Relative reference: Foxtail millet offers clues for assembling the switchgrass genomeMay 14, 2012
Arranging DNA fragments into a genome sequence that scientists can interpret is a challenge often compared to assembling a puzzle, except there is no box to provide an idea of what the picture is even supposed to be. Sometimes there's guidance in the form of other publicly-available DNA sequences from related organisms that can be used to guide the assembly process, but its usefulness depends on how closely related any two sequences are to one another. For example, a reference genome might be so distantly related from the one being assembled, it would be akin to comparing a Model-T to a contemporary hybrid car.
For researchers interested in switchgrass, a perennial grass that the U.S. Department of Energy (DOE) is investigating as a prospective biofuels feedstock, assembling the plant genome poses an even more complicated puzzle than usual because it has multiple copies of its chromosomes. The DOE Joint Genome Institute (JGI), in an international partnership that includes the DOE BioEnergy Science Center (BESC) and the DOE Joint BioEnergy Institute (JBEI), two of the three DOE Bioenergy Research Centers, has sequenced plant genomes of related candidate bioenergy crops such as sorghum and the model grass Brachypodium. Both plants have been used as references for switchgrass, however sorghum last shared a common ancestor with switchgrass more than 20 million years ago while Brachypodium last shared a common ancestor with switchgrass more than 50 million years ago. The genome of a much closer switchgrass relative--foxtail millet (Setaria italica)--is described in the May 13, 2012 edition of Nature Biotechnology. All three genomes, along with those of other plants sequenced by the DOE JGI are publicly accessible on www.phytozome.net.
"We're not thinking of Setaria as a biofuel crop per se but as a very informative model since its genome is so structurally close to switchgrass," said Jeff Bennetzen, a BESC researcher, the study's co-first author and a professor at the University of Georgia. He originally proposed that the DOE JGI sequence the foxtail millet genome under the 2008 Community Sequencing Program.
One of the challenges in studying grasses for bioenergy applications is that they typically have long lifecycles and complex genomes. Jeremy Schmutz, head of the DOE JGI Plant Program at the HudsonAlpha Institute of Biotechnology, pointed out that foxtail millet has several advantages as a model. It's a compact genome roughly half a billion bases in size, and large quantities of it can be grown in small spaces in just a few months.
Schmutz said that roughly 80 percent of the foxtail millet genome has been assembled using the tried-and-true Sanger sequencing platform, along with more than 95 percent of the gene space--the functional regions of the genome. "The Setaria genome is a high quality reference genome," he said. "If you want to conduct functional studies that require knowing all the genes and how they are localized relative to one another, then use this genome."
One such area of study is adaptation. Since it is found all over the world, Setaria is considered a good model for learning how grasses can adapt and thrive under various environmental conditions. Additionally it appears to have independently evolved a pathway for photosynthesis that is separate from that used by maize and sorghum. "With the sequencing of the Setaria genome," the team noted in their paper, "evolutionary geneticists now have an annual, temperate, C4, drought- and cold-tolerant grass that they can comprehensively compare to other plants that have or have not yet evolved these adaptions." C4 plants are distinguished by their ability to conduct photosynthesis faster than C3 plants under high light intensity and high temperatures.
Schmutz also noted that the Setaria genome is a good experimental model in the lab for studying switchgrass traits such as cell wall formation. As a member of BESC, Bennetzen explained how using the Setaria genome could aid one of his team's bioenergy projects: "The biggest cost and bottleneck in biofuel production is converting lignocellulose to simple sugars. We're looking at traits associated with reduced recalcitrance (i.e., easier access to sugars) and looking for variations that alter cell wall composition. If it works in Setaria then the same approach will work in switchgrass."
For Tom Brutnell, a co-author on the study and director of the Enterprise Institute for Renewable Fuels at the Donald Danforth Plant Center, the Setaria genome is the starting point for his own research interests. "Now that we have the genome sequence, we can kickstart the development of genetic tools for Setaria." His proposal under the DOE JGI's 2012 Community Sequencing Program builds off the availability of two Setaria genomes, that of foxtail millet and its wild ancestor green foxtail (S. viridis), which is also described in the paper. "What we really want is an Arabidopsis for the Panicoid grasses," he said, referring to the ubiquitous plant model used by many researchers. "Green foxtail is smaller than foxtail millet--we can get it to flower when it's just six inches tall and you go from seed to seed in six to eight weeks. In contrast, foxtail millet is a proper crop, so it's taller, has a longer generation time of four months, and no one has really developed efficient transformation methods for it. Our project with the DOE JGI allows us to tap the Setaria genomes to fast track S. viridis as a model genetic system."
