Loblolly pine's immense genome conquered

The massive genome sequence of the loblolly pine the most commercially important tree species in the United States and the source of most American paper products has been completed by a nationwide research team, led by a UC Davis scientist.

The draft genome approximately seven times bigger than the human genome is the largest genome sequenced to date and the most complete conifer genome sequence ever published. The sequencing was accomplished by using, for the first time, a faster and more efficient analytical process. The achievement is described in two papers in the March 2014 issue of GENETICS and in one paper in the open access journal Genome Biology.

The genome sequence will help scientists breed improved varieties of the loblolly pine, which also is being developed as a feedstock for biofuel. The newly sequenced genome also provides a better understanding of the evolution and diversity of plants.

Its a huge genome. But the challenge isnt just collecting all the sequence data. The problem is assembling that sequence into order, said David Neale, a professor of plant sciences at the University of California, Davis, who led the loblolly pine genome project and is an author on the GENETICS and Genome Biology articles.

To tackle the enormous size of the loblolly pines genome, which until recently has been an obstacle to sequencing efforts, the research team used a new method that can speed up genome assembly by compressing the raw sequence data 100-fold.

Modern genome sequencing methods make it relatively easy to read the individual letters in DNA, but only in short fragments. In the case of the loblolly, 16 billion separate fragments had to be fit back together a computational puzzle called genome assembly.

We were able to assemble the human genome, but that was close to the limit of our ability; seven times bigger was just too much, said Steven Salzberg, professor of medicine and biostatistics at Johns Hopkins University, one of the directors of the loblolly genome assembly team and an author on the papers.

The key to the solution was using a new method, developed by researchers at the University of Maryland, which pre-processes the sequence data, eliminates redundancies and yields 100 times less sequence data. This approach, tested for the first time in this study, allowed the team to assemble a much more complete genome sequence than the draft assemblies of two other conifer species reported last year.

The size of the pieces of consecutive sequence that we assembled are orders of magnitude larger than whats been previously published, said Neale, noting that the loblolly now provides a high-quality reference genome that considerably speeds along future conifer genome projects.

The loblolly genome research was conducted in an open-access manner, benefiting the research community even before the genome sequencing effort was completed and published. Data have been freely available throughout the project, with three public releases starting in June 2012.

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Loblolly pine's immense genome conquered