15 years of GDR: New data and functionality in the Genome Database for Rosaceae

Abstract The Genome Database for Rosaceae (GDR, https://www.rosaceae.org) is an integrated web-based community database resource providing access to publicly available genomics, genetics and breeding data and data-mining tools to facilitate basic, translational and applied research in Rosaceae. The volume of data in GDR has increased greatly over the last 5 years. The GDR now houses multiple versions of whole genome assembly and annotation data from 14 species, made available by recent advances in sequencing technology. Annotated and searchable reference transcriptomes, RefTrans, combining peer-reviewed published RNA-Seq as well as EST datasets, are newly available for major crop species. Significantly more quantitative trait loci, genetic maps and markers are available in MapViewer, a new visualization tool that better integrates with other pages in GDR. Pathways can be accessed through the new GDR Cyc Pathways databases, and synteny among the newest genome assemblies from eight species can be viewed through the new synteny browser, SynView. Collated single-nucleotide polymorphism diversity data and phenotypic data from publicly available breeding datasets are integrated with other relevant data. Also, the new Breeding Information Management System allows breeders to upload, manage and analyze their private breeding data within the secure GDR server with an option to release data publicly.

[1]  Dorrie Main,et al.  Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm , 2012, PloS one.

[2]  P. Karp,et al.  The challenge of constructing, classifying, and representing metabolic pathways. , 2013, FEMS microbiology letters.

[3]  D. Rokhsar,et al.  Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies , 2012, BMC Genomics.

[4]  X. Huang,et al.  CAP3: A DNA sequence assembly program. , 1999, Genome research.

[5]  P. Green,et al.  Consed: a graphical tool for sequence finishing. , 1998, Genome research.

[6]  S. Tabata,et al.  Genome structure of Rosa multiflora, a wild ancestor of cultivated roses , 2017, DNA research : an international journal for rapid publication of reports on genes and genomes.

[7]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[8]  Christina E. Wells,et al.  The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution , 2013, Nature Genetics.

[9]  M. González-Agüero,et al.  Differential expression of ethylene biosynthesis genes in drupelets and receptacle of raspberry (Rubus idaeus). , 2015, Journal of plant physiology.

[10]  Riccardo Velasco,et al.  Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple , 2012, PloS one.

[11]  Stephen P. Ficklin,et al.  Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases , 2013, Database J. Biol. Databases Curation.

[12]  Jeremy D. DeBarry,et al.  MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity , 2012, Nucleic acids research.

[13]  J. Slovin,et al.  Re-annotation of the woodland strawberry (Fragaria vesca) genome , 2015, BMC Genomics.

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

[15]  Lincoln Stein,et al.  CMap 1.01: a comparative mapping application for the Internet , 2009, Bioinform..

[16]  K. Evans,et al.  APPLE BREEDING IN THE PACIFIC NORTHWEST , 2013 .

[17]  Riccardo Velasco,et al.  Development and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh) , 2014, PloS one.

[18]  Stephen P. Ficklin,et al.  Tripal: a construction toolkit for online genome databases , 2011, Database J. Biol. Databases Curation.

[19]  S. Isobe,et al.  The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding , 2017, DNA research : an international journal for rapid publication of reports on genes and genomes.

[20]  Luca Bianco,et al.  Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa , 2015, BMC Genomics.

[21]  The Gene Ontology Consortium.  Expansion of the Gene Ontology knowledgebase and resources , 2016, Nucleic Acids Res..

[22]  Henry D. Priest,et al.  The genome of black raspberry (Rubus occidentalis). , 2016, The Plant journal : for cell and molecular biology.

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

[24]  Jeffrey P. Mower,et al.  Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity , 2017, GigaScience.

[25]  S. Kuhara,et al.  Dissection of the Octoploid Strawberry Genome by Deep Sequencing of the Genomes of Fragaria Species , 2013, DNA research : an international journal for rapid publication of reports on genes and genomes.

