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International Team Sequences Banana Genome

NEW YORK (GenomeWeb News) – An international team led by investigators in France has sequenced and started analyzing the draft genome for the banana species Musa acuminata.

As they reported online today in Nature, the researchers used a combination of Roche 454, Sanger, and Illumina sequencing strategies to tackle the genome of a doubled-haploid M. acuminata banana plant. From the 523 million base draft genome sequence generated, they then went on to begin exploring the plant's evolutionary history and relationships to other plants.

"The reference Musa genome sequence represents a major advance in the quest to unravel the complex genetics of this vital crop, whose breeding is particularly challenging," senior author Patrick Wincker, a researcher affiliated with Genoscope, the University of Évry, and France's National Center for Scientific Research (CNRS), and co-authors wrote, calling the draft sequence a "crucial stepping stone for genetic improvement of banana."

A good deal of interbreeding between Musa species and sub-species has occurred since banana domestication began some 7,000 years ago, Wincker and his colleagues explained. Combined with selection for plants that produce seedless fruit without fertilization, such hybridization has contributed to the development of diploid and triploid banana cultivars comprised of both M. acuminata and M. balbisiana genomes.

For the current study, researchers focused on a doubled-haploid banana accession known as Pahang that was generated by culturing a wild M. acuminata plant from the malaccensis sub-species. The wild plant's haploid genome is one of three Musa genomes found in the widely cultivated triploid banana plant called Cavendish, they explained, whose somaclones account for around half of the bananas produced at present.

Using Sanger sequencing and high-throughput shotgun sequencing with the Roche 454 GS FLX and Illumina GAIIx platforms, the team generated a draft assembly covering roughly 90 percent of the Pahang plant's genome.

Their subsequent analysis of this assembly uncovered 36,542 predicted protein-coding genes and 235 microRNAs. Also figuring prominently in the genome were transposable elements, which comprised around half of the sequence.

The researchers tracked down almost 7,700 gene clusters that are shared between Musa plants and plants from other lineages such as Arabidopsis, date palm, rice, sorghum, and Brachypodium. They also detected clusters that were specific to certain plants, including Musa-specific genes related to transcription factor function, defense, and metabolism.

The banana genome harbored sequences from a plant pest too: the double-stranded DNA virus known as banana streak virus turned up at two-dozen loci in the genome. In contrast to the banana streak viruses found in the banana species B. balbisiana, though, these viruses do not appear to have the genetic wherewithal to form independent infectious particles, researchers noted.

Pahang chromosome patterns were consistent with the notion that whole-genome duplications have occurred both within the Musa lineage and in the ancestral plants that gave rise to other plants in the same flowering plant order, known as Zingiberales.

But the group's chromosomal and phylogenetic analyses also indicate that the whole-genome duplications in Zingiberales were independent from those affecting another flowering plant order called Poales, which includes grasses, pointing to whole-genome duplications after the Zingiberales-Poales split.

Finally, the researchers' RNA sequence data offered insight into some of the transcriptional changes that accompany banana fruit ripening — a process that can be induced using the plant hormone gas ethylene. For instance, they reported, banana ripening involved a jump in the expression of genes coding for enzymes that alter the plant cell wall and a dip in the levels of starch producing enzymes.

The transcriptome information also allowed a look at some of the genes contributing to banana defense, which is another area of economic interest given the viral and fungal pests banana plants face and the pesticide treatments currently used to try to keep these pathogens in check.