying; Dai, Can; Liu, Fan; Wu, Qijia; Song, Chi; Zhou, Yadong; Huang, Weichang; Jiang, Kai; Wang, Qi; Yang, Yong; Zhong, Zhixiang; Yang, Ming; Yan, Xue; Hu, Guangwan; Hou, Chen; Su, Yingjuan; Feng, Shixiu; Yang, Ji; Yan, Jijun; Chu, Jinfang; Chen, Fan; Ran, Jinhua; Wang, Xiaoquan; Van de Peer, Yves; Leitch, Andrew R.; Wang, Qingfeng (Nature Research, 2021)
    The gymnosperm Welwitschia mirabilis belongs to the ancient, enigmatic gnetophyte lineage. It is a unique desert plant with extreme longevity and two ever-elongating leaves. We present a chromosome-level assembly of its ...
  • Whole-genome microsynteny-based phylogeny of angiosperms 
    Zhao, Tao; Zwaenepoel, Arthur; Xue, Jia-Yu; Kao, Shu-Min; Li, Zhen; Schranz, M. Eric; Van de Peer, Yves (Nature Research, 2021-06)
    Plant genomes vary greatly in size, organization, and architecture. Such structural differences may be highly relevant for inference of genome evolution dynamics and phylogeny. Indeed, microsynteny—the conservation of ...
  • “Winter is coming” : how did polyploid plants survive? 
    Li, Zhen; Van de Peer, Yves (Elsevier, 2020-01)
    No abstract available.
  • Wolfberry genomes and the evolution of Lycium (Solanaceae) 
    Cao, You-Long; Li, Yan-long; Fan, Yun-Fang; Li, Zhen; Yoshida, Kouki; Wang, Jie-Yu; Ma, Xiao-Kai; Wang, Ning; Mitsuda, Nobutaka; Kotake, Toshihisa; Ishimizu, Takeshi; Tsai, Kun-Chan; Niu, Shan-Ce; Zhang, Diyang; Sun, Wei-Hong; Luo, Qing; Zhao, Jian-Hua; Yin, Yue; Zhang, Bo; Wang, Jun-Yi; Qin, Ken; An, Wei; He, Jun; Dai, Guo-Li; Wang, Ya-Jun; Shi, Zhi-Gang; Jiao, En-Ning; Wu, Peng-Ju; Liu, Xuedie; Liu, Bin; Liao, Xing-Yu; Jiang, Yu-Ting; Yu, Xia; Hao, Yang; Xu, Xin-Yu; Zou, Shuang-Quan; Li, Ming-He; Hsiao, Yu-Yun; Lin, Yu-Fu; Liang, Chieh-Kai; Chen, You-Yi; Wu, Wan-Lin; Lu, Hsiang-Chai; Lan, Si-Ren; Wang, Zhi-Wen; Zhao, Xiang; Zhong, Wen-Ying; Yeh, Chuan-Ming; Tsai, Wen-Chieh; Van de Peer, Yves; Liu, Zhong-Jian (Nature Research, 2021-06)
    Wolfberry Lycium, an economically important genus of the Solanaceae family, contains approximately 80 species and shows a fragmented distribution pattern among the Northern and Southern Hemispheres. Although several ...