The maize W22 genome provides a foundation for functional genomics and transposon biology

[1]  Axel Himmelbach,et al.  Wild emmer genome architecture and diversity elucidate wheat evolution and domestication , 2017, Science.

[2]  James C. Schnable,et al.  A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize , 2017, Front. Plant Sci..

[3]  T. Sultana,et al.  Integration site selection by retroviruses and transposable elements in eukaryotes , 2017, Nature Reviews Genetics.

[4]  James C. Schnable,et al.  Evolutionarily Conserved Alternative Splicing Across Monocots , 2017, Genetics.

[5]  Ryan F. McCormick,et al.  The Sorghum bicolor reference genome: improved assembly and annotations, a transcriptome atlas, and signatures of genome organization , 2017, bioRxiv.

[6]  Kevin L. Schneider,et al.  Improved maize reference genome with single-molecule technologies , 2017, Nature.

[7]  Silvio C. E. Tosatto,et al.  InterPro in 2017—beyond protein family and domain annotations , 2016, Nucleic Acids Res..

[8]  Kevin L. Childs,et al.  Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize[OPEN] , 2016, Plant Cell.

[9]  J. Gershenzon,et al.  Characterization of Biosynthetic Pathways for the Production of the Volatile Homoterpenes DMNT and TMTT in Zea mays[OPEN] , 2016, Plant Cell.

[10]  K. Koch,et al.  Transposon Mutagenesis and Analysis of Mutants in UniformMu Maize (Zea mays). , 2016, Current protocols in plant biology.

[11]  Tyson A. Clark,et al.  Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing , 2016, Nature Communications.

[12]  Peggy G. Lemaux,et al.  Advancing Crop Transformation in the Era of Genome Editing[OPEN] , 2016, Plant Cell.

[13]  Albert J. Vilella,et al.  Ensembl comparative genomics resources , 2016, Database J. Biol. Databases Curation.

[14]  Guoli Ji,et al.  detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes , 2016, Scientific Reports.

[15]  Hanlee P. Ji,et al.  Haplotyping germline and cancer genomes using high-throughput linked-read sequencing , 2015, Nature Biotechnology.

[16]  Lincoln Stein,et al.  Gramene 2016: comparative plant genomics and pathway resources , 2015, Nucleic Acids Res..

[17]  A. Hastie,et al.  Optical Nano-mapping and Analysis of Plant Genomes. , 2016, Methods in molecular biology.

[18]  James C. Schnable,et al.  SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand , 2015, Genome biology and evolution.

[19]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[20]  L. Mueller,et al.  Dynamic Maize Responses to Aphid Feeding Are Revealed by a Time Series of Transcriptomic and Metabolomic Assays1[OPEN] , 2015, Plant Physiology.

[21]  James C. Schnable,et al.  Genome evolution in maize: from genomes back to genes. , 2015, Annual review of plant biology.

[22]  Peter J. Bradbury,et al.  High-resolution genetic mapping of maize pan-genome sequence anchors , 2015, Nature Communications.

[23]  Jawon Song,et al.  Examining the Causes and Consequences of Context-Specific Differential DNA Methylation in Maize1[OPEN] , 2015, Plant Physiology.

[24]  R. Dawe,et al.  Genetic and Genomic Toolbox of Zea mays , 2015, Genetics.

[25]  P. Schembri,et al.  Correction: Corrigendum: Coralligenous and maërl habitats: predictive modelling to identify their spatial distributions across the Mediterranean Sea , 2014, Scientific Reports.

[26]  Jikai Lei,et al.  Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes1[OPEN] , 2014, Plant Physiology.

[27]  Xiandong Meng,et al.  A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing , 2014, Scientific Reports.

[28]  M. Pindo,et al.  A MITE Transposon Insertion Is Associated with Differential Methylation at the Maize Flowering Time QTL Vgt1 , 2014, G3: Genes, Genomes, Genetics.

[29]  M. A. Pedraza,et al.  Insights into the Maize Pan-Genome and Pan-Transcriptome[W][OPEN] , 2014, Plant Cell.

[30]  Carolyn J. Lawrence-Dill,et al.  MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations1[W][OPEN] , 2013, Plant Physiology.

[31]  K. Koch,et al.  Mu-seq: Sequence-Based Mapping and Identification of Transposon Induced Mutations , 2013, PloS one.

[32]  Xiaohong Yang,et al.  CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the postdomestication spread of maize , 2013, Proceedings of the National Academy of Sciences.

[33]  J. Kendall,et al.  The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA , 2013, Genome research.

[34]  Xiaoyu Zhang,et al.  CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize , 2013, Genome research.

[35]  H. Dooner,et al.  Gene tagging with engineered Ds elements in maize. , 2013, Methods in molecular biology.

[36]  Zhengwei Zhu,et al.  CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..

[37]  Peter J. Bradbury,et al.  Maize HapMap2 identifies extant variation from a genome in flux , 2012, Nature Genetics.

[38]  C. Scheuring,et al.  Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research , 2012, Nature Protocols.

[39]  Jeffrey Ross-Ibarra,et al.  Identification of a functional transposon insertion in the maize domestication gene tb1 , 2011, Nature Genetics.

[40]  Bernd Weisshaar,et al.  Targeted Identification of Short Interspersed Nuclear Element Families Shows Their Widespread Existence and Extreme Heterogeneity in Plant Genomes[W] , 2011, Plant Cell.

