Whole-genome sequencing and SNV genotyping of ‘Nebbiolo’ (Vitis vinifera L.) clones

[1]  J. Franco-Zorrilla,et al.  Catastrophic Unbalanced Genome Rearrangements Cause Somatic Loss of Berry Color in Grapevine1 , 2017, Plant Physiology.

[2]  C. Fields,et al.  Whole genome comparative analysis of four Georgian grape cultivars , 2017, Molecular Genetics and Genomics.

[3]  S. Camiolo,et al.  Sequence Polymorphisms and Structural Variations among Four Grapevine (Vitis vinifera L.) Cultivars Representing Sardinian Agriculture , 2017, Front. Plant Sci..

[4]  M. Crespan,et al.  Structural dynamics at the berry colour locus in Vitis vinifera L. somatic variants. , 2017 .

[5]  I. Gribaudo,et al.  Cultivar-specific gene modulation in Vitis vinifera: analysis of the promoters regulating the expression of WOX transcription factors , 2017, Scientific Reports.

[6]  R. Viola,et al.  DNA-Free Genetically Edited Grapevine and Apple Protoplast Using CRISPR/Cas9 Ribonucleoproteins , 2016, Front. Plant Sci..

[7]  P Neveu,et al.  Towards an open grapevine information system , 2016, Horticulture Research.

[8]  Can Alkan,et al.  Inter-varietal structural variation in grapevine genomes. , 2016, The Plant journal : for cell and molecular biology.

[9]  Shaohua Li,et al.  CRISPR/Cas9-mediated efficient targeted mutagenesis in Chardonnay (Vitis vinifera L.) , 2016, Scientific Reports.

[10]  M. Schatz,et al.  Phased diploid genome assembly with single-molecule real-time sequencing , 2016, Nature Methods.

[11]  S. Raimondi,et al.  The key role of “Moscato bianco” and “Malvasia aromatica di Parma” in the parentage of traditional aromatic grape varieties , 2016, Tree Genetics & Genomes.

[12]  P. Carbonell-Bejerano,et al.  Developmental, transcriptome, and genetic alterations associated with parthenocarpy in the grapevine seedless somatic variant Corinto bianco. , 2016, Journal of experimental botany.

[13]  P. Hinrichsen,et al.  Molecular diversity within clones of cv. Tannat (Vitis vinifera) , 2015 .

[14]  N. Patron,et al.  Editing plant genomes with CRISPR/Cas9. , 2015, Current opinion in biotechnology.

[15]  V. Dumas,et al.  Chromosome Replacement and Deletion Lead to Clonal Polymorphism of Berry Color in Grapevine , 2015, PLoS genetics.

[16]  Xin Li,et al.  NLRs in plants. , 2015, Current opinion in immunology.

[17]  G. Valle,et al.  A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress condition and genotype , 2014, BMC Plant Biology.

[18]  D. Bosco,et al.  Flavescence dorée phytoplasma titre in field‐infected Barbera and Nebbiolo grapevines , 2014 .

[19]  Mario Pezzotti,et al.  The grapevine gene nomenclature system , 2013, BMC Genomics.

[20]  A. Calò,et al.  Genetic Variability and Geographic Typicality of Italian Former Prosecco Grape Variety Using PCR-Derived Molecular Markers , 2014, Molecular Biotechnology.

[21]  A. Maass,et al.  Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants , 2014, BMC Plant Biology.

[22]  M. Delledonne,et al.  The High Polyphenol Content of Grapevine Cultivar Tannat Berries Is Conferred Primarily by Genes That Are Not Shared with the Reference Genome[W] , 2013, Plant Cell.

[23]  Colin N. Dewey,et al.  De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis , 2013, Nature Protocols.

[24]  B. Walter,et al.  Stable MSAP Markers for the Distinction of Vitis vinifera cv Pinot Noir Clones , 2013, Molecular Biotechnology.

[25]  Mara Miculan.  Detection of somatic variants from next-generation sequencing data in grapevine bud sports , 2013 .

[26]  M. S. Grando,et al.  Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape , 2013, BMC Plant Biology.

[27]  M. Delledonne,et al.  De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity , 2013, BMC Genomics.

[28]  R. Velasco,et al.  Pinot blanc and Pinot gris arose as independent somatic mutations of Pinot noir , 2012, Journal of experimental botany.

[29]  Jancis Robinson,et al.  Wine Grapes: A Complete Guide to 1,368 Vine Varieties, Including Their Origins and Flavours , 2012 .

[30]  M. Schatz,et al.  Current challenges in de novo plant genome sequencing and assembly , 2012, Genome Biology.

[31]  Pablo Cingolani,et al.  © 2012 Landes Bioscience. Do not distribute. , 2022 .

[32]  L. Audeguin,et al.  Transposable Elements Are a Major Cause of Somatic Polymorphism in Vitis vinifera L. , 2012, PloS one.

[33]  S. Ramachandran,et al.  Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor) , 2011, Genome Biology.

[34]  Javier Ibáñez,et al.  A 48 SNP set for grapevine cultivar identification , 2011, BMC Plant Biology.

[35]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[36]  Vipin T. Sreedharan,et al.  Multiple reference genomes and transcriptomes for Arabidopsis thaliana , 2011, Nature.

[37]  Edward S. Buckler,et al.  Genetic structure and domestication history of the grape , 2011, Proceedings of the National Academy of Sciences.

[38]  J. Boursiquot,et al.  An efficient and rapid protocol for plant nuclear DNA preparation suitable for next generation sequencing methods. , 2011, American journal of botany.

[39]  I. Gribaudo,et al.  Characterization of expression dynamics of WOX homeodomain transcription factors during somatic embryogenesis in Vitis vinifera. , 2011, Journal of experimental botany.

[40]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[41]  F. Pelsy.  Molecular and cellular mechanisms of diversity within grapevine varieties , 2010, Heredity.

[42]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[43]  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.

[44]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[45]  A. Forneck,et al.  Clonal Variation in Pinot noir Revealed by S-SAP Involving Universal Retrotransposon-Based Sequences , 2009, American Journal of Enology and Viticulture.

[46]  J. Jakše,et al.  Highly variable AFLP and S-SAP markers for the identification of 'Malbec' and 'Syrah' clones , 2009 .

[47]  J. Martínez-Zapater,et al.  High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology , 2007, BMC Genomics.

[48]  Yi-An Chen,et al.  An optimized procedure greatly improves EST vector contamination removal , 2007, BMC Genomics.

[49]  J. Poulain,et al.  The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla , 2007, Nature.

[50]  Michele Morgante,et al.  Transposable elements and the plant pan-genomes. , 2007, Current opinion in plant biology.

[51]  Alexander F. Auch,et al.  MEGAN analysis of metagenomic data. , 2007, Genome research.

[52]  D. Merdinoglu,et al.  Genetic diversity and geographical dispersal in grapevine clones revealed by microsatellite markers. , 2006, Genome.

[53]  A. R. Walker,et al.  Two new grape cultivars, bud sports of Cabernet Sauvignon bearing pale-coloured berries, are the result of deletion of two regulatory genes of the berry colour locus , 2006, Plant Molecular Biology.

[54]  M. S. Grando,et al.  Multiple origins of cultivated grapevine (Vitis vinifera L. ssp. sativa) based on chloroplast DNA polymorphisms , 2006, Molecular ecology.

[55]  Juan Miguel García-Gómez,et al.  BIOINFORMATICS APPLICATIONS NOTE Sequence analysis Manipulation of FASTQ data with Galaxy , 2005 .

[56]  Martin Kuiper,et al.  BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks , 2005, Bioinform..

[57]  A. Bressan,et al.  Acquisition efficiency of Flavescence dorée phytoplasma by Scaphoideus titanus Ball from infected tolerant or susceptible grapevine cultivars or experimental host plants , 2005 .

[58]  T. Lacombe,et al.  Development of a standard set of microsatellite reference alleles for identification of grape cultivars , 2004, Theoretical and Applied Genetics.

[59]  V. Dumas,et al.  Diversification within grapevine cultivars goes through chimeric states. , 2004, Genome.

[60]  Stephen M. Mount,et al.  Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. , 2003, Nucleic acids research.

[61]  A. Schneider,et al.  Genetic relationships among grapevine cultivars from North-Western Italy , 2003 .

[62]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[63]  A. Schneider,et al.  Within cultivar grapevine variability studied by morphometrical and molecular marker based techniques. , 2000 .

[64]  H. Bandelt,et al.  Median-joining networks for inferring intraspecific phylogenies. , 1999, Molecular biology and evolution.

[65]  H. Bleiholder,et al.  Growth Stages of the Grapevine: Phenological growth stages of the grapevine (Vitis vinifera L. ssp. vinifera)—Codes and descriptions according to the extended BBCH scale† , 1995 .

[66]  B. G. Coombe,et al.  Growth Stages of the Grapevine: Adoption of a system for identifying grapevine growth stages , 1995 .

[67]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.