Coffee tree genome sequenced

November 5, 2014, Institut de Recherche pour le Développement (IRD)
Coffea canephora. Credit: IRD / G. Villegier

In the study published in Science, the researchers were interested in Robusta coffee because of its average sized genome (710 million pairs of DNA bases) and its diploid nature (contrary to Coffea arabica, which is tetraploid). The genetic map of the coffee tree studied, produced in the 1980s by IRD in Cote d'Ivoire, also had the advantage of being a homozygous plant (two identical sets of eleven chromosomes), which is easier to analyse than natural heterozygotes.

By using several sequencing technologies, Genoscope (CEA) coordinated the mapping of the DNA sequence for the coffee tree, assembled in large fragments able to be used in various types of analysis. The IRD and CIRAD teams then anchored these sequence fragments to a high-density genetic card to reconstruct the pseudo-chromosomes. A catalogue of genes and repeated sequences was then created and validated, allowing for a comparison with other plants.

A critical stage

Thus, the researchers established a reference sequence for coffee trees (including for the species Coffea arabica), and more generally for the Rubiaceae, one of the largest families of flowering plants (containing nearly 12,500 species).

A of genomes by the international consortium also revealed that the organisation of the coffee tree genome is best preserved in the Asteridae (the family to which potatoes and tomatoes belong) and is very close to that of the ancestral species from which all true Dicotyledons (or Eudicotyledons) descended through evolution. Lastly, the study of the genome improves knowledge of the secondary metabolism of plants and its diversification. A comparative analysis with the cacao tree genome also shows that the biosynthesis of caffeine is due to enzymes unique to each species, which appeared at various moments in their evolution.

Over the longer term, the identification of the coffee tree genome sequence opens up new possibilities for varietal improvement, knowledge of the specific functions of the genes (in particular those specific to coffee trees), the possibility of transferring results to other species, and refining diagnostic tools for the function of the plant.

It will facilitate the completion of applied projects, such as the selection or creation of coffee tree varieties with improved technological and/or qualitative characteristics; more resistant to environmental constraints and to bioagressors, such as for example orange leaf rust. In fact, this disease still has a considerable impact on coffee cultivation and the economy of small producer countries in Central America such as Guatemala, Honduras, and Costa Rica. Lastly, it should help guide producers toward ecologically intensive agriculture.

Explore further: Coffee genome sheds light on the evolution of caffeine

More information: F. Denoeud et al. "The Coffee Genome Provides Insight into Convergent Evolution of Caffeine Biosynthesis," Science, 5 Sept 2014.

Related Stories

New genetic variants associated with coffee drinking

October 7, 2014

A new, large-scale study has identified six new genetic variants associated with habitual coffee drinking. The genome-wide meta-analysis, led by Harvard School of Public Health and Brigham and Women's Hospital researchers, ...

Researchers complete genome sequencing of the Jujube tree

October 29, 2014

BGI Tech and Hebei Agricultural University jointly announced the complete, high quality sequencing of the Jujube genome. Jujube is the most economically important member of the Rhamnaceae family, and the Jujube genome is ...

Blame coffee farm rust fungus for rising coffee prices

September 30, 2014

Wonder why that cup o' joe is so expensive? The culprit, says ecologist Ivette Perfecto of the University of Michigan, is a fungus sweeping through coffee plantations in Mexico and Central America, limiting coffee production ...

Recommended for you

Study suggests trees are crucial to the future of our cities

March 25, 2019

The shade of a single tree can provide welcome relief from the hot summer sun. But when that single tree is part of a small forest, it creates a profound cooling effect. According to a study published today in the Proceedings ...

Matter waves and quantum splinters

March 25, 2019

Physicists in the United States, Austria and Brazil have shown that shaking ultracold Bose-Einstein condensates (BECs) can cause them to either divide into uniform segments or shatter into unpredictable splinters, depending ...

Apple pivot led by star-packed video service

March 25, 2019

With Hollywood stars galore, Apple unveiled its streaming video plans Monday along with news and game subscription offerings as part of an effort to shift its focus to digital content and services to break free of its reliance ...


Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.