Genomics and bioinformatics resources for translational science in Rosaceae

Recent technological advances in biology promise unprecedented opportunities for rapid and sustainable advancement of crop quality. Following this trend, the Rosaceae research community continues to generate large amounts of genomic, genetic and breeding data. These include annotated whole genome sequences, transcriptome and expression data, proteomic and metabolomic data, genotypic and phenotypic data, and genetic and physical maps. Analysis, storage, integration and dissemination of these data using bioinformatics tools and databases are essential to provide utility of the data for basic, translational and applied research. This review discusses the currently available genomics and bioinformatics resources for the Rosaceae family.

• Publication year

  2013

• Venue

  Plant Biotechnology Reports

• Publication date

  2013-05-21

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1007/s11816-013-0282-3PMID 24634697PMCID 3951882
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2013cited by this paper
• Evaluation of the hormonal state of columnar apple trees (Malus x domestica) based on high throughput gene expression studies

  2013cited by this paper
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  2013cited by this paper
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  2012influential reference
• Development and Evaluation of a Genome-Wide 6K SNP Array for Diploid Sweet Cherry and Tetraploid Sour Cherry

  2012cited by this paper
• Multiple plant hormones and cell wall metabolism regulate apple fruit maturation patterns and texture attributes

  2012cited by this paper
• Gene Ontology Annotations and Resources

  2012cited by this paper
• Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm

  2012cited by this paper
• Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies

  2012cited by this paper
• A high-throughput apple SNP genotyping platform using the GoldenGate™ assay.

  2012cited by this paper
• Rootstock-regulated gene expression patterns associated with fire blight resistance in apple

  2012cited by this paper
• A transposase strategy for creating libraries of circularly permuted proteins

  2012cited by this paper
• P3DB: An Integrated Database for Plant Protein Phosphorylation

  2012cited by this paper
• GenBank

  2012cited by this paper
• Facing growth in the European Nucleotide Archive

  2012cited by this paper
• EUROPEAN SMALL BERRIES GENETIC RESOURCES, GENBERRY: TESTING A PROTOCOL FOR DETECTING FRUIT NUTRITIONAL QUALITY IN EU STRAWBERRY GERMPLASM COLLECTIONS

  2012cited by this paper
• The draft genome of a diploid cotton Gossypium raimondii

  2012cited by this paper
• Microarray analysis of differentially expressed genes engaged in fruit development between Prunus mume and Prunus armeniaca.

  2012cited by this paper
• Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple

  2012cited by this paper
• The draft genome of sweet orange (Citrus sinensis)

  2012cited by this paper
• PGDD: a database of gene and genome duplication in plants

  2012cited by this paper
• MaizeGDB: curation and outreach go hand-in-hand

  2011cited by this paper
• InterPro in 2011: new developments in the family and domain prediction database

  2011cited by this paper
• Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform1[W]

  2011cited by this paper
• The genome of woodland strawberry (Fragaria vesca)

  2011influential reference
• Genome-wide analysis of the RING finger gene family in apple

  2011cited by this paper
• Towards a unified genetic map for diploid roses

  2011cited by this paper
• New approaches to Prunus transcriptome analysis

  2011cited by this paper
• The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

  2011cited by this paper
• Simple Sequence Repeat Marker Development and Mapping Targeted to Previously Unmapped Regions of the Strawberry Genome Sequence

  2011cited by this paper
• The Biomolecular Interaction Network Database in PSI-MI 2.5

  2011cited by this paper
• The Pfam protein families database

  2011cited by this paper
• Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection

  2011cited by this paper
• Reorganizing the protein space at the Universal Protein Resource (UniProt)

  2011cited by this paper
• PDBe: Protein Data Bank in Europe

  2010cited by this paper
• Signaling Pathways Mediating the Induction of Apple Fruitlet Abscission1[C][W][OA]

  2010cited by this paper
• The genome of the domesticated apple (Malus × domestica Borkh.)

