The Coffee Flavor Mystery 

Last week, one of the most feared moments in an office morning happened: there was something wrong with the coffee. Several colleagues noticed an off-taste that defies all description; nearest comes a bit of coconut and a blend of mint. Hesitation, doubts, ughs, and people turned into brave tasters and thorough detectives.

Very different coffee flavor profiles in spite of low genetic variation

As we chattered about the source for this coffee “flavor”, a Nature Communications study shed light on the genetic basis of the very different flavor notes of the most commonly sold coffee variety Arabica. In "All arabica coffee is genetically similar: how can beans taste so different?", the researchers around Michele Morgante published the most complete genome sequence of the arabica cultivar yet, accessing previously unexplored genomic regions.

The whole genome sequence was compared between 174 arabica varieties, and the researchers confirmed the previously reported low genetic variation that leaves the reasons unknown for the variation in disease resistances and the markedly different flavor profiles that coffee connoisseurs can easily taste. This is because the species Coffea arabica is considered relatively young, deriving from a rather fixed genetic makeup of a single plant only 50,000 years ago (a hybrid between the other success variety robusta and a not widely cultivated species Coffea eugenioides). But the new study now revealed evidence of substantial chromosomal rearrangements: for example, deletions in which large parts of chromosomes are entirely missing, genes being present in multiple copies, and even instances in which entire chromosomes were absent.

Uncovering hidden genomic variations

The study underscores the importance of investigating broader genetic variation to gain deeper insights into plant traits.

The complete coffee genome can now open the door for genotyping long and complex variants even from short read sequencing data, facilitating fine mapping of traits and the development of novel markers or gene editing targets. At Computomics, we believe in the transformative power of latest sequencing technology to generate whole genome sequences - and to compare them in a Pangenome to explore variation beyond what is commonly looked at. Our interactive pangenome graph browser Pantograph visually and interactively supports such analyses. Pantograph comprehensively combines public and proprietary assemblies, long and short read sequencing data, markers, multiple gene annotations, gene expression data, QTLs, and phenotypic data into a genomics discovery and trait knowledge co-pilot.

Pantograph, our interactive pangenome graph browser

So - whether it's coffee, or any other plant you wish to investigate - reach out to Jörg Hagmann for more information on how our platform can propel your research forward!

Dr. Jörg Hagmann, Product Manager Pantograph

By the way, the off-taste of our morning coffee remained as mysterious as the true genetic basis of coffee flavor — so far. In any case, we will get a new coffee machine.

 
Title photo by Rodrigo Flores on Unsplash