Cocoa Genome Hub

Cocoa Genome Hub provides centralized access to genomic resources and reference genome sequences for Theobroma cacao L. to support genomic, comparative genomics, and genetic studies.

Key Features:

• Reference Criollo genome assembly v2: Hosts the improved Criollo assembly derived from the Belizian Criollo B97-61/B2 cultivar (version 2).
• Sequencing data integration: Assembly integrated four Illumina large insert size mate-paired libraries with Pacific Biosciences long reads at 52x coverage.
• Assembly improvements: Reduced scaffold count from 4,792 to 554 and increased scaffold N50 from 0.47 Mb to 6.5 Mb.
• Chromosomal anchoring: Achieved 96.7% of the genome anchored to the ten chromosomes compared to 66.8% in the previous version.
• Genotyping by sequencing (GBS): Used to assist chromosomal anchoring and reduce unknown sites from 10.8% to 5.7%.
• Functional and structural annotation: Provides updated functional annotations and new RefSeq structural annotations based on RNAseq evidence.
• Draft genome context: References the 2011 draft genome that covered ~76% of the estimated genome with 82% anchored to ten chromosomes.
• Gene family analysis: Documents expansions of gene families, including flavonoid-related genes.

Scientific Applications:

• Complex trait genomics: Enable exploration of complex traits at the genomic level in cacao.
• Comparative genomics and evolutionary analysis: Support comparative genomics studies and investigation of evolutionary scenarios such as chromosome fusions from an ancestral genome.
• Gene family and candidate gene identification: Facilitate identification of expanded gene families (e.g., flavonoid-related genes) and candidate genes for crop improvement.
• Genetic improvement and breeding research: Inform genetic improvement strategies for cacao breeding.

Methodology:

Genome assembly used an NGS-based approach integrating four Illumina large insert size mate-paired libraries with Pacific Biosciences long reads at 52x coverage; genotyping by sequencing (GBS) was used for anchoring and RNAseq evidence supported RefSeq structural annotations.