The road to sequencing the banana genome

Anne Vézina Monday, 06 August 2012

The recent news that the banana genome had been sequenced and published in Nature is said to have had “scientists breaking out the banana daiquiris.” My guess is that they more likely reached for their computer to download the sequence, but the point is the same. If ever a crop needed help from genomics research, it is the difficult-to-breed-and-to-study-using-classical-genetics banana. It also explains the early interest in sequencing its genome.

Plans to sequence the banana genome started taking shape in 2001, when Bioversity International brought together a group of scientists to form the Global Musa Genomics Consortium. At the time, the only plant whose genome had been sequenced was Arabidopsis, with rice close behind. It seemed only fitting that the banana should ride the next wave of sequencing. As the then coordinator of the Consortium told Nature, research on banana was lagging behind, compared to better-funded crops, and genomics represented the best opportunity to rapidly make up for the backlog.

Fortunately, the sequence was not necessary to begin catching up. One of the first things the Consortium did is set up a website and a distribution arm, the Musa Genome Resource Centre, for the genomics resources developed by its members; things like BAC and cDNA libraries. Starting in 2005, it is invited to organize an annual Musa genomics workshop at the Plant and Animal Genome conference, during which scientists present their latest findings and discuss opportunities and challenges. Online tools are also developed to manage the mass of data generated by genomics projects.

Despite the progress, funding to sequence the genome remained elusive until 2008 when a workshop on the project is held at the U.S. Department of Energy’s Joint Genome Institute (JGI) in January of that year. This is where the deputy director of the French sequencing centre Genoscope announces that his institute would produce a sequence covering the genome four times over, using the reliable but expensive Sanger technology, if another centre did the other half to achieve the desired 8x coverage. JGI was interested in being that partner but the DoE, which had final say, passed on the banana in favour of species that were considered a better fit to investigate alternative fuels and bioremediation.

The plan looked as if it would unravel, but thanks to funding from the French National Research Agency, Genoscope later announced that it would sequence the whole genome with CIRAD. In the meantime, cheaper and faster next-generation sequencing techniques had become available and had been added to the original plan to increase the coverage. The strategy allowed the scientists to produce a high-quality reference sequence in two years.

For the journal article that followed, several collaborators, including Bioversity bioinformaticians, were brought in to provide additional analyses. When the Nature paper was put online, a new version of GreenPhyl, a platform that uses phylogenomics to predict the function of a gene based on its relationship with a gene of known function in another species, was released with the banana genome in it. Originally developed by CIRAD, the platform was expanded by Bioversity to its current collection of 22 genomes spanning the plant kingdom, including the cassava one.

As for celebrations, at least one group of people took a break to mark the occasion. They didn’t break out the banana daiquiris, but they did pop champagne corks. You guessed it. The revellers were the French scientists to whom we owe this achievement.