New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing

[1]  M. Cáccamo,et al.  Characterization of repetitive DNA landscape in wheat homeologous group 4 chromosomes , 2015, BMC Genomics.

[2]  Hadi Quesneville,et al.  Structural and functional partitioning of bread wheat chromosome 3B , 2014, Science.

[3]  J. Batley,et al.  A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome , 2014, Science.

[4]  J. Doležel,et al.  Common Wheat Chromosome 5B Composition Analysis Using Low‐Coverage 454 Sequencing , 2014 .

[5]  Hana Šimková,et al.  The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution , 2013, Genome Biology.

[6]  Robert P. Davey,et al.  Sequencing quality assessment tools to enable data-driven informatics for high throughput genomics , 2013, Front. Genet..

[7]  R. Philippe,et al.  The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution , 2013, Genome Biology.

[8]  J. Rogers,et al.  Sequence-Based Analysis of Translocations and Inversions in Bread Wheat (Triticum aestivum L.) , 2013, PloS one.

[9]  H. Kanamori,et al.  Next-Generation Survey Sequencing and the Molecular Organization of Wheat Chromosome 6B , 2013, DNA research : an international journal for rapid publication of reports on genes and genomes.

[10]  V. Echenique,et al.  Identification, mapping and evolutionary course of wheat lipoxygenase-1 genes located on the A genome , 2013 .

[11]  H. Quesneville,et al.  The wheat powdery mildew genome shows the unique evolution of an obligate biotroph , 2013, Nature Genetics.

[12]  Shichen Wang,et al.  Sequence-Based Mapping of the Polyploid Wheat Genome , 2013, G3: Genes, Genomes, Genetics.

[13]  Mihaela M. Martis,et al.  A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat , 2013, Genome Biology.

[14]  Mihaela M. Martis,et al.  A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor , 2013, Proceedings of the National Academy of Sciences.

[15]  Zohar B. Weinstein,et al.  Physical Mapping Integrated with Syntenic Analysis to Characterize the Gene Space of the Long Arm of Wheat Chromosome 1A , 2013, PloS one.

[16]  Hana Šimková,et al.  Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat , 2013, BMC Genomics.

[17]  Wenlong Yang,et al.  Draft genome of the wheat A-genome progenitor Triticum urartu , 2013, Nature.

[18]  Yadan Luo,et al.  Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation , 2013, Nature.

[19]  Yaqin Ma,et al.  Comparative Analysis of Syntenic Genes in Grass Genomes Reveals Accelerated Rates of Gene Structure and Coding Sequence Evolution in Polyploid Wheat1[W][OA] , 2012, Plant Physiology.

[20]  P. Kersey,et al.  Analysis of the bread wheat genome using whole genome shotgun sequencing , 2012, Nature.

[21]  P. Huybers,et al.  Reckoning wheat yield trends , 2012 .

[22]  A. Chan,et al.  Chromosome arm-specific BAC end sequences permit comparative analysis of homoeologous chromosomes and genomes of polyploid wheat , 2012, BMC Plant Biology.

[23]  Gabriel Dorado,et al.  Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content. , 2012, The Plant journal : for cell and molecular biology.

[24]  Adam Skarshewski,et al.  Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation , 2012, Theoretical and Applied Genetics.

[25]  T. Flutre,et al.  TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes , 2012, Front. Plant Sci..

[26]  Laura R. Emery,et al.  Protein Phylogenetic Analysis of Ca2+/cation Antiporters and Insights into their Evolution in Plants , 2012, Front. Plant Sci..

[27]  N. Ramankutty,et al.  Recent patterns of crop yield growth and stagnation , 2012, Nature Communications.

[28]  V. Allard,et al.  Genome-wide association analysis to identify chromosomal regions determining components of earliness in wheat , 2011, Theoretical and Applied Genetics.

[29]  J. Batley,et al.  Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. , 2011, Plant biotechnology journal.

[30]  Mihaela M. Martis,et al.  Frequent Gene Movement and Pseudogene Evolution Is Common to the Large and Complex Genomes of Wheat, Barley, and Their Relatives[W][OA] , 2011, Plant Cell.

[31]  Uwe Scholz,et al.  Unlocking the Barley Genome by Chromosomal and Comparative Genomics[W][OA] , 2011, Plant Cell.

[32]  J. Rogers,et al.  Crop genome sequencing: lessons and rationales. , 2011, Trends in plant science.

[33]  G. Valle,et al.  First Survey of the Wheat Chromosome 5A Composition through a Next Generation Sequencing Approach , 2010, PloS one.

[34]  N. Wu,et al.  Molecular analysis of lipoxygenase (LOX) genes in common wheat and phylogenetic investigation of LOX proteins from model and crop plants , 2010 .

[35]  Anton Nekrutenko,et al.  Manipulation of FASTQ data with Galaxy , 2010, Bioinform..

[36]  M. Hayden,et al.  An introgression on wheat chromosome 4DL in RL6077 (Thatcher*6/PI 250413) confers adult plant resistance to stripe rust and leaf rust (Lr67) , 2010, Theoretical and Applied Genetics.

[37]  Hikmet Budak,et al.  Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces[W] , 2010, Plant Cell.

[38]  J. Doležel,et al.  Development of Chromosome-Specific BAC Resources for Genomics of Bread Wheat , 2010, Cytogenetic and Genome Research.

[39]  R. Varshney,et al.  From genome studies to agricultural biotechnology: closing the gap between basic plant science and applied agriculture. , 2010, Current opinion in plant biology.

