UB participates in coffee plant genome sequencing and analysis

Julio Rozas, professor from the Department of Genetics of the Faculty of Biology at UB and ICREA Academia researcher, and Pablo Lirando, UB postdoctoral researcher, have participated in the analysis of coffee DNA sequences as members of the international research team led by the Institute of Research for Development (IRD, France), the National Sequencing Center (CEA-Genoscope, France) and the University at Buffalo (United States).

Coffee is the principal agricultural product of many tropical countries. According to estimates by the International Coffee Organization, more than 8.7 million tons of coffee was produced in 2013, revenue from exports amounted to $15.4 billion in 2009-2010, and the sector employed nearly 26 million people in 52 countries during 2010.

“Coffee is as important to everyday early risers as it is to the global economy. Accordingly, a genome sequence could be a significant step toward improving coffee”, said Philippe Lashermes, researcher at IRD. “By looking at the coffee genome and genes specific to coffee, we were able to draw some conclusions about what makes coffee special”, he pointed out.

Software developed at UB

The research team created a high-quality draft of the genome of Coffea canephora, which accounts for about 30% of the worldʼs coffee production. Then, scientists looked at how coffeeʼs genetic make-up is distinct from other species.

In order to carry out this analysis, UB researchers created and used a piece of biosoftware named BadiRate. It enables to analyse gene gains and losses throughout evolution. “We have used BadiRate to determine the type of genes that have significantly increased the number of duplications in coffee lineage. The types of genes that have expanded in coffee lineage are potential candidates to understand the particularities and the molecular evolution of the species”, explains Pablo Lirando, member of the Molecular Evolutionary Genetics Group of UB.

Caffeine does not have a common ancestor

Victor Albert, professor from the University at Buffalo, affirmed: “By looking at which families of genes expanded in the plant, and the relationship between the genome structure of coffee and other species, we were able to learn about coffeeʼs independent pathway in evolution, including the story of caffeine”.

Compared to several other plant species including grape and tomato, coffee harbours larger families of genes that relate to the production of alkaloid and flavonoid compounds, which contribute to qualities such as coffee aroma and bitterness.

Coffeeʼs genome structure is different from other plant families

The new study provides the opportunity to better understand the evolution of coffeeʼs genome structure. “It turns out that, over evolutionary time, coffee genome wasnʼt triplicated as in its relatives: tomato and chilli pepper. Instead it maintained a structure similar to grapes”, said Patrick Winker, researcher at CEA-Genoscope. “As such —he added—, evolutionary diversification of coffee genome was likely more driven by duplications in particular gene families as opposed to when all genes in the genome duplicate”. 

This stands in contrast to what has been suggested for several other large plant, where other investigators have noted correlations between high species diversity in a group and the presence of whole genome doublings or triplings.“Coffee lies in the plant family Rubiaceae, which has about 13,000 species and is the worldʼs fourth largest; thus, with no genome duplication at its root, it appears to break the mold of a genome duplication link to high biodiversity”, concludes France Denoeud, researcher at CEA-Genoscope.