Under the peel

Under the peel is the blog of the ProMusa community. The views expressed are those of the authors. Non-registered users can post comments, but only registered ones can post blog items. When logged in, click on the pencil+ icon to start a post. We welcome contributions in French or Spanish. If you need help, contact the InfoMus@ editor at infomusa@promusa.org.

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.

The 'best genomics Venn diagram ever' deconstructed

Anne Vézina Sunday, 15 July 2012

It didn’t take long after the journal Nature put online the article on the banana genome sequence for bloggers to start commenting on the Venn diagram featuring a a bright yellow banana. David Ng at Popperfont qualified it as, “quite possibly the most complicated (and therefore awesome) Venn Diagram ever”. Jonathan Eisen, the scientist who coined the term phylogenomics, said that it was “perhaps the best genomics Venn diagram ever”, while Joe, of the It’s okay to be smart blog wrote that it is “a pretty genius way of delivering a bunch of banana data all at once”. He added that it was the first time he ever saw a six-way Venn diagram. Joe is right to be impressed, but the truth is that this is not the first ever six-way Venn diagram.

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Breeding superior cooking bananas

Jim Lorenzen Tuesday, 03 July 2012

Banana breeders are familiar with the routine of climbing a ladder in the early morning to collect male flowers and carrying them, and the ladder, over to the intended female plants to hand-pollinate female flowers. Since flowers open sequentially each day, each floral bunch is pollinated daily for a week. You could say that banana breeders serve as surrogates to natural pollinators, in this case bats.

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Blogging your way out of anonymity

Inge Van den Bergh Wednesday, 23 May 2012

There are some notable exceptions, but most scientists only exploit one way to share their research results: they publish a paper in a scientific journal. And these papers often tend to be … well, let’s admit it … quite dry, as Adam Ruben recently described it in his blog post about “How to write like a scientist”. Aside from the occasional presentation at a scientific conference (which, unless the scientist is an especially good speaker or presents ground-breaking results, are usually readily forgotten), most of us don’t take advantage of the wide range of other media that are available these days, such as videos, status updates, blog posts, blog comments, interactive graphs and maps, tweets, etc.

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Remembering the world's most famous banana scientist

Anne Vézina Friday, 11 May 2012

I never met Norman Simmonds, on whom I recently did a page in Musapedia. He died six months before I joined INIBAP in July 2002. Prior to doing a page on him I was glad he had shared so much of his vast knowledge of bananas (I keep my copies of Bananas and The Evolution of the Bananas at arm’s length since they are the first things I check whenever I am looking for information on bananas, even though new data have since poked holes in some of his hypotheses, like his account of domestication). But having read what people said about him after his death, at 79, I now regret having narrowly missed the opportunity to pick his brains (he apparently remained active right until his last weeks). I can only imagine how intimidating it would have been. He is said to have refused an entry in Who’s Who because their letter to him was sloppily written.

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World Banana Forum: getting down to business

Alistair Smith Tuesday, 20 March 2012

Some 200 people took part in the second global conference of the World Banana Forum in Guayaquil, business capital of Ecuador, at the end of February. International fruit companies, national producers, small farmers' organisations, trade unions of plantation workers, retailers, government representatives, scientists, certification bodies and NGOs met around an agenda for change in the industry that had been set 2 years earlier in Rome at the launch of the Forum.

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Student farm bananas, update

Gabriel Sachter-Smith Wednesday, 23 November 2011

Things are going well! We have our first two plants flowering after only 7 months in the ground. This recent photo was taken at about 8 months after planting. It is gaining a lot of attention on our campus, and we already started to expand it, and will be adding even more soon as well.

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Banana scientists gather in Brazil for the fourth ISHS-ProMusa symposium

Inge Van den Bergh Wednesday, 02 November 2011

The first ISHS-ProMusa symposium ended with Richard Markham, then chair of the ISHS Section on Banana and Plantain, reminding participants “of our limited success over the past 20 years in providing workable solutions to the major crop protection problems of farmers”. We all know what these are: leaf spot diseases, Fusarium wilt, bacterial wilts, viruses, nematodes and weevils. This fourth symposium, hosted by Embrapa, similarly provided sobering accounts of the challenges scientists still face in addressing these problems. And rightly so. We should not underestimate the scale of the task at hand. But symposia also play a non-negligible role in lifting our spirits by reminding us that the steady progress of science is also punctuated by the occasional leap.

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