Banana Genome Hub
Gaëtan Droc1†*, Delphine Larivière1,2†, Valentin Guignon3, Nabila Yahiaoui1, Dominique This2, Olivier Garsmeur1, Alexis Dereeper4, Chantal Hamelin1, Xavier Argout1, Jean-François Dufayard1, Juliette Lengelle1‡,
Franc-Christophe Baurens1, Alberto Cenci3, Bertrand Pitollat1, Angélique D’Hont1, Manuel Ruiz1, Mathieu Rouard3, Stéphanie Bocs1
(1) CIRAD, UMR AGAP, F-34398 Montpellier, France. (2) Montpellier SupAgro, UMR AGAP, F-34060 Montpellier, France. (3) Bioversity International, Commodity systems & genetic resources programme, F-34397 Montpellier, France.
(4) IRD, UMR RPB, F-34394 Montpellier, France. *Correspondence: gaetan.droc@cirad.fr
†Contributed equally. ‡Present address: Université de Toulouse UPS, UMR5546, F-31326 Castanet-Tolosan, France.
http://banana-genome.cirad.fr/
(1) A. D'Hont et al., The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature, 488:213, 2012. (2) G. Droc et al., The Banana Genome Hub. Database: the journal of biological databases and curation, 2013, Submitted revision (manuscript ID DATABASE-2012-0102.R1). BGH is supported by South Green Bioinformatics Platform http://southgreen.cirad.fr/
Hub Components
bio mart
Metabolic Pathways
Gene
Families AnnotationEditor
Genomic Workflow manager
Query Builder Web Front End & Feature Report Community Annotation System Banana Genome Browser Transcriptome Analysis Rice Browser Map Comparison Macrosynteny Karyotype Synteny Dotplot Banana is one of the world’s favorite fruits and one of the
most important crops for
deve-loping countries. The banana
refe-rence genome sequence (Musa acuminata) was recently released (1). To support genome studies, we developed a hub (2) that enhances inte-r o p e inte-r a b i l i t y between informa-tion systems contai-ning genomics data on banana. Such hub is generic and is being extended to other species (Cacao, Coffee). Musa paralogous regions coloured according to ancestral blocks
Annotation System
The sequence is analysed with pipelines predicting genes & repetitive elements. Results are structured with the Sequence Ontology & controlled vocabularies & formatted in GFF3 before insertion into Chado and GBrowse databases using Perl loaders.
Hub Achitecture
Gene reports are accessible via Tripal, GBrowse, BioMart. Polypeptides
are analyzed with GreenPhylDB, Galaxy, MusaCyc, OryGenesDB. Genetic markers with CMAP & TropGeneDB linked to the Musa Germplasm
Infor-mation System (MGIS). SNiPlay is dedicated to SNPs.
GMOD Component SouthGreen Component
Other Information System Data interoperability Data Source Data Transfert GBrowse2 Artemis Galaxy Metabolic Pathway SNiPlay Tripal Gene Report CMAP TropGeneDB MGIS ITC Genebank BioMart ESTtik GreenPhyl Advanced Search PGDD SAM Pathway Tool Flat File ChadoController PGDD CMAP GBrowse MySQL BioMart Chado Tripal PostGreSQL chromosome fasta fasta gff3 gff3 repeat_region gff3 repeat_region LTR_retrotransposon target_site_duplication RR_tract gene mRNA polypeptide CDS exon protein_match match RepeatMasker Censor LTRHarvest tBlastX Blastn Mreps TRF FGenesH SNAP Genewise GeneId G-Mo.R-Se Est2genome GAZE fasta BlastP InterProScan gff3 product functional_completeness gene evidence evidence_code EC_number status REPET-TEannot gff3 rpt_label rpt_completeness rpt_family rpt_superfamily rpt_type rpt_order rpt_class status Controlled vocabulary Program Combiner MySQL Gbrowse Sequence Ontology File format Database model PostGreSQL Chado
(3) V. Guignon et al., Chado Controller: advanced annotation management with a community annotation system. Bioinformatics, 28:1054, 2012.
Artemis
The annotation tool is linked to the Chado database. It allows the manual curation and, for authorized users, the
update of the DB. unctionnal annota-tion uses controled vocabulary.The cura-tion is tracked by
ins-pection of all the modifications that are historized (3).
Galaxy
Sequences can be
imported directly into Galaxy from the
Advanced Search or GreenPhylDB.
obsolete