Michael Freeling, a researcher at the University of California, Berkeley who works on plant comparative genomics, said that the Setaria genome "adds much to the power of 'grasses as a single genetic system' and the plant biology community is fortunate that DOE Joint Genome Institute has completed its draft sequence." He added that foxtail millet's location in the grass phylogenetic tree is crucial. "[It's] far enough away from rice to assure that functionless sequences have randomized, but not so far that small conserved regulatory sites are unrecognizable. Being in the sister tribe to the crops sorghum and maize, Setaria serves as a particularly valuable outgroup. Further, Setaria is nested into a region of grasses where C3 and C4 photosynthetic styles seem almost interchangeable, so insight is expected. C4 photosynthesis, with its distinctive anatomy including the famous bundle sheath, is particularly efficient. Setaria is now the model for all the other members of its tribe, including switchgrass."
"This work not only represents an important milestone in our goal to render the production of biofuels from lignocellulosic crops such as switchgrass more cost effective, but it also serves to illustrate how collaborations between centers such as BESC, JBEI and the JGI can significantly impact the frontiers of research for the whole plant research community," said BESC director Paul Gilna.
The U.S. Department of Energy Joint Genome Institute, supported by the DOE Office of Science, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI, headquartered in Walnut Creek, Calif., provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @doe_jgi on Twitter.
BESC and JBEI are two of three DOE Bioenergy Research Centers established by the DOE's Office of Science in 2007. The centers support multidisciplinary, multi-institutional research teams pursuing the fundamental scientific breakthroughs needed to make production of cellulosic biofuels, or biofuels from nonfood plant fiber, cost-effective on a national scale. The centers are led by ORNL, Lawrence Berkeley National Laboratory and the University of Wisconsin-Madison in partnership with Michigan State University.
DOE's Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.
DOE/Joint Genome Institute
Related Genome Articles:
An international consortium, with the participation of the Helmholtz Zentrum München, Plant Genome and Systems Biology Department (PGSB), has published methodologically significant data on the barley genome.
Looking for a better beer or single malt Scotch whiskey?
Chronic lung infections can be devastating for patients with cystic fibrosis (CF), and infection by Burkholderia cenocepacia, one of the most common species found in cystic fibrosis patients, is often antibiotic resistant.
Cells face a daunting task. They have to neatly pack a several meter-long thread of genetic material into a nucleus that measures only five micrometers across.
A study by San Diego Zoo Global reveals that the prospects for recovery of the critically endangered northern white rhinoceros -- of which only three individuals remain -- will reside with the genetic resources that have been banked at San Diego Zoo Global's Frozen Zoo®.
Precise, economical genome editing tools such as CRISPR have made it possible to make targeted changes in genes, which could be applied to human embryos to correct mutations, prevent disease, or alter traits.
How do pathogens such as bacteria or parasites manage to hide from their host's immune system?
An international team of scientists, led by researchers from A*STAR's Genome Institute of Singapore and the Bioinformatics Institute, have developed SIFT 4G (SIFT for Genomes) -- a software that can lead to faster genome analysis.
Single-cell techniques have been used to investigate histone replacement and chromatin remodeling in developing oocytes.
Dinoflagellates live free-floating in the ocean or symbiotically with corals, serving up -- or as -- lunch to a host of mollusks, tiny fish and coral species.
Related Genome Reading:
Genome (The Extinction Files Book 2)
by A.G. Riddle (Author)
The thrilling conclusion to THE EXTINCTION FILES is finally here!
* * *
A code hidden in the human genome...
Will reveal the ultimate secret of human existence.
And could hold humanity's only hope of survival.
* * *
In 2003, the first human genome was sequenced. But the secrets it held were never revealed.
