The coffee genome hub: a resource for coffee genomes

The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently released. In the context of the C. canephora genome sequencing project and to support post-genomics efforts, we developed the Coffee Genome Hub (http://coffee-genome.org/), an integrative genome information system that allows centralized access to genomics and genetics data and analysis tools to facilitate translational and applied research in coffee. We provide the complete genome sequence of C. canephora along with gene structure, gene product information, metabolism, gene families, transcriptomics, syntenic blocks, genetic markers and genetic maps. The hub relies on generic software (e.g. GMOD tools) for easy querying, visualizing and downloading research data. It includes a Genome Browser enhanced by a Community Annotation System, enabling the improvement of automatic gene annotation through an annotation editor. In addition, the hub aims at developing interoperability among other existing South Green tools managing coffee data (phylogenomics resources, SNPs) and/or supporting data analyses with the Galaxy workflow manager.

[1]  Dany Severac,et al.  Contribution of subgenomes to the transcriptome and their intertwined regulation in the allopolyploid Coffea arabica grown at contrasted temperatures. , 2013, The New phytologist.

[2]  Oscar Westesson,et al.  Visualizing next-generation sequencing data with JBrowse , 2013, Briefings Bioinform..

[3]  Dany Severac,et al.  Genome rearrangements derived from homoeologous recombination following allopolyploidy speciation in coffee. , 2014, The Plant journal : for cell and molecular biology.

[4]  Manuel Ruiz,et al.  SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects , 2011, BMC Bioinformatics.

[5]  C. Claudel-Renard,et al.  Enzyme-specific profiles for genome annotation: PRIAM. , 2003, Nucleic acids research.

[6]  Valentin Guignon,et al.  Chado Controller: advanced annotation management with a community annotation system , 2012, Bioinform..

[7]  R. Durbin,et al.  GAZE: a generic framework for the integration of gene-prediction data by dynamic programming. , 2002, Genome research.

[8]  F. Denoeud,et al.  Annotating genomes with massive-scale RNA sequencing , 2008, Genome Biology.

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

[10]  Arek Kasprzyk,et al.  BioMart: driving a paradigm change in biological data management , 2011, Database J. Biol. Databases Curation.

[11]  Lincoln Stein,et al.  Using GBrowse 2.0 to visualize and share next-generation sequence data , 2013, Briefings Bioinform..

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

[13]  Chris Mungall,et al.  A Chado case study: an ontology-based modular schema for representing genome-associated biological information , 2007, ISMB/ECCB.

[14]  Matthew Berriman,et al.  Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database , 2008, Bioinform..

[15]  Peter D. Karp,et al.  Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology , 2015, Briefings Bioinform..

[16]  Daniel J. Blankenberg,et al.  Galaxy: a platform for interactive large-scale genome analysis. , 2005, Genome research.

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

[18]  Dan M. Bolser,et al.  Gramene 2013: comparative plant genomics resources , 2013, Nucleic Acids Res..

[19]  Daniel W. A. Buchan,et al.  The tomato genome sequence provides insights into fleshy fruit evolution , 2012, Nature.

[20]  L. Stein,et al.  JBrowse: a next-generation genome browser. , 2009, Genome research.

[21]  Maido Remm,et al.  Enhancements and modifications of primer design program Primer3 , 2007, Bioinform..

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

[23]  Ping Zheng,et al.  CottonGen: a genomics, genetics and breeding database for cotton research , 2013, Nucleic Acids Res..

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

[25]  Robert M. Buels,et al.  The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl , 2010, Nucleic Acids Res..

[26]  Claudine Campa,et al.  MoccaDB - an integrative database for functional, comparative and diversity studies in the Rubiaceae family , 2009, BMC Plant Biology.

[27]  Daniel R. Zerbino,et al.  Ensembl 2014 , 2013, Nucleic Acids Res..

[28]  Yeting Zhang,et al.  A genome triplication associated with early diversification of the core eudicots , 2012, Genome Biology.

[29]  Benoît Bertrand,et al.  Caffeine-based gold(I) N-heterocyclic carbenes as possible anticancer agents: synthesis and biological properties. , 2014, Inorganic chemistry.

[30]  Christian M. Zmasek,et al.  GreenPhylDB v2.0: comparative and functional genomics in plants , 2010, Nucleic Acids Res..

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

[32]  T. Flutre,et al.  Considering Transposable Element Diversification in De Novo Annotation Approaches , 2011, PloS one.

[33]  Thierry Leroy,et al.  Developing core collections to optimize the management and the exploitation of diversity of the coffee Coffea canephora , 2014, Genetica.

[34]  Isabelle Privat,et al.  The 'PUCE CAFE' Project: the First 15K Coffee Microarray, a New Tool for Discovering Candidate Genes correlated to Agronomic and Quality Traits , 2011, BMC Genomics.

[35]  Jayarama,et al.  The coffee genome provides insight into the convergent evolution of caffeine biosynthesis , 2014, Science.

[36]  Tanya Z. Berardini,et al.  The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools , 2011, Nucleic Acids Res..

[37]  Valentin Guignon,et al.  The Banana Genome Hub , 2013, Database J. Biol. Databases Curation.

[38]  Katja Baerenfaller,et al.  Taking the Next Step: Building an Arabidopsis Information Portal[OA] , 2012, Plant Cell.

[39]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[40]  Tae-Ho Lee,et al.  PGDD: a database of gene and genome duplication in plants , 2012, Nucleic Acids Res..

[41]  B. Mueller‐Roeber,et al.  Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity , 2010, Genome biology and evolution.

[42]  Amélie Bardil,et al.  Genomic expression dominance in the natural allopolyploid Coffea arabica is massively affected by growth temperature. , 2011, The New phytologist.

[43]  Derek Y. Chiang,et al.  MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery , 2010, Nucleic acids research.