NEW YORK (GenomeWeb News) – A research team involving investigators from five continents reported online yesterday in Nature Genetics that it has sequenced a draft version of the wild strawberry genome.
The researchers used a combination of high-throughput sequencing platforms to tackle the genome of the woodland strawberry, Fragaria vesca, a perennial plant related to cultivated strawberries and to apple, peach, pear, and raspberry plants. The wild strawberry was selected, in part, because its genome is more compact than that of its domesticated counterpart.
"We achieved coverage exclusively with short-read technologies and did assembly without a physical reference, demonstrating that a contiguous plant genome sequence can be assembled and characterized using solely these technologies," senior author Kevin Folta, a plant science researcher at the University of Florida, and his co-authors wrote. "Moreover, this genome was sequenced using an open-access community model."
The team used Roche 454, Illumina, and Life Technologies' SOLiD platforms to sequence the 240 million base pair genome of a F. vesca sub-species vesca line called Hawaii 4 to 39 times coverage, on average. They then assembled strawberry sequence scaffolds into seven pseudochromosomes using Illumina sequencing to help track down SNP markers in the genome.
The researchers' analyses of the wild strawberry genome turned up 34,809 predicted protein-coding genes, including around 25,000 genes that have been preliminarily annotated so far.
They also detected 569 transfer RNAs, 76 microRNAs, numerous other RNAs, and thousands of transposable elements making up more than one-fifth of the genome.
But in contrast with other plants sequenced so far, the team noted, the strawberry genome does not show evidence of large duplication events.
"All members of the rosid clade share an ancient triplication, first documented in grape and found in all other rosid genomes, including apple," they wrote. "In strawberry, chromosome rearrangement and genome size reduction (perhaps accompanied by preferential loss of duplicated genes) may obscure the signature of the ancient triplication."
By looking at how 389 markers from the so-called "rosaceous conserved ortholog set" corresponded to the woodland strawberry genome, the researchers were also able to glean information about the shared common ancestor of Rosaceae plants. From their data so far, they concluded that plants in this family likely descended from an ancestral plant with nine chromosomes.
Finally, their comparative studies also hinted that another model organism, Populus, may be improperly classified and may be more similar to Arabidopsis and related plants than to legume plants.
Their transcriptional studies of the plant, meanwhile, which were based on complementary DNA sequences, suggest that 2,151 genes are highly expressed in the plant's root, compared with 1,753 in the fruit.
Many of the genes with elevated expression in fruit were involved in processes such as carbohydrate metabolism, and fruit, flower, and embryo-related processes, the researchers reported, while those that were especially well represented in the roots included many transcription factor, signaling, and stress response genes.
With the strawberry genome in hand, those involved in the study hope to begin using the sequence to not only learn more about plant biology, but also for improving the quality of cultivated strawberry plants and for coming up with strategies to combat pests that damage commercial strawberry crops — particularly the pathogen Verticilium dahliae, which causes a disease called strawberry wilt.
"This will accelerate research that will lead to improved crops, particularly commercial strawberries," co-author Todd Mockler, a plant molecular biologist at Oregon State University, said in a statement. "It could lead to fruit that resists pests, smells better, tolerates heat, requires less fertilizer, has a longer shelf life, tastes better or has an improved appearance."