The truth was discovered thirty years ago, almost by accident. Dr. Paul Kraus had spent his entire career searching for what he called humanity's lost tribes--human ancestors who had gone extinct. When... View Details
Genome: The Autobiography of a Species in 23 Chapters
by Matt Ridley (Author)
The genome's been mapped.
But what does it mean?
Arguably the most significant scientific discovery of the new century, the mapping of the twenty-three pairs of chromosomes that make up the human genome raises almost as many questions as it answers. Questions that will profoundly impact the way we think about disease, about longevity, and about free will. Questions that will affect the rest of your life.
Genome offers extraordinary insight into the ramifications of this incredible breakthrough. By picking one newly discovered gene from each pair of chromosomes and... View Details
Adam and the Genome: Reading Scripture after Genetic Science
by Scot McKnight (Author), Dennis R. Venema (Author), Daniel Harrell (Afterword), Tremper Longman III (Afterword)
Genomic science indicates that humans descend not from an individual pair but from a large population. What does this mean for the basic claim of many Christians: that humans descend from Adam and Eve?
Leading evangelical geneticist Dennis Venema and popular New Testament scholar Scot McKnight combine their expertise to offer informed guidance and answers to questions pertaining to evolution, genomic science, and the historical Adam. Some of the questions they explore include:
- Is there credible evidence for evolution?
- Do we descend from a population or are we the offspring of... View Details
The Gene: An Intimate History
by Siddhartha Mukherjee (Author)
THE #1 NEW YORK TIMES BESTSELLER
A New York Times Notable Book
A Washington Post and Seattle Times Best Book of the Year
From the Pulitzer Prize-winning author of The Emperor of All Maladies—a fascinating history of the gene and “a magisterial account of how human minds have laboriously, ingeniously picked apart what makes us tick” (Elle).
“Dr. Siddhartha Mukherjee dazzled readers with his Pulitzer Prize-winning The Emperor of All Maladies in 2010. That achievement was evidently just a warm-up for... View Details
Genetics: From Genes to Genomes, 5th edition
by Leland H. Hartwell (Author), Michael L. Goldberg (Author), Janice A. Fischer (Author), Leroy Hood (Author), Charles F. Aquadro (Author)
Genetics: From Genes to Genomes is a cutting-edge, introductory genetics text authored by an unparalleled author team, including Nobel Prize winner, Leland Hartwell. The 5th edition continues to build upon the integration of Mendelian and molecular principles, providing students with the links between the early understanding of genetics and the new molecular discoveries that have changed the way the field of genetics is viewed.
Users who purchase Connect Plus receive access to the full online ebook version of the textbook as well as SmartBook. View Details
The Genome War: How Craig Venter Tried to Capture the Code of Life and Save the World
by James Shreeve (Author)
The long-awaited story of the science, the business, the politics, the intrigue behind the scenes of the most ferocious competition in the history of modern science—the race to map the human genome.
On May 10, 1998, biologist Craig Venter, director of the Institute for Genomic Research, announced that he was forming a private company that within three years would unravel the complete genetic code of human life—seven years before the projected finish of the U.S. government’s Human Genome Project. Venter hoped that by decoding the genome ahead of schedule, he would speed up the pace of... View Details
The Developing Genome: An Introduction to Behavioral Epigenetics
by David S. Moore (Author)
Why do we grow up to look, act, and feel as we do? Through most of the twentieth century, scientists and laypeople answered this question by referring to two factors alone: our experiences and our genes. But recent discoveries about how genes work have revealed a new way to understand the developmental origins of our characteristics. These discoveries have emerged from the new science of behavioral epigenetics--and just as the whole world has now heard of DNA, "epigenetics" will be a household word in the near future.
Behavioral epigenetics is important because it explains how our... View Details
The Deeper Genome: Why there is more to the human genome than meets the eye
by John Parrington (Author)
Over a decade ago, as the Human Genome Project completed its mapping of the entire human genome, hopes ran high that we would rapidly be able to use our knowledge of human genes to tackle many inherited diseases, and understand what makes us unique among animals. But things didn't turn out that way. For a start, we turned out to have far fewer genes than originally thought -- just over 20,000, the same sort of number as a fruit fly or worm. What's more, the proportion of DNA consisting of genes coding for proteins was a mere 2%. So, was the rest of the genome accumulated 'junk'?... View