Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Maize genome pilot sequencing project results in six-fold reduction of effective size of maize genome

08.03.2004


Cutting corn down to size


A team of scientists reports a major advance in seqencing large genomes. And they have done their work on the plant that made the Midwest famous - maize, or corn, if you will



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.

A team of scientists reports a major advance in seqencing large genomes. And they have done their work on the plant that made the Midwest famous - maize, or corn, if you will.
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 www.danforthcenter.org for additional information.

Tony Fitzpatrick | WUSTL
Further information:
http://news-info.wustl.edu/tips/page/normal/697.html

More articles from Life Sciences:

nachricht During HIV infection, antibody can block B cells from fighting pathogens
14.08.2018 | NIH/National Institute of Allergy and Infectious Diseases

nachricht First study on physical properties of giant cancer cells may inform new treatments
14.08.2018 | Brown University

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: New interactive machine learning tool makes car designs more aerodynamic

Scientists develop first tool to use machine learning methods to compute flow around interactively designable 3D objects. Tool will be presented at this year’s prestigious SIGGRAPH conference.

When engineers or designers want to test the aerodynamic properties of the newly designed shape of a car, airplane, or other object, they would normally model...

Im Focus: Robots as 'pump attendants': TU Graz develops robot-controlled rapid charging system for e-vehicles

Researchers from TU Graz and their industry partners have unveiled a world first: the prototype of a robot-controlled, high-speed combined charging system (CCS) for electric vehicles that enables series charging of cars in various parking positions.

Global demand for electric vehicles is forecast to rise sharply: by 2025, the number of new vehicle registrations is expected to reach 25 million per year....

Im Focus: The “TRiC” to folding actin

Proteins must be folded correctly to fulfill their molecular functions in cells. Molecular assistants called chaperones help proteins exploit their inbuilt folding potential and reach the correct three-dimensional structure. Researchers at the Max Planck Institute of Biochemistry (MPIB) have demonstrated that actin, the most abundant protein in higher developed cells, does not have the inbuilt potential to fold and instead requires special assistance to fold into its active state. The chaperone TRiC uses a previously undescribed mechanism to perform actin folding. The study was recently published in the journal Cell.

Actin is the most abundant protein in highly developed cells and has diverse functions in processes like cell stabilization, cell division and muscle...

Im Focus: Lining up surprising behaviors of superconductor with one of the world's strongest magnets

Scientists have discovered that the electrical resistance of a copper-oxide compound depends on the magnetic field in a very unusual way -- a finding that could help direct the search for materials that can perfectly conduct electricity at room temperatur

What happens when really powerful magnets--capable of producing magnetic fields nearly two million times stronger than Earth's--are applied to materials that...

Im Focus: World record: Fastest 3-D tomographic images at BESSY II

The quality of materials often depends on the manufacturing process. In casting and welding, for example, the rate at which melts solidify and the resulting microstructure of the alloy is important. With metallic foams as well, it depends on exactly how the foaming process takes place. To understand these processes fully requires fast sensing capability. The fastest 3D tomographic images to date have now been achieved at the BESSY II X-ray source operated by the Helmholtz-Zentrum Berlin.

Dr. Francisco Garcia-Moreno and his team have designed a turntable that rotates ultra-stably about its axis at a constant rotational speed. This really depends...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

Within reach of the Universe

08.08.2018 | Event News

A journey through the history of microscopy – new exhibition opens at the MDC

27.07.2018 | Event News

2018 Work Research Conference

25.07.2018 | Event News

 
Latest News

'Building up' stretchable electronics to be as multipurpose as your smartphone

14.08.2018 | Information Technology

During HIV infection, antibody can block B cells from fighting pathogens

14.08.2018 | Life Sciences

First study on physical properties of giant cancer cells may inform new treatments

14.08.2018 | Life Sciences

VideoLinks
Science & Research
Overview of more VideoLinks >>>