[41]  Jian Wang,et al.  Genome-wide patterns of genetic variation among elite maize inbred lines , 2010, Nature Genetics.

[42]  Peter Tiffin,et al.  Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. , 2010, Genome research.

[43]  V. Brendel,et al.  Genome-Wide Distribution of Transposed Dissociation Elements in Maize[W][OA] , 2010, Plant Cell.

[44]  Nicholas Stiffler,et al.  Use of Illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy Mutator lines of maize. , 2010, The Plant journal : for cell and molecular biology.

[45]  Dawn H. Nagel,et al.  The B73 Maize Genome: Complexity, Diversity, and Dynamics , 2009, Science.

[46]  Patrick S. Schnable,et al.  Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content , 2009, PLoS genetics.

[47]  Sanzhen Liu,et al.  Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome , 2009, PLoS genetics.

[48]  J. Gershenzon,et al.  Monoterpene and sesquiterpene synthases and the origin of terpene skeletal diversity in plants. , 2009, Phytochemistry.

[49]  S. Wessler,et al.  TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences , 2009, Nucleic acids research.

[50]  Albert J. Vilella,et al.  EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. , 2009, Genome research.

[51]  H. Dooner,et al.  Maize Genome Structure Variation: Interplay between Retrotransposon Polymorphisms and Genic Recombination[W] , 2008, The Plant Cell Online.

[52]  Stefan Kurtz,et al.  LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons , 2008, BMC Bioinformatics.

[53]  J. Bennetzen,et al.  A unified classification system for eukaryotic transposable elements , 2007, Nature Reviews Genetics.

[54]  Joachim Messing,et al.  Sequence-indexed mutations in maize using the UniformMu transposon-tagging population , 2007, BMC Genomics.

[55]  Burkhard Morgenstern,et al.  AUGUSTUS: ab initio prediction of alternative transcripts , 2006, Nucleic Acids Res..

[56]  Joachim Messing,et al.  Organization and variability of the maize genome. , 2006, Current opinion in plant biology.

[57]  P. Schnable,et al.  Thebz-rcy allele of theCy transposable element system ofZea mays contains aMu-like element insertion , 1989, Molecular and General Genetics MGG.

[58]  K. Koch,et al.  Steady-state transposon mutagenesis in inbred maize. , 2005, The Plant journal : for cell and molecular biology.

[59]  V. Chandler,et al.  Mu transposable elements are structurally diverse and distributed throughout the genusZea , 1989, Journal of Molecular Evolution.

[60]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[61]  T. Brutnell,et al.  Transposon tagging using Activator (Ac) in maize. , 2003, Methods in molecular biology.

[62]  H. Fu,et al.  Intraspecific violation of genetic colinearity and its implications in maize , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[63]  D. Ashlock,et al.  Maize Mu transposons are targeted to the 5' untranslated region of the gl8 gene and sequences flanking Mu target-site duplications exhibit nonrandom nucleotide composition throughout the genome. , 2002, Genetics.

[64]  D. Lisch.  Mutator transposons. , 2002, Trends in plant science.

[65]  V. Walbot,et al.  Saturation mutagenesis using maize transposons. , 2000, Current opinion in plant biology.

[66]  V. Solovyev,et al.  Ab initio gene finding in Drosophila genomic DNA. , 2000, Genome research.

[67]  J. Bennetzen.  The Mutator transposable element system of maize. , 1996, Current topics in microbiology and immunology.

[68]  V. Chandler,et al.  The Mu elements of Zea mays. , 1992, Advances in genetics.

[69]  V. Walbot,et al.  Mutator activity in maize correlates with the presence and expression of the Mu transposable element Mu9. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[70]  M. Freeling,et al.  Identification of a regulatory transposon that controls the Mutator transposable element system in maize. , 1991, Genetics.

[71]  S. Wessler,et al.  Nucleotide sequence of the maize Mutator element, Mu8. , 1990, Nucleic acids research.

[72]  M. Freeling,et al.  A New Mu Element from a Robertson’s Mutator Line , 1988 .

[73]  V. Walbot,et al.  Isolation and characterization of a 1.7-kb transposable element from a mutator line of maize. , 1987, Genetics.

[74]  S. Dellaporta,et al.  Transposition of Ac from the P locus of maize into unreplicated chromosomal sites. , 1987, Genetics.

[75]  E. Ralston,et al.  A Single Genetic Unit Specifies Two Transposition Functions in the Maize Element Activator , 1986, Science.

[76]  N. Fedoroff,et al.  Cloning of the bronze locus in maize by a simple and generalizable procedure using the transposable controlling element Activator (Ac). , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[77]  J. Bennetzen.  Transposable element Mu1 is found in multiple copies only in Robertson's Mutator maize lines. , 1984, Journal of molecular and applied genetics.

[78]  D. Robertson.  Characterization of a mutator system in maize , 1978 .

[79]  J. Kermicle.  Dependence of the R-mottled aleurone phenotype in maize on mode of sexual transmission. , 1970, Genetics.

[80]  R. A. Brink,et al.  Paramutation: directed genetic change. Paramutation occurs in somatic cells and heritably alters the functional state of a locus. , 1968, Science.

[81]  E. Mertz,et al.  Mutant Gene That Changes Protein Composition and Increases Lysine Content of Maize Endosperm , 1964, Science.