Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Loblolly pine's immense genome conquered

20.03.2014

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 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.

Credit: Ron Billings/Texas A&M Forest Service

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.

"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.

To tackle the enormous size of the loblolly pine's 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 what's 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.

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 genome sequencing also revealed the location of genes that may be involved in fighting off pathogens, which will help scientists understand more about disease resistance in pines.

For example, researchers from the Forest Service Southern Institute for Forest Genetics identified an important candidate gene for resistance to fusiform rust, the most damaging disease of southern pines. A molecular understanding of genetic resistance is a valuable tool for forest managers as they select trees that will develop into healthy stands.

"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," said Dana Nelson, the institute's project leader. "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," she said.

Sonny Ramaswamy, director of USDA's National Institute of Food and Agriculture, which funded the research, noted that the loblolly pine plays an important role in American forestry.

"Now that we've unlocked its genetic secrets, loblolly pine will take on even greater importance as we look for new sources of biomass to drive our nation's bio-economy, and ways to increase carbon sequestration and mitigate climate change," Ramaswamy said.

The loblolly genome project was led by a UC Davis team, and the assembly stages were led by Johns Hopkins University and the University of Maryland. Other collaborating institutions include Indiana University, Bloomington; Texas A&M University; Children's Hospital Oakland Research Institute; and Washington State University.

###

The work was supported in part by the US Department of Agriculture's National Institute of Food and Agriculture through its flagship competitive grants program, the Agriculture and Food Research Initiative.

About UC Davis:

For more than 100 years, UC Davis has been one place where people are bettering humanity and our natural world while seeking solutions to some of our most pressing challenges. Located near the state capital, UC Davis has more than 33,000 students, over 2,500 faculty and more than 21,000 staff, an annual research budget of over $750 million, a comprehensive health system and 13 specialized research centers. The university offers interdisciplinary graduate study and more than 100 undergraduate majors in four colleges — Agricultural and Environmental Sciences, Biological Sciences, Engineering, and Letters and Science. It also houses six professional schools — Education, Law, Management, Medicine, Veterinary Medicine and the Betty Irene Moore School of Nursing.

Media contact(s):

-- David Neale, UC Davis Plant Sciences, dbneale@ucdavis.edu

-- Jennifer Martin, USDA National Institute of Food and Agriculture, (202) 720-8188, jmartin@nifa.usda.gov

-- Cristy Gelling, Genetics Society of America, (412) 327-6343, cgelling@thegsajournals.org

-- Anna Perman, Genome Biology/BioMed Central, +44 (0)20 3192 2, Anna.Perman@biomedcentral.com

-- Pat Bailey, UC Davis News Service, (530) 752-9843, pjbailey@ucdavis.edu

Pat Bailey | EurekAlert!
Further information:
http://www.ucdavis.edu

Further reports about: Biology DNA Food Genetics Genome Loblolly Medicine fragments resistance sequence

More articles from Agricultural and Forestry Science:

nachricht Fighting a destructive crop disease with mathematics
21.06.2017 | University of Cambridge

nachricht Unusual soybean coloration sheds a light on gene silencing
20.06.2017 | University of Illinois College of Agricultural, Consumer and Environmental Sciences

All articles from Agricultural and Forestry Science >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Can we see monkeys from space? Emerging technologies to map biodiversity

An international team of scientists has proposed a new multi-disciplinary approach in which an array of new technologies will allow us to map biodiversity and the risks that wildlife is facing at the scale of whole landscapes. The findings are published in Nature Ecology and Evolution. This international research is led by the Kunming Institute of Zoology from China, University of East Anglia, University of Leicester and the Leibniz Institute for Zoo and Wildlife Research.

Using a combination of satellite and ground data, the team proposes that it is now possible to map biodiversity with an accuracy that has not been previously...

Im Focus: Climate satellite: Tracking methane with robust laser technology

Heatwaves in the Arctic, longer periods of vegetation in Europe, severe floods in West Africa – starting in 2021, scientists want to explore the emissions of the greenhouse gas methane with the German-French satellite MERLIN. This is made possible by a new robust laser system of the Fraunhofer Institute for Laser Technology ILT in Aachen, which achieves unprecedented measurement accuracy.

Methane is primarily the result of the decomposition of organic matter. The gas has a 25 times greater warming potential than carbon dioxide, but is not as...

Im Focus: How protons move through a fuel cell

Hydrogen is regarded as the energy source of the future: It is produced with solar power and can be used to generate heat and electricity in fuel cells. Empa researchers have now succeeded in decoding the movement of hydrogen ions in crystals – a key step towards more efficient energy conversion in the hydrogen industry of tomorrow.

As charge carriers, electrons and ions play the leading role in electrochemical energy storage devices and converters such as batteries and fuel cells. Proton...

Im Focus: A unique data centre for cosmological simulations

Scientists from the Excellence Cluster Universe at the Ludwig-Maximilians-Universität Munich have establised "Cosmowebportal", a unique data centre for cosmological simulations located at the Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences. The complete results of a series of large hydrodynamical cosmological simulations are available, with data volumes typically exceeding several hundred terabytes. Scientists worldwide can interactively explore these complex simulations via a web interface and directly access the results.

With current telescopes, scientists can observe our Universe’s galaxies and galaxy clusters and their distribution along an invisible cosmic web. From the...

Im Focus: Scientists develop molecular thermometer for contactless measurement using infrared light

Temperature measurements possible even on the smallest scale / Molecular ruby for use in material sciences, biology, and medicine

Chemists at Johannes Gutenberg University Mainz (JGU) in cooperation with researchers of the German Federal Institute for Materials Research and Testing (BAM)...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Plants are networkers

19.06.2017 | Event News

Digital Survival Training for Executives

13.06.2017 | Event News

Global Learning Council Summit 2017

13.06.2017 | Event News

 
Latest News

Quantum thermometer or optical refrigerator?

23.06.2017 | Physics and Astronomy

A 100-year-old physics problem has been solved at EPFL

23.06.2017 | Physics and Astronomy

Equipping form with function

23.06.2017 | Information Technology

VideoLinks
B2B-VideoLinks
More VideoLinks >>>