[26]  Dorrie Main,et al.  Development and Evaluation of a Genome-Wide 6K SNP Array for Diploid Sweet Cherry and Tetraploid Sour Cherry , 2012, PloS one.

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

[28]  Stephen P. Ficklin,et al.  AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture , 2018, Database J. Biol. Databases Curation.

[29]  Dorrie Main,et al.  GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data , 2007, Nucleic Acids Res..

[30]  Stephen P. Ficklin,et al.  GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research , 2004, BMC Bioinform..

[31]  Ping Zheng,et al.  The Genome Database for Rosaceae (GDR): year 10 update , 2013, Nucleic Acids Res..

[32]  H. Quesneville,et al.  A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits , 2018, Nature Plants.

[33]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[34]  S. Shu,et al.  The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity , 2017, BMC Genomics.

[35]  A. Oshlack,et al.  Corset: enabling differential gene expression analysis for de novo assembled transcriptomes , 2014, Genome Biology.

[36]  H. Quesneville,et al.  A high-quality sequence of Rosa chinensis to elucidate genome structure and ornamental traits , 2018, bioRxiv.

[37]  Dorrie Main,et al.  Multiple Models for Rosaceae Genomics[OA] , 2008, Plant Physiology.

[38]  Stephen P. Ficklin,et al.  Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases , 2017, Database J. Biol. Databases Curation.

[39]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

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

[41]  Henry D. Priest,et al.  The genome of woodland strawberry (Fragaria vesca) , 2011, Nature Genetics.

[42]  Jesse Poland,et al.  Field Book: An Open‐Source Application for Field Data Collection on Android , 2014 .

[43]  J. Gouzy,et al.  High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development , 2017, Nature Genetics.

[44]  Jacob A. Tennessen,et al.  Evolutionary Origins and Dynamics of Octoploid Strawberry Subgenomes Revealed by Dense Targeted Capture Linkage Maps , 2014, Genome biology and evolution.

[45]  R. Hellens,et al.  The Draft Genome Sequence of European Pear (Pyrus communis L. ‘Bartlett’) , 2014, PloS one.

[46]  P. Wincker,et al.  The Rosa genome provides new insights into the domestication of modern roses , 2018, Nature Genetics.

[47]  Eugene Zhang,et al.  The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics , 2017, Nucleic Acids Res..

[48]  Michael Banf,et al.  Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants1[OPEN] , 2017, Plant Physiology.

[49]  T. Mockler,et al.  Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data , 2018, Horticulture Research.

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

[51]  Xiao Zhou,et al.  New extension software modules to enhance searching and display of transcriptome data in Tripal databases , 2017, Database J. Biol. Databases Curation.

[52]  Satoshi Yuhara.  Draft Genome Sequence of European Pear ( Pyrus communis L) , 2013 .

[53]  Roger E Bumgarner,et al.  The genome of the domesticated apple (Malus × domestica Borkh.) , 2010, Nature Genetics.

[54]  The Gene Ontology Consortium,et al.  Expansion of the Gene Ontology knowledgebase and resources , 2016, Nucleic Acids Res..

[55]  Riccardo Velasco,et al.  Development and validation of the Axiom(®) Apple480K SNP genotyping array. , 2016, The Plant journal : for cell and molecular biology.

[56]  Zhongchi Liu,et al.  Genome re-annotation of the wild strawberry Fragaria vesca using extensive Illumina- and SMRT-based RNA-seq datasets , 2017, DNA research : an international journal for rapid publication of reports on genes and genomes.

[57]  Suzanna E Lewis,et al.  JBrowse: a dynamic web platform for genome visualization and analysis , 2016, Genome Biology.

[58]  M. Borodovsky,et al.  The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry) , 2017, GigaScience.

[59]  F. Krens,et al.  Using RNA-Seq to assemble a rose transcriptome with more than 13,000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.) , 2015, Front. Plant Sci..