Featured Research

from universities, journals, and other organizations

Sequencing Project Results In Six-fold Reduction Of Effective Size Of Maize Genome

Date:
March 9, 2004
Source:
Washington University In St. Louis
Summary:
A team of scientists that includes a Washington University in St. Louis biologist, has evaluated and validated a gene-enrichment strategy for genome sequencing and has reported a major advance in sequencing large genomes.

A team of scientists that includes a Washington University in St. Louis biologist, has evaluated and validated a gene-enrichment strategy for genome sequencing and has reported a major advance in sequencing large genomes. The team showed a six-fold reduction of the effective size of the Zea mays (maize or corn) genome while creating a four-fold increase in the gene identification rate when compared to standard whole-genome sequencing methods.

The Maize Genomics Consortium reported their results in the December 19, 2003 issue of Science magazine. Karel R. Schubert, Ph.D., Washington University affiliate professor of biology in Arts & Sciences, was the principal investigator of the study. Schubert is vice president of technology management and science administration at the Donald Danforth Plant Science Center in St. Louis.

The Maize Genomics Consortium, consisting of The Donald Danforth Plant Science Center, The Institute for Genomic Research (TIGR), Purdue University, and Orion Genomics, was awarded a two-year, $6 million plant genome grant on September 20, 2002 by the National Science Foundation (NSF) to develop and evaluate high-throughput and robust strategies to isolate and sequence maize genes. The two gene-enrichment methods used in the research published in Science are methyl-filtration and high-Cot selection.

According to Schubert and W. Brad Barbazuk, Ph.D., senior bioinformatics specialist and assistant domain member, both at the Donald Danforth Plant Science Center, the overall goal of the pilot sequencing project in maize is to derive an effective strategy to sequence the maize genome. To meet this goal, the Maize Genomics Consortium will generate approximately 800,000 total sequence reads using the methyl-filtration and high-Cot methods, with the results published in Science describing the analysis of the first 200,000 sequence reads.

It is a challenging effort to sequence the maize genome, as its size and structure preclude using the standard whole-genome methods for sequence analysis and alignment. At about 2 to 3 billion base pairs, the maize genome is estimated to be 20 times larger than Arabidopsis, an experimental plant that is the first plant genome to be completely sequenced. However, maize probably has only twice as many genes as Arabidopsis. The rest of the maize genome is made up of a large amount of highly repetitive DNA including many mobile DNA elements. Unlike Arabidopsis genes, the maize genes are not spaced evenly throughout the genome but instead are clustered in "islands" floating in a large "sea" of repeat-sequence DNA.

To sequence these "islands", the Maize Consortium used two methods for gene-enrichment, methyl-filtration and high-Cot selection. The methyl-filtration method was developed at Cold Spring Harbor Laboratory in Long Island, New York, and has been exclusively licensed to St. Louis-based Orion Genomics. It is based on the finding that highly repetitive DNA is modified (methylated) while genes are largely free of such modification. The well-established high-Cot selection method was applied at Purdue University and exploits the fact that gene sequences are in relatively low abundance compared with the large amount of repeated non-genic sequences. These methods target overlapping, but non-identical fractions of the genome that are highly enriched for genes sequences.

###

Washington University in St. Louis is part of the alliance that makes The Donald Danforth Plant Science Center. The Center is a not-for-profit research institution that was founded in 1998 as the product of a unique and innovative alliance joining the University of Illinois at Urbana-Champaign, the Missouri Botanical Garden, the University of Missouri-Columbia, Monsanto Company, Purdue University, and Washington University in St. Louis. The mission of the Danforth Center is to increase understanding of basic plant biology; to apply new knowledge for the benefit of human nutrition and health and to improve the sustainability of agriculture worldwide; to facilitate the rapid development and commercialization of promising technologies and products; and to contribute to the education and training of graduate and postdoctoral students, scientists, and technicians from around the world. Please visit http://www.danforthcenter.org for additional information.


Story Source:

The above story is based on materials provided by Washington University In St. Louis. Note: Materials may be edited for content and length.


Cite This Page:

Washington University In St. Louis. "Sequencing Project Results In Six-fold Reduction Of Effective Size Of Maize Genome." ScienceDaily. ScienceDaily, 9 March 2004. <www.sciencedaily.com/releases/2004/03/040309074545.htm>.
Washington University In St. Louis. (2004, March 9). Sequencing Project Results In Six-fold Reduction Of Effective Size Of Maize Genome. ScienceDaily. Retrieved July 23, 2014 from www.sciencedaily.com/releases/2004/03/040309074545.htm
Washington University In St. Louis. "Sequencing Project Results In Six-fold Reduction Of Effective Size Of Maize Genome." ScienceDaily. www.sciencedaily.com/releases/2004/03/040309074545.htm (accessed July 23, 2014).

Share This




More Plants & Animals News

Wednesday, July 23, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Michigan Plant's Goal: Flower and Die

Michigan Plant's Goal: Flower and Die

AP (July 22, 2014) An 80-year-old agave plant, which is blooming for the first and only time at a University of Michigan conservatory, will die when it's done (July 22) Video provided by AP
Powered by NewsLook.com
San Diego Zoo Welcomes New, Rare Rhino Calf

San Diego Zoo Welcomes New, Rare Rhino Calf

Reuters - US Online Video (July 21, 2014) An endangered black rhino baby is the newest resident at the San Diego Zoo. Sasha Salama reports. Video provided by Reuters
Powered by NewsLook.com
Shark Sightings a Big Catch for Cape Tourism

Shark Sightings a Big Catch for Cape Tourism

AP (July 21, 2014) A rise in shark sightings along the shores of Chatham, Massachusetts is driving a surge of eager vacationers to the beach town looking to catch a glimpse of a great white. (July 21) Video provided by AP
Powered by NewsLook.com
$23.6 Billion Awarded To Widow In Smoking Lawsuit

$23.6 Billion Awarded To Widow In Smoking Lawsuit

Newsy (July 20, 2014) Cynthia Robinson claims R.J. Reynolds Tobacco Company hid the health and addiction risks of its products, leading to the death of her husband in 1996. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins