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3 results on '"Baifang Qin"'

1. The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses

Author

Claude Scarpelli, Thomas Schiex, Ghislaine Magdelenat, Michael K. Udvardi, Baifang Qin, Xinbin Dai, Jeff J. Doyle, Patrick X. Zhao, Hélène Bergès, Vagner A. Benedito, Arvind K. Bharti, Chrystel Gibelin, Dong-Hoon Jeong, Stéphane De Mita, Stephane Rombauts, Mingyi Wang, Nathalie Choisne, Simone L. Macmil, Patrick Wincker, Senjuti Sinharoy, Sylvie Samain, Christopher D. Town, Susan R. Singer, Heidrun Gundlach, Anne Berger, Jane Rogers, Kathrin Klee, Sarah Sims, Nevin D. Young, Stéphanie Fouteau, Claire Riddle, Iryna Sanders, John Gish, Limei Yang, René Geurts, Gregory D. May, Shiguo Zhou, Shweta Deshpande, David C. Schwartz, Anika Jöcker, Christine Nicholson, Ton Bisseling, Klaus F. X. Mayer, Antoine Zuber, Roxanne Denny, Chunting Lang, Carolien Franken, Douglas R. Cook, Ruihua Shi, Frédéric Debellé, Valérie Barbe, Giles E. D. Oldroyd, Foo Cheung, Lucy Matthews, Blake C. Meyers, Jeremy D. Murray, Dong-Jin Kim, Joann Mudge, Agnès Viollet, Heiko Schoof, Graham B. Wiley, Benjamin D. Rosen, Jean Dénarié, Florent Prion, Keqin Wang, Arnaud Bellec, Béatrice Segurens, Jeong Hwan Mun, Ernest F. Retzel, Sean Humphray, Andrew Farmer, D. Janine Sherrier, Lieven Sterck, Richard A. Dixon, Steven B. Cannon, Steve Kenton, Philippe Bardou, Alvaro J. González, Haibao Tang, Julie Poulain, Arnaud Couloux, Majesta O'Bleness, Pamela J. Green, Manuel Spannagl, Shelby L. Bidwell, Jixian Zhai, Asis Hallab, Anne Marie Dudez, Michael Bechner, Marina Naoumkina, James D. White, Francis Quetier, Marijke Hartog, Erin L. Monaghan, Charles Paule, Chunmei Qu, Andrew J. Severin, Céline Noirot, Fu Ying, Shaoping Lin, Ziyun Yao, Vivek Krishnakumar, Steven A. Goldstein, Axin Hua, Erika Sallet, Bing Bing Wang, Peng Zhou, Hongshing Lai, Yanbo Xing, Nicolas Samson, Jamison McCorrison, Doug White, Yi Jing, Olivier Saurat, Liping Zhou, Kevin A. T. Silverstein, Jean Weissenbach, Bruce A. Roe, Sebastian Proost, Yves Van de Peer, Xiaohong Wang, Jens Warfsmann, Jérôme Gouzy, Fares Z. Najar, University of Minnesota [Twin Cities] (UMN), University of Minnesota System, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Department of Disease and Stress Biology, John Innes Centre [Norwich], Laboratory of Molecular Biology, Department of Plant Science, Wageningen University and Research [Wageningen] (WUR), Corn Insects and Crop Genetics Research Unit, USDA-ARS : Agricultural Research Service, Department of Agronomy, Purdue University [West Lafayette], Plant Biology Division, The Samuel Roberts Noble Foundation, West Virginia University, German Research Center for Environmental Health - Helmholtz Center München (GmbH), Centre National de la Recherche Scientifique (CNRS), Rheinische Friedrich-Wilhelms-Universität Bonn, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Department plant pathology, Pennsylvania State University (Penn State), Penn State System-Penn State System, University of Delaware [Newark], J. Craig Venter Institute [La Jolla, USA] (JCVI), Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, National center for genome resources (NCGR), BBSRC John Innes Centre, Partenaires INRAE, Bayer Cropscience, Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), College of Science [Swansea], Swansea University, University of Oklahoma (OU), Department of Plant Biology, Royal Veterinary and Agricultural University = Kongelige Veterinær- og Landbohøjskole (KVL ), Max Planck Institute for Plant Breeding Research (MPIPZ), Wageningen University and Research Centre (WUR), Wellcome Trust, International Institute of Tropical Agriculture, Department of Plant Pathology, University of Kentucky, Rural Development Administration, Unité de Biométrie et Intelligence Artificielle (UBIA), Carleton College, Funding support to N.D.Y., C. D. T. and B. A. R. from The Noble Foundation and NSF-PGRP 0321460, 0604966, to N.D.Y., J.M. and G. D. M. from NSF-PGRP 0820005, to C. D. T. from NSF-PGRP 0821966, to F. D., G.E.D.O., R. G., K. F. X. M., T. B., J. Denarie, F. Q. and J. R. from FP6 EU project GLIP/Grain Legumes FOOD-CT-2004-506223, to G.E.D.O. and J.R. from BBSRC BBS/B/11524, to F. D. and F. Q. from ANR project SEQMEDIC 2006-01122, to R. G. from the Dutch Science Organization VIDI 864.06.007, ERA-PG FP-06.038A, to Y.V.d.P. from the Belgian Federal Science Policy Office IUAP P6/25, Fund for Scientific Research Flanders, Institute for the Promotion of Innovation by Science and Technology in Flanders and Ghent University (MRP N2N), to D. R. C. from NSF IOS-0531408, IOS-0605251, to D.J.S., B. C. M. and P.J.G. from USDA CSREES 2006-03567, and to J. Gouzy from 'Laboratoire d'Excellence' (LABEX) TULIP (ANR-10-LABX-41). We also acknowledge technical support from the University of Minnesota Supercomputer Institute and thank Y.W. Nam for a BamHI BAC library used by Genoscope, S. Park and M. Accerbi for RNA isolation, T. Paape for statistical consulting, and M. Harrison for supplying myc infected and control root tissues used to make small RNA libraries.

Subjects
0106 biological sciences, multidisciplinary science, 01 natural sciences, Genome, genomic, flavonoid biosynthesis, Vitis, genes, 2. Zero hunger, 0303 health sciences, Multidisciplinary, Medicago, biology, truncatula, food and beverages, Biological Evolution, Medicago truncatula, plant science, duplications, Rhizobium, Laboratory of Molecular Biology, Genome, Plant, signal-transduction, science and technology, Lotus japonicus, Molecular Sequence Data, Genomics, Synteny, tetraploidy, Article, 03 medical and health sciences, Nitrogen Fixation, Botany, evolution, expression, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Laboratorium voor Moleculaire Biologie, Medicago sativa, Symbiosis, 030304 developmental biology, fungi, Fabaceae, sequence, biology.organism_classification, arabidopsis, leguminosae, Soybeans, genetic, EPS, 010606 plant biology & botany
Abstract

Chantier qualité GA; International audience; Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation1. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species2. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing ~94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa’s genomic toolbox.

Published
2011
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2. Duplication and divergence offgf8 functions in teleost development and evolution

Author

Ruihua Shi, Xinjun He, Baifang Qin, Richard Jovelin, Angel Amores, Yi-Lin Yan, Bruce A. Roe, John H. Postlethwait, and William A. Cresko

Subjects
Apical ectodermal ridge, animal structures, Evolution, Molecular, FGF8, stomatognathic system, Genes, Duplicate, Phylogenetics, Gene Duplication, Gene duplication, Genetics, Animals, Limb development, Zebrafish, Phylogeny, Ecology, Evolution, Behavior and Systematics, biology, Gene Expression Profiling, Fishes, Gene Expression Regulation, Developmental, Stickleback, biology.organism_classification, Fibroblast Growth Factors, Gene expression profiling, embryonic structures, Molecular Medicine, Animal Science and Zoology, Signal Transduction, Developmental Biology
Abstract

Fibroblast growth factors play critical roles in many aspects of embryo patterning that are conserved across broad phylogenetic distances. To help understand the evolution of fibroblast growth factor functions, we identified members of the Fgf8/17/18-subfamily in the three-spine stickleback Gasterosteus aculeatus, and investigated their evolutionary relationships and expression patterns. We found that fgf17b is the ortholog of tetrapod Fgf17, whereas the teleost genes called fgf8 and fgf17a are duplicates of the tetrapod gene Fgf8, and thus should be called fgf8a and fgf8b. Phylogenetic analysis supports the view that the Fgf8/17/18-subfamily expanded during the ray-fin fish genome duplication. In situ hybridization experiments showed that stickleback fgf8 duplicates exhibited common and unique expression patterns, indicating that tissue specialization followed the gene duplication event. Moreover, direct comparison of stickleback and zebrafish embryonic expression patterns of fgf8 co-orthologs suggested lineage-specific independent subfunction partitioning and the acquisition or the loss of ortholog functions. In tetrapods, Fgf8 plays an important role in the apical ectodermal ridge of the developing pectoral appendage. Surprisingly, differences in the expression of fgf8a in the apical ectodermal ridge of the pectoral fin bud in zebrafish and stickleback, coupled with the role of fgf16 and fgf24 in teleost pectoral appendage show that different Fgf genes may play similar roles in limb development in various vertebrates.

Published
2007
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3. The Fanconi anemia gene network is conserved from zebrafish to human

Author

John H. Postlethwait, Baifang Qin, Daniel Selvig, Bruce A. Roe, Amber M. Starks, Catherine Wilson, and Tom A. Titus

Subjects
Genetics, Chromosomes, Artificial, Bacterial, animal structures, Sequence Homology, Amino Acid, biology, Fanconi Anemia Complementation Group D2 Protein, Molecular Sequence Data, General Medicine, biology.organism_classification, FANCA, FANCB, Fanconi Anemia, FANCF, FANCG, FANCD2, Animals, Humans, Amino Acid Sequence, Gene, Zebrafish, Genomic organization
Abstract

Fanconi anemia (FA) is a complex disease involving nine identified and two unidentified loci that define a network essential for maintaining genomic stability. To test the hypothesis that the FA network is conserved in vertebrate genomes, we cloned and sequenced zebrafish (Danio rerio) cDNAs and/or genomic BAC clones orthologous to all nine cloned FA genes (FANCA, FANCB, FANCC, FANCD1, FANCD2, FANCE, FANCF, FANCG, and FANCL), and identified orthologs in the genome database for the pufferfish Tetraodon nigroviridis. Genomic organization of exons and introns was nearly identical between zebrafish and human for all genes examined. Hydrophobicity plots revealed conservation of FA protein structure. Evolutionarily conserved regions identified functionally important domains, since many amino acid residues mutated in human disease alleles or shown to be critical in targeted mutagenesis studies are identical in zebrafish and human. Comparative genomic analysis demonstrated conserved syntenies for all FA genes. We conclude that the FA gene network has remained intact since the last common ancestor of zebrafish and human lineages. The application of powerful genetic, cellular, and embryological methodologies make zebrafish a useful model for discovering FA gene functions, identifying new genes in the network, and identifying therapeutic compounds.

Published
2006
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