A listing and summary of the major cacao genome resource websites. Thanks to Andrew Fister for this analysis.

Cacao Criollo Genome V2 @ CIRAD France
Criollo Genome Assembly V2 @NCBI
Criollo Genome Database V1

Genome of genotype B97-61/B2. Has GBrowse, BLAST, Primer BLAST, Interpro Domain Search. Accesses genome sequence data, sequencing of transcript libraries to support gene models, EST libraries from ESTtik.

Forastero Genome Database

Genome of genotype Matina 1-6. Current version is 1.1 Has GBrowse, BLAST. Accesses genome sequence, sequencing of transcript libraries. Not all tracks are available for version 1.1 data (i.e. transcript libraries, protein similarity)

Plant Antisense Transcripts Database

Contains data on small RNA abundance in cacao more than 70 other plant species. Can use GO annotation and network analysis to examine small RNA function. Data source is TcaGI Release 3.0 (2009)

Plaza Comparative Genomics (Cacao page)

Broad tool for comparative plant genomics. Allows gene family identification within and between species. Synteny mapping tool, whole genome dotplot, functional gene classification through GO annotations and Interpro information. Data source is Phytozome 9.1 (Matina v1.1)

NCBI Cacao Genome Assembly Database

Repository of Criollo genome sequencing data.

EnsemblPlants (cacao page)

Access to data from Matina 1-6 sequencing project. Can download nucleotide and protein alignments with other plant species.

Plant Resistance Gene Wiki

Currently contains list of 153 R genes. List has not yet been updated, very few have structural classifications predicted. Data sources are UniGene (references to ESTtik) and NCBI.

Phytozome (cacao page)

Data source is Matina 1-6 project. Contains description of genome and assembly, and allows downloading of gene models. Allows multispecies BLAST searches.

Plant Genome Duplication Database

Enables locus searches and synteny plots to identify gene duplication products within and between species. Data source is B97-61/B2.

VISTA Tools for Comparative Genomics (cacao page)

Synteny plotting tools for cacao and ~20 other species. Data source is Matina 1-6.

Plant Methylome db (cacao page)
Center for Innovation of Cacao, Peru, Germplasm Database
The Gene Ontology (GO) Panther

THE GENE ONTOLOGY RESOURCE The mission of the GO Consortium is to develop a comprehensive, computational model of biological systems, ranging from the molecular to the organism level, across the multiplicity of species in the tree of life. The Gene Ontology (GO) knowledgebase is the world’s largest source of information on the functions of genes. This knowledge is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research. This site contains cacao data.

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