The strawberry genome
An international consortium of researchers, led by scientists at the Virginia Bioinformatics Institute and the Department of Horticulture at Virginia Tech, has cracked the genetic code of the woodland strawberry, Fragaria vesca.
Plant genomes can be tricky to sequence. They tend to be large, highly complex, and contain lots of repetitive DNA sequences that pose significant challenges for whole-genome sequencing. To stand a chance, researchers have to choose the right organism to work on and use state-of-the-art genome sequencing technologies.
The woodland strawberry has one of the smallest genomes of economically significant plants. With 14 chromosomes, it still comes in at a hefty 206 million base pairs (Mbp) per cell of DNA. That’s where next-generation sequencing power comes in. In January 2007, the Core Laboratory Facility at the Virginia Bioinformatics Institute (VBI) received the first-of-its-kind Roche GS-FLX next-generation genome sequencer, funded by the Virginia Commonwealth Research Initiative. Since then, the new machine has been cranking out DNA nucleotide sequences for different projects — more than 60 billion base pairs a year, including the complete sequence of the woodland strawberry genome.
“The genome sequence data will be an invaluable tool for researchers around the world looking to improve strawberry and other fruit crops through genomics,” says Vladimir Shulaev, VBI associate professor and one of the leaders of research into strawberry genetics at Virginia Tech.
The consortium of scientists who sequenced the strawberry genome is part of the Rosaceae genomics initiative (see main article). Roche Applied Sciences, the New Zealand Institute for Plant and Food Research Limited, the University of Florida, and the Institute for Advanced Learning and Research in Danville provided invaluable support for the sequencing effort. Otto Folkerts, associate director of technology development at VBI, says, “The strawberry sequencing project is a great example of a community-driven sequencing effort that has benefited from the generous contributions of a wide range of consortium participants. The availability of the Roche GS-FLX genome sequencing technology at VBI has created exciting new opportunities for collaborative whole-genome sequencing projects.”
Now that the 206 million nucleotides of the sequence are in place, the researchers are working to assemble all the data into a meaningful array of the various genetic elements that comprise a genome. Once this step is complete, the treasure trove of genetic information will help spur the next wave of research into strawberry crop improvement.
Clive Evans, associate director of the Virginia Bioinformatics Institute's Core Laboratory Facility, and Otto Folkerts, associate director of technology development at VBI, make good use of the Institute's Roche GS-FLX next-generation genome sequencer. Photo by Ivan Morozov, Virginia Bioinformatics Institute.