Publications des agents du Cirad


The Banana Genome Hub : [W079]

Droc G., Larivière D., Guignon V., Yahiaoui N., This D., Garsmeur O., Dereeper A., Hamelin C., Argout X., Dufayard J.F., Lengellé J., Baurens F.C., Cenci A., Pitollat B., D'Hont A., Ruiz M., Rouard M., Bocs S.. 2014. In : Plant and Animal Genomes Conference XXII Conference, San diego, United States, San Diego, United States, January 11-15, 2014. s.l. : s.n.. Plant and Animal Genome Conference. 22, 2014-01-11/2014-01-15, San Diego (Etats-Unis).

The banana (Musa acuminata DH Pahang) reference genome sequence was released. To support postsequencing efforts, an integrative genome information system, accessible through the South Green Bioinformatics Platform, was articulated around a Community Annotation System. Our strategy was to exploit, whenever possible, generic software (e.g. GMOD tools) interconnected to establish a reliable framework. It is composed as follow. A core comprises a relational database connected to a genome browser with an advanced search and an annotation editor. A controller allows access restriction, annotation quality and history. Authenticated curators can thus improve the automatic annotation of genes and transposable elements. A gene report allows quick search and fosters interoperability with other South Green tools that manage molecular makers,genetic maps, gene families, ESTs, SNPs, metabolic pathways and cross-genome syntenic dotplots; and give access to sequence analysis workflows. Thus, the Banana Genome Hub (BGH) aggregates various information systems and projects like the sequencing of the genome, in order to provide a unified access, which in turn encourages the integration of new tools. It can sustain re-sequencing efforts as recently done for the Musa balbisiana PKW. We described use cases that illustrate the use of the BGH to retrieve data, benefit from pre-computed analyses, edit incorrect predictions, update analyses in order to refine the gene evolutionary history and the polypeptide function and finally to help to solve issues of agronomic interest. Since the BGH launch mid- 2012, about 728 out of 36,542 genes were manually curated. Training on Musa bioinformatics was done in November 2013.

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