Open Access
Grapevine gene nomenclature system
Jérôme Grimplet,Anne-Françoise Adam-Blondon,Pierre-François Bert,Oliver Bitz,Dario Cantu,Grant R. Cramer,Christopher Davies,Serge Delrot,Mario Pezzotti,Stephane Rombauts +9 more
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Fleshy Fruit Development & Ripening (COST Action FA1106 QualityFruit) conference was held in Chania (Grecia) del 22 al 25 de septiembre de 2013.Abstract:
Poster presentado en la 2nd Annual ConferenceFleshy Fruit Development & Ripening (COST Action FA1106 QualityFruit), celebrada en Chania (Grecia) del 22 al 25 de septiembre de 2013.read more
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A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3).
Aurélie Canaguier,Aurélie Canaguier,Jérôme Grimplet,G. Di Gaspero,Simone Scalabrin,Eric Duchêne,Nathalie Choisne,Nacer Mohellibi,Cécile Guichard,Cécile Guichard,Stephane Rombauts,I. Le Clainche,I. Le Clainche,Aurélie Bérard,A. Chauveau,Rémi Bounon,Rémi Bounon,C Rustenholz,Michele Morgante,M-C Le Paslier,Dominique Brunel,A-F Adam-Blondon,A-F Adam-Blondon +22 more
TL;DR: A new version of the grapevine reference genome assembly and of its annotation and its VCost.v3 gene annotation in Genbank format is presented.
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Genome-wide characterisation and expression profile of the grapevine ATL ubiquitin ligase family reveal biotic and abiotic stress-responsive and development-related members.
Pietro Ariani,Alice Regaiolo,Arianna Lovato,Alejandro Giorgetti,Andrea Porceddu,Salvatore Camiolo,Darren Wong,Simone D. Castellarin,Elodie Vandelle,Annalisa Polverari +9 more
TL;DR: The data offer the first genome-wide overview and annotation of the grapevine ATL family, and provide a basis for investigating the roles of specific family members in grapevine physiology and stress responses, as well as potential biotechnological applications.
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A systems-oriented analysis of the grapevine R2R3-MYB transcription factor family uncovers new insights into the regulation of stilbene accumulation
Darren C. J. Wong,Rudolf O. Schlechter,Alessandro Vannozzi,Janine Höll,Ibrahim Hmmam,Jochen Bogs,Giovanni Battista Tornielli,Simone D. Castellarin,José Tomás Matus +8 more
TL;DR: A comprehensive analysis of different MYB binding motifs in the promoters of co-expressed genes predicted grape R2R3-MYB binding preferences and supported evidence for putative downstream targets, and enrichment of cis-regulatory motifs for diverse TFs reinforced the notion of transcriptional coordination and interaction between MYBs and other regulators.
Journal ArticleDOI
Transcriptomic analysis of the late stages of grapevine ( Vitis vinifera cv. Cabernet Sauvignon) berry ripening reveals significant induction of ethylene signaling and flavor pathways in the skin
Grant R. Cramer,Ryan Ghan,Karen Schlauch,Richard L. Tillett,Hildegarde Heymann,Alberto Ferrarini,Massimo Delledonne,Sara Zenoni,Marianna Fasoli,Mario Pezzotti +9 more
TL;DR: Analysis of the transcriptome dynamics during late stages of ripening of grapevine berries revealed that these berries went through massive transcriptional changes in gene ontology categories involving chemical signaling and metabolism in both the pulp and skin, particularly in the skin.
Journal ArticleDOI
Structural and Functional Analysis of the GRAS Gene Family in Grapevine Indicates a Role of GRAS Proteins in the Control of Development and Stress Responses
Jérôme Grimplet,Patricia Agudelo-Romero,Rita Teresa Teixeira,José M. Martínez-Zapater,Ana Margarida Fortes +4 more
TL;DR: Comparisons of tomato and grapevine GRAS genes identified candidate genes that might constitute conserved transcriptional regulators of both climacteric and non-climacteric fruit ripening and robust candidate genes for future functional analysis aiming at improving the quality of fleshy fruits are identified.
References
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MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
Koichiro Tamura,Daniel S. Peterson,Nicholas Peterson,Glen Stecher,Masatoshi Nei,Sudhir Kumar +5 more
TL;DR: The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
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MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
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The rapid generation of mutation data matrices from protein sequences
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Phylogeny.fr: robust phylogenetic analysis for the non-specialist
Alexis Dereeper,Valentin Guignon,Guillaume Blanc,Stéphane Audic,S. Buffet,François Chevenet,Jean-François Dufayard,Stéphane Guindon,Vincent Lefort,Magali Lescot,Jean-Michel Claverie,Olivier Gascuel +11 more
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