Low-cost assembly of a cacao crop genome is able to resolve complex heterozygous bubbles

• Published in: Horticulture research Vol. 6; no. 1; p. 44
• Main Authors: Morrissey, Joe, Stack, J. Conrad, Valls, Rebecca, Motamayor, Juan Carlos
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 06.04.2019; Oxford University Press
• Subjects: 631/208; 631/61/212; Agricultural economics; Agriculture; Assembly; Biomedical and Life Sciences; Chocolate; Crop improvement; Cultivars; Deoxyribonucleic acid; DNA; Ecology; Gene mapping; Genetic engineering; Genetics; Genomes; Heterozygosity; Hybrids; Land use; Life Sciences; Modernization; Parents; Plant breeding; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Plant Sciences; Reagents
• ISSN: 2052-7276; 2052-7276
• DOI: 10.1038/s41438-019-0125-7

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 F 1 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. A sweet solution for studying cacao genetics Genomic insights from an efficient, low-cost DNA sequencing strategy could enable more sustainable cacao cultivation. Growing demand for chocolate is currently being satisfied by increasing land use. A richer understanding of this plant’s genome could enable development of more productive strains, and Juan Carlos Motamayor and colleagues at Mars Chocolate have demonstrated a method for rapidly collecting such data. Most sequencing platforms produce vast multitudes of short DNA sequences which must then be assembled into a final map—a particular challenge for cacao, whose genome contains complex repetitive regions that are tough to reconstruct. Using a newer platform known as MinION, which produces far longer sequence reads, Motamayor’s team assembled a detailed genome map for a widely-used cacao cultivar within months for under $5,000. This approach could facilitate genetic engineering efforts to improve crop performance.