[40]  S. Robinson,et al.  Food Security: The Challenge of Feeding 9 Billion People , 2010, Science.

[41]  Pierre Sourdille,et al.  Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat. , 2010, Plant biotechnology journal.

[42]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[43]  Uwe Scholz,et al.  Gene Content and Virtual Gene Order of Barley Chromosome 1H1[C][W][OA] , 2009, Plant Physiology.

[44]  Kazuo Shinozaki,et al.  TriFLDB: A Database of Clustered Full-Length Coding Sequences from Triticeae with Applications to Comparative Grass Genomics[C][W][OA] , 2009, Plant Physiology.

[45]  D. Laurie,et al.  Meta-QTL analysis of the genetic control of ear emergence in elite European winter wheat germplasm , 2009, Theoretical and Applied Genetics.

[46]  G. Slafer,et al.  Raising yield potential in wheat. , 2009, Journal of experimental botany.

[47]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[48]  U. Lohwasser,et al.  Molecular mapping of quantitative trait loci (QTLs) controlling aluminium tolerance in bread wheat , 2009, Euphytica.

[49]  A. Steed,et al.  Semi-dwarfing Rht-B1 and Rht-D1 loci of wheat differ significantly in their influence on resistance to Fusarium head blight , 2009, Theoretical and Applied Genetics.

[50]  J. Dubcovsky,et al.  Genetic and Molecular Characterization of the VRN2 Loci in Tetraploid Wheat1[W][OA] , 2008, Plant Physiology.

[51]  S. Xue,et al.  A high-density intervarietal map of the wheat genome enriched with markers derived from expressed sequence tags , 2008, Theoretical and Applied Genetics.

[52]  T. Friesen,et al.  Whole genome mapping in a wheat doubled haploid population using SSRs and TRAPs and the identification of QTL for agronomic traits , 2008, Molecular Breeding.

[53]  E. Mardis The impact of next-generation sequencing technology on genetics. , 2008, Trends in genetics : TIG.

[54]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[55]  D. Somers,et al.  Microsatellite mapping of adult-plant leaf rust resistance gene Lr22a in wheat , 2007, Theoretical and Applied Genetics.

[56]  M. Tester,et al.  HKT1;5-Like Cation Transporters Linked to Na+ Exclusion Loci in Wheat, Nax2 and Kna11[OA] , 2007, Plant Physiology.

[57]  Christine G Elsik,et al.  Community annotation: procedures, protocols, and supporting tools. , 2006, Genome research.

[58]  Jianxin Ma,et al.  Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[59]  Xiue Wang,et al.  Development and characterization of a Triticum aestivum-Haynaldia villosa translocation line T4VS⋅4DL conferring resistance to wheat spindle streak mosaic virus , 2005, Euphytica.

[60]  Miftahudin,et al.  Analysis of Expressed Sequence Tag Loci on Wheat Chromosome Group 4 , 2004, Genetics.

[61]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[62]  J. Doležel,et al.  Analysis and sorting of rye (Secale cereale L.) chromosomes using flow cytometry. , 2003, Genome.

[63]  C. Stoeckert,et al.  OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.

[64]  S. Salzberg,et al.  Using MUMmer to Identify Similar Regions in Large Sequence Sets , 2003, Current protocols in bioinformatics.

[65]  R. Haselkorn,et al.  Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[66]  Rolf Apweiler,et al.  InterProScan - an integration platform for the signature-recognition methods in InterPro , 2001, Bioinform..

[67]  J. Doležel,et al.  Flow sorting of mitotic chromosomes in common wheat (Triticum aestivum L.). , 2000, Genetics.

[68]  I. Leitch,et al.  Nuclear DNA Amounts in Angiosperms and their Modern Uses—807 New Estimates , 2000 .

[69]  M. Sorrells,et al.  Mapping Yr28 and Other Genes for Resistance to Stripe Rust in Wheat , 2000 .

[70]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[71]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[72]  P. Christou,et al.  ‘Green revolution’ genes encode mutant gibberellin response modulators , 1999, Nature.

[73]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[74]  J. Dvorak,et al.  Structural evolution of wheat chromosomes 4A, 5A, and 7B and its impact on recombination , 1995, Theoretical and Applied Genetics.

[75]  B. Gill,et al.  Registration of KS93WGRC27 Wheat Streak Mosaic Virus Resistant T4DL‐4Ai#2S Wheat Germplasm , 1995 .

[76]  J. S. Heslop-Harrison,et al.  Nuclear dna amounts in angiosperms. , 1976, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[77]  R. Flavell,et al.  Characterisation of the wheat genome by renaturation kinetics , 1975, Chromosoma.

[78]  BMC Genomics BioMed Central Methodology article Coupling amplified DNA from flow-sorted chromosomes to , 2008 .

[79]  A. Distelfeld,et al.  Genetic and Molecular Characterization of the VRN2 loci in Tetraploid Wheat , 2008 .

[80]  M. Tester,et al.  HKT 1 ; 5-Like Cation Transporters Linked to Na 1 Exclusion Loci in Wheat , Nax 2 and Kna 1 1 [ OA ] , 2007 .

[81]  J. Bennetzen,et al.  Mechanisms of recent genome size variation in flowering plants. , 2005, Annals of botany.

[82]  Juan Miguel García-Gómez,et al.  Sequence analysis Blast 2 GO : a universal tool for annotation , visualization and analysis in functional genomics research , 2005 .

[83]  Z. Yang,et al.  Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. , 2000, Molecular biology and evolution.