Loblolly Pine Genome Is 7 Times Bigger Than Human Genome

By Shweta Iyer on March 20, 2014 1:04 PM EDT

loblolly pine
The loblolly pine -- whose genome is the largest ever sequenced -- is the most commercially important tree species in the United States and the source of most American paper products. (Photo: Ron Billings/Texas A&M Forest )

The genetic sequence of the second most common species of tree in the United States - the loblolly pine - was recently completed by an all-American research team headed by a University of California, Davis (UC Davis) scientist.  The loblolly pine is commercially important and is used for pulpwood and timber. Understanding the tree's genome will help scientists grow more resistant and improved varieties of pine.

The loblolly conifer genome was a challenge to sequence due to its massive size and complexity. But the scientists completed the sequencing by using a fast and sophisticated technology. The draft genome of the tree was about seven times bigger than the human genome and the largest genome to be sequenced till date. It is also the most complete conifer genome sequence ever published. The research has been published this month in Genetics and Genome Biology.

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"It's a huge genome. But the challenge isn't just collecting all the sequence data. The problem is assembling that sequence into order," said David Neale, a professor of plant sciences at the UC Davis and the main researcher of this project, according to a press release Thursday.

To effectively sequence the loblolly's massive genome, the team used a new method that can speed up genome assembly by compressing the raw sequence data by 100 times. Present day genome sequencing tools easily decipher the DNA but do so in short fragments. The loblolly had 16 billion separate fragments, which had to be sequenced and then put back together in a process 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, a coauthor on the papers.

This problem was solved when the scientists used the 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 method was used here for the first time and allowed the scientists to assemble a much more complete genome sequence, than had been attempted before.

"The size of the pieces of consecutive sequence that we assembled are orders of magnitude larger than what's been previously published," said Neale. This sequence can be now used as a high quality "reference" genome to facilitate genome sequencing in other conifers.

The new sequencing confirmed that 82 percent of the loblolly genome is made up of invasive DNA elements and other DNA fragments that copied themselves around the genome. The sequencing also highlighted the location of genes that may be involved in disease resistance. For example, researchers from the Forest Service Southern Institute for Forest Genetics, identified an important candidate gene for resistance to fusiform rust, that causes untold damage to southern pines.

Understanding the genetic resistance in plants can be of huge benefit to scientists and forest managers who can select trees with an inherent resistance to pathogens.

"The fusiform rust mapping that our scientists did as part of this project provides significant information for land managers, since more than 500 million loblolly pine seedlings with these resistance genes are planted every year. The group selected loblolly pine for sequencing because of the relatively long history of genetic research from the institute and others on the loblolly's complex traits such as disease resistance," said Dana Nelson, the institute's project leader.

The loblolly genome project was an open-access project and the scientists shared the results from the experiments with the research community.

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