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The cocoa genome hub, an integrated platform to access the Criollo genome V2

Argout X., Martin G., Droc G.. 2017. In : Booklet of abstracts of the first International Symposium on Cocoa Research ISCR 2017. Lima : ICCO, p. 214-215. International Symposium on Cocoa Research ¿ ISCR 2017 : Promoting Advances in Research to Enhance the Profitability of Cocoa Farming. 1, 2017-11-13/2017-11-17, Lima (Pérou).

The first draft genome of the species, from the Belizian Criollo B97-61/B2 cultivar, was published in 2011. Although a useful resource, some improvements were possible, including to identify misassemblies, to reduce the number of scaffolds and gaps, and to anchor un-anchored sequences to the 10 chromosomes. In 2017, we used a combination Next Generation Sequencing data to produce the version 2 of the assembly. We corrected misassembled regions and reduced the number of scaffolds from 4,792 in assembly V1 to 554 in V2 with a N50 increased from 0.47 Mb in V1 to 6.5 Mb in V2. A total of 96.7% of the assembly was anchored to the 10 chromosomes compared to 66.8% in the previous version. Unknown sites (Ns) were reduced from 10.8% to 5.7%. In addition, we updated the functional annotations and performed a new RefSeq structural annotation based on RNAseq evidence. In that context and to support post-genomics efforts, we developed the Cocoa Genome Hub (http://cocoagenome- hub.southgreen.fr/), an integrated web-based database providing centralized access to T. cacao genome and analysis tools to facilitate basic, translational and applied research in cocoa. We provide access to the complete criollo genome sequence V2 along with gene structure, gene product information, metabolism, gene families, transcriptomics (ESTs, RNA-Seq), 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.

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