Abstract
Cacao (Theobroma cacao) is a tropical tree that produces the essential raw material for chocolate. Because yields have been stagnant, land use has expanded to provide for increasing chocolate demand. Assembled genomes of key parents could modernize breeding programs in the remote and under-resourced locations where cacao is grown. The MinION, a long read sequencer that runs off of a laptop computer, has the potential to facilitate the assembly of the complex genomes of high-yielding F1 hybrids. Here, we validate the MinION’s application to heterozygous crops by creating a de novo genome assembly of a key parent in breeding programs, the clone Pound 7. Our MinION-only assembly was 20% larger than the latest released cacao genome, with 10-fold greater contiguity, and the resolution of complex heterozygosity and repetitive elements. Polishing with Illumina short reads brought the predicted completeness of our assembly to similar levels to the previously released cacao genome assemblies. In contrast to previous cacao genome projects, our assembly required only a small scientific team and limited reagents. Our sequencing and assembly methods could easily be adopted by under-resourced breeding programs, speeding crop improvement in the developing world.
Highlights
Cacao is a diploid tree that produces the raw material for the chocolate industry, and is grown primarily in the tropics of West Africa, Southeast Asia, and South and Central America
We present a highly contiguous, and high-quality genome assembly for the Pound 7 cacao clone
To better test if the MinION would function in remote cacao breeding sites, the DNA preparation was simplified as much as possible
Summary
Cacao is a diploid tree that produces the raw material for the chocolate industry, and is grown primarily in the tropics of West Africa, Southeast Asia, and South and Central America. While recent production levels have increased, this has come from expansion of the land devoted to cacao. In contrast, has stagnated (Fig. 1a, b). The killing of fragile tropical ecosystems to expanded cacao production could be prevented by modernizing under-resourced breeding programs in the developing world using genomics technologies, improving yields on existing farms. Genomic approaches are readily utilized to advance breeding programs in staple crops[1], and can even impact the production of tropical commodities like oil palm[2].
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