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Genome Yields Clues to Polyploidization Effects in Canola Plants

NEW YORK (GenomeWeb) – An international team led by investigators in Australia, China, Canada, France, and the US has sequenced and started analyzing the genome of the canola plant Brassica napus, an oilseed source descended from a hybridization event between B. rapa and B. oleracea plants that occurred some 7,500 years ago.

As they reported today in Science, the researchers used a combination of Sanger, Roche 454, and Illumina HiSeq approaches to tackle the 1.13-billion-base genome of the B. napus cultivar called Darmor-bzh. By examining the resulting assembly, which spanned almost 80 percent of the genome, they got a look at the gene content, functional capabilities, and expression patterns associated with the B. rapa- and B. oleracea-related sub-genomes that make up B. napus' allopolyploid genome.

The new genome assembly and related resources are expected to offer "unique perspectives on the early evolution of a domesticated polyploid and will facilitate the manipulation of useful variation, contributing to sustainable increases in oilseed crop production to meet growing demands for both edible and biofuel oils," the researchers wrote.

Canola is a widely cultivated oilseed plant domesticated during the Middle Ages in Europe. Through diversifying selection, the study's authors explained, related plants such as kale and rutabaga have become specialized for growing other food and fodder sources.

For the current study, the team used a combination of genome mapping, sequencing, and assembly approaches to put together the canola plant's allopolyploid genome, which is composed of sub-genomes that resemble sequence from the Asian cabbage/turnip B. rapa and the Mediterranean cabbage B. oleracea.

After generating long Roche 454 GS FLX+ and Sanger reads, together with shorter Illumina HiSeq reads, for example, the researchers put together a 849.7-million-base canola genome assembly that was anchored using SNP maps and assigned to the so-called An or Cn sub-genomes with the help of sequences from the parental plant species.

Those sub-genome assemblies differed in both their size and gene content, the team noted, with the B. oleracea-related Cn sub-genome spanning almost 526 million bases and the B. rapa-related An sub-genome made up of just over 314 million bases.

In both sub-genomes, the team saw expansions to gene sets involved in lipid production relative to B. rapa and B. oleracea progenitor plants, though a few lipid-related genes appear to have been deleted or experienced gene conversions in the canola sub-genomes.

Selective pressures applied to canola since its domestication seem to have diminished the plant's production of nutritionally unappealing compounds such as sulfur-laden plant defense metabolites known as glucosinolates, the researchers reported, while boosting lipid composition and oil content in seeds.

By folding in RNA sequencing data for B. napus, the team identified more than 101,000 gene models in the plant, along with tissue-specific expression patterns and alternative splicing profiles.

Comparisons between the canola genome and those of several other sequenced plant species highlighted the rampant genome duplication that characterizes the newly-sequenced oilseed, which has a genome that's undergone an estimated 72 genome multiplications in its evolutionary history, according to the study's authors.

Finally, the team's analysis revealed a range of homologous sequence exchanges between the canola sub-genomes, which seem to have contributed to some diversification and restructuring of these component sequences and the advent of new features and functional adaptations.

"Human cultivation and breeding of B. napus morphotypes may have selected favorable [homologous exchanges], causing sub-genome restructuring of regions containing genes controlling valuable agronomic traits," the study's authors explained.

"Because B. napus is a young allopolyploid beginning gene loss and genome reorganization, further partitioning of expression may become a key determinant for the long-term preservation of its duplicated genes," they concluded.