  2010cited by this paper
• Generation and analysis of ESTs from strawberry (Fragaria xananassa) fruits and evaluation of their utility in genetic and molecular studies

  2010cited by this paper
• Gramene database in 2010: updates and extensions

  2010cited by this paper
• Extending CATH: increasing coverage of the protein structure universe and linking structure with function

  2010cited by this paper
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  2010cited by this paper
• Genome-wide mapping of alternative splicing in Arabidopsis thaliana.

  2010cited by this paper
• DDBJ progress report

  2010cited by this paper
• The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl

  2010cited by this paper
• Decision tree supported substructure prediction of metabolites from GC-MS profiles

  2010cited by this paper
• Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening

  2010cited by this paper
• Using the Generic Synteny Browser (GBrowse_syn)

  2010cited by this paper
• Genome sequence of the palaeopolyploid soybean

  2010cited by this paper
• GreenPhylDB v2.0: comparative and functional genomics in plants

  2010influential reference
• RosBREED: Enabling marker-assisted breeding in Rosaceae

  2010influential reference
• PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

  2009cited by this paper
• A Bayesian QTL linkage analysis of the common dataset from the 12th QTLMAS workshop

  2009cited by this paper
• Comparative analysis of expressed sequence tags from tissues in ripening stages of peach (Prunus persica L. Batsch)

  2009cited by this paper
• The B73 Maize Genome: Complexity, Diversity, and Dynamics

  2009cited by this paper
• Comparative EST transcript profiling of peach fruits under different post-harvest conditions reveals candidate genes associated with peach fruit quality

  2009cited by this paper
• Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers

  2009cited by this paper
• The Sorghum bicolor genome and the diversification of grasses

  2009cited by this paper
• MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays.

  2009cited by this paper
• AtMetExpress Development: A Phytochemical Atlas of Arabidopsis Development[W][OA]

  2009cited by this paper
• ISAFRUIT - study of the genetic basis of Prunus fruit quality in two peach and two apricot populations.

  2009cited by this paper
• The genome of the cucumber, Cucumis sativus L.

  2009cited by this paper
• SALAD database: a motif-based database of protein annotations for plant comparative genomics

  2009cited by this paper
• An integrated strategy to identify key genes in almond adventitious shoot regeneration.

  2009cited by this paper
• How to usefully compare homologous plant genes and chromosomes as DNA sequences.

  2008cited by this paper
• Discovery and revision of Arabidopsis genes by proteogenomics

  2008cited by this paper
• TreeGenes: A Forest Tree Genome Database

  2008cited by this paper
• Version VI of the ESTree db: an improved tool for peach transcriptome analysis

  2008cited by this paper
• Global gene expression analysis of apple fruit development from the floral bud to ripe fruit

  2008cited by this paper
• Multiple Models for Rosaceae Genomics[OA]

  2008cited by this paper
• Development of ChillPeach genomic tools and identification of cold-responsive genes in peach fruit

  2008cited by this paper
• Synteny and Collinearity in Plant Genomes

  2008cited by this paper
• Highly integrated single-base resolution maps of the epigenome in Arabidopsis.

  2008cited by this paper
• Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics

  2008cited by this paper
• Jasmonate-induced transcriptional changes suggest a negative interference with the ripening syndrome in peach fruit.

  2008cited by this paper
• i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles

  2008cited by this paper
• A framework physical map for peach, a model Rosaceae species

  2008cited by this paper
• SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny

  2008cited by this paper
• GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data

  2007influential reference
• The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

  2007cited by this paper
• The Pfam protein families database

  2007cited by this paper
• Microarray analysis of apple gene expression engaged in early fruit development

  2007influential reference
• Sampling the Arabidopsis Transcriptome with Massively Parallel Pyrosequencing1[W][OA]

  2007cited by this paper
• Data growth and its impact on the SCOP database: new developments

  2007cited by this paper
• Using the Generic Genome Browser (GBrowse)

  2007cited by this paper
• A Predicted Interactome for Arabidopsis1[C][W][OA]

  2007cited by this paper
• Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays

  2007cited by this paper
• A Genomics Approach Reveals That Aroma Production in Apple Is Controlled by Ethylene Predominantly at the Final Step in Each Biosynthetic Pathway[W]

  2007cited by this paper
• Aligning multiple whole genomes with Mercator and MAVID.

