An international research consortium including researchers from the University of Helsinki and Nanyang Technological University in Singapore has compiled the genome of three coffee species from DNA sequences of coffee plant leaf cells. The genome of Arabica, or Coffea arabica, was assembled in Singapore and Helsinki, and those of Robusta (C. canephora) and C. eugenioides were assemled at Cornell University in the United States.
“The aim is to find traits that improve yield and quality. Cultivated Arabica is less genetically diverse, and therefore more susceptible to disease,” says Salojärvi, an assistant professor at Nanyang Technological University.
Salojärvi holds positions both at Nanyang Technological University and the University of Helsinki. The very broad and international research team makes extensive use of computational resources and databases in both countries.
Establishing a chromosome-level assembly required also the determination of the three-dimensional structure of the chromosomes. The computing resources of the CSC– IT Center for Science, the Finnish ELIXIR Node, were used for this task. In the process the contiguous coffee genome sequences assembled in earlier steps were combined into chromosome-length scaffolds.
“This process means that a chromosome is made up of fully sequenced fragments and empty spaces in between. Among other things, the structural analysis will reveal the connection with genes and the regions of the genome that regulate them.”
All three coffee genomes have been shared via EBI/NCBI. Additionally, these annotations have been made accessible via ORCAE, a database with tools to further work on the gene structures, and containing annotations of diverse eukaryote genomes. It is operated by the Belgian ELIXIR Node.
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ELIXIR is partly funded by the European Commission