A tale of two banana sequences

Anne Vézina Thursday, 07 November 2013

The recent publication by Belgian and Malaysian scientists of a draft Musa balbisiana genome sequence in BMC Genomics went largely unnoticed, at least compared to the media attention that surrounded last year’s publication of the Musa acuminata genome sequence. The media may have a limited appetite for banana genomics but not Musa scientists. They knew from the beginning that the so-called A genome was not the whole story. No sooner had its sequence been released that French and Chinese scientists were discussing joining forces to produce a reference sequence for the edible banana’s other founding genome, the B genome donated by Musa balbisiana, which is often associated with tolerance to abiotic stresses. It looks as if they have been beaten to the finish line, but the fact is that the two scientific teams were pursuing different strategies.

Image Both teams used a genebank accession called Pisang Klutuk Wulung (PKW), characterized by a black pseudostem. But while the Belgian-Malaysian team extracted the DNA directly from plantlets obtained from the ITC, the French-Chinese team extracted the DNA from a doubled haploid (DH) PKW plant produced by scientists at the French Agricultural Research Centre for Development (CIRAD).

When sequencing the first genome of a species, scientists often use a homozygous derivative (a doubled haploid) to facilitate the assembling of the reference sequence. By doing so, however, they forego capturing allelic diversity (the alternative forms – alleles – of the same gene). This typically comes later during resequencing efforts that compare closely related genomes to the reference one, which is how the draft balbisiana sequence was obtained. The Belgian-Malaysian scientists used the acuminata reference sequence generated from DH Pahang as a template onto which they aligned their fragments of balbisiana DNA.

In addition to predicting 36,638 genes, the scientists found more than 18 million SNPs (DNA markers that have a single nucleotide difference between individuals), which by definition cannot be detected in DH plants. They also looked for microRNA (small non-coding RNA molecule that are encoded by DNA and play a role in the regulation of gene expression) and found new microRNA families, some of which are unique to the B genome. All the sequence data have been uploaded to The Banana Genome Hub where they are available for browsing and downloading by the scientific community to further annotate and investigate.

Meanwhile, the French-Chinese team is continuing its work on the reference sequence which will go one step further and position the genes on the balbisiana chromosomes by using the genetic map being developed by CIRAD scientists as part of RTB’s genotyping activities. Knowing where the genes and transposable elements are located on the chromosomes is important in understanding how the B genome is organized and to what extent it is structurally similar to the A genome.

The balbisiana reference sequence anchored to the species’ 11 chromosomes is being produced by the CATAS’ Institute of Tropical Bioscience and Biotechnology in collaboration with the Beijing Genomics Institute and CIRAD, in the framework of the Global Musa Genomics Consortium.

The draft balbisiana sequence is the result of a collaboration between KU Leuven’s Laboratory of Fruit Breeding and Biotechnology and the University of Malaya’s Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences.