Category Archives: Transhuman News

According to the study, the sequencing of the loblolly pine's genome was completed by using a faster and more efficient analytical process, including advanced computer technology. The genome sequence of the tree, which is the most commercially important tree species in the U.S., is expected to help scientists breed improved varieties of the pine and better understand the evolution and diversity of plants.

Its a huge genome, David Neale of the University of California, Davis, who led the research, said in a statement. But the challenge isnt just collecting all the sequence data. The problem is assembling that sequence into order.

The loblolly pine is one of several pines native to the southeastern U.S., spreading eastward from central Texas to Florida, and northward to Delaware and southern New Jersey. The tree is milled for building lumber and paper, while it is also the primary source of pulpwood and saw timber for the country's forest products industry.

To tackle the enormous size of the loblolly pine genome, which has 22 billion base pairs compared to only 3 billion in the human genome, scientists used a new method that could speed up genome assembly by compressing the raw sequence data 100-fold, according to the study, which has been published in two papers in the March 2014 issue of Genetics, and in one paper in the open access journal, Genome Biology.

As part of the study, scientists also looked for genes that control resistance to fusiform rust, a disease that infects southern pines and renders them unfit for use. According to scientists, they found a whole family of resistant genes in the loblolly pines genome.

Commercially, it is the most economically devastating disease of the southern pines, John M. Davis of the University of Florida, said in a statement. If growers didnt have genetic resistance, we would have no pine plantations its that important.

Floridas nearly 16 million acres of timberland supported economic activities that generated $14.7 billion in economic impact in recent years while providing nearly 90,000 full- and part-time jobs. A molecular understanding of genetic resistance is a valuable tool for forest managers as it allows them to select trees that can develop into healthy groves.

See the rest here:
Largest Genome Sequenced: Loblolly Pine's Genetic Code Is 7 Times Larger Than A Humans

The massive genome of the loblolly pine -- around seven times bigger than the human genome -- is the largest genome sequenced to date and the most complete conifer genome sequence ever published. This achievement marks the first big test of a new analysis method that can speed up genome assembly by compressing the raw sequence data 100-fold.

The draft genome is described in the March 2014 issue of the journal Genetics and the journal Genome Biology.

Loblolly pine is the most commercially important tree species in the United States and the source of most American paper products. The tree is also being developed as a feedstock for biofuel. The genome sequence will help scientists breed improved varieties and understand the evolution and diversity of plants. But the enormous size of the pine's genome had been an obstacle to sequencing efforts until recently. "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 University of California, Davis, who led the loblolly pine genome project and is an author on the GENETICS and Genome Biology articles.

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 it 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, who was also an author on the papers.

The scale of the problem can be compared to shredding thousands of copies of the same book and then trying to read the story. "You have this big pile of tiny pieces and now you have to reassemble the book," Salzberg said.

The key to the solution was using a new method to pre-process the gargantuan pile of sequence data so that it could all fit within the working memory of a single super-computer. The method, developed by researchers at the University of Maryland, compiles many overlapping fragments of sequence into much larger chunks, then throws away all the redundant information. Eliminating the redundancies leaves the computer with 100 times less sequence data to deal with.

This approach 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 what's been previously published," said Neale. This will enable the loblolly to serve as a high-quality "reference" genome that considerably speeds along future conifer genome projects.

The loblolly genome data have also been freely available throughout the project, with public releases starting back in June 2012. "Our project has had great benefits to the community long before publication," said Neale.

The new sequence confirmed that the loblolly genome is so large because it is crammed full of invasive DNA elements that copied themselves around the genome. Approximately 82% of the genome is made up of these and other repetitive fragments of sequence.

Continue reading here:
Loblolly pine genome is largest ever sequenced: Seven times bigger than the human genome

March 20, 2014

Image Caption: Conifers are the predominant members of the 300 million year old Gymnosperm clade. Conifers are also distinguished by their leviathan genomes. The reference genome sequence of Loblolly pine is published in the March issue of the journal GENETICS, published by the Genetics Society of America. Its 22-Gb genome size, makes it the largest genome sequenced and assembled to date. Credit: Dr. Ronald Billings, Texas A&M Forest Service

Genetics Society of America

The massive genome of the loblolly pinearound seven times bigger than the human genomeis the largest genome sequenced to date and the most complete conifer genome sequence ever published. This achievement marks the first big test of a new analysis method that can speed up genome assembly by compressing the raw sequence data 100-fold.

The draft genome is described in the March 2014 issue of GENETICS and the journal Genome Biology.

Loblolly pine is the most commercially important tree species in the United States and the source of most American paper products. The tree is also being developed as a feedstock for biofuel. The genome sequence will help scientists breed improved varieties and understand the evolution and diversity of plants.

But the enormous size of the pines genome had been an obstacle to sequencing efforts until recently. 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.

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 togethera computational puzzle called genome assembly.

We were able to assemble the human genome, but it 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, who was also an author on the papers.

The scale of the problem can be compared to shredding thousands of copies of the same book and then trying to read the story. You have this big pile of tiny pieces and now you have to reassemble the book, Salzberg said.

Read more here:
Loblolly Pine Genome Largest Ever Sequenced