  2007influential reference
• The Golm Metabolome Database: a database for GC-MS based metabolite profiling

  2007cited by this paper
• Running head: Analyses of Expressed Sequence Tags from Apple.

  2006cited by this paper
• The Plant Structure Ontology, a Unified Vocabulary of Anatomy and Morphology of a Flowering Plant1[W][OA]

  2006cited by this paper
• Development and Evaluation

  2006influential reference
• The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

  2006cited by this paper
• Analyses of Expressed Sequence Tags from Apple1

  2006influential reference
• Database resources of the National Center for Biotechnology Information

  2006cited by this paper
• SUBA: the Arabidopsis Subcellular Database

  2006cited by this paper
• Candidate gene database and transcript map for peach, a model species for fruit trees

  2005cited by this paper
• The map-based sequence of the rice genome

  2005cited by this paper
• Mapping With a Few Plants: Using Selective Mapping for Microsatellite Saturation of the Prunus Reference Map

  2005cited by this paper
• Using the KEGG Database Resource

  2005influential reference

• Characterization of β-Tubulin Genes in Prunus persica and Prunus dulcis for Fingerprinting of their Interspecific Hybrids

  2022cites this paper
• Genetic diversity for developing climate-resilient wheats to achieve food security goals

  2022cites this paper
• Multi-Omic Approaches to Investigate Molecular Mechanisms in Peach Post-Harvest Ripening

  2022cites this paper
• Comparative analyses of chloroplast genomes in ‘Red Fuji’ apples: low rate of chloroplast genome mutations

  2022cites this paper
• Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members

  2022cites this paper
• Complete chloroplast genome of a rare and endangered plant species Osteomeles subrotunda: genomic features and phylogenetic relationships with other Rosaceae plants

  2021cites this paper
• Challenges and Strategies for Developing Climate-Smart Apple Varieties Through Genomic Approaches

  2020cites this paper
• Omics Technologies for Abiotic Stress Tolerance in Plants: Current Status and Prospects

  2019cites this paper
• Recent Approaches in Omics for Plant Resilience to Climate Change

  2019cites this paper
• Virus-induced gene silencing in Prunus fruit and nut tree species by Apple latent spherical virus vector 2017

  2018cites this paper
• Augmentation of crop productivity through interventions of omics technologies in India: challenges and opportunities

  2018cites this paper
• Plum ( Prunus spp.) Breeding

  2018cites this paper
• Sequence and Analysis of the Black Raspberry (Rubus occidentalis) Genome

  2018cites this paper
• Rosaceae Fruit Development, Ripening and Post-harvest: An Epigenetic Perspective

  2017cites this paper
• DNA-informed breeding of rosaceous crops: promises, progress and prospects

  2017cites this paper
• Virus-induced gene silencing in Prunus fruit and nut tree species by Apple latent spherical virus vector

  2017cites this paper
• Identification of Sugar Beet Flowering Genes Based on Arabidopsis Homologous Genes

  2017cites this paper
• Rose hip as an underutilized functional food: Evidence-based review

  2017cites this paper
• Omics and System Biology Approaches in Plant Stress Research

  2017cites this paper
• Development and evaluation of software for applied clinical genomics

  2016cites this paper
• Genetic mapping and phenotyping plant characteristics, fruit quality and disease resistance traits in octoploid strawberry (Fragaria × ananassa)

  2016influential citation
• Comparing Genetic Mechanisms of Bud Chilling Fulfillment and Seed Cold Stratification: A Role for Peach (Prunus persica)?

  2015cites this paper
• Dynamic software design for clinical exome and genome analyses: insights from bioinformaticians, clinical geneticists, and genetic counselors

  2015cites this paper
• Genomic resources in fruit plants: an assessment of current status

  2015cites this paper
• Advances in Plant Dormancy

  2015cites this paper
• Whole Genome Sequencing of Fruit Tree Species

  2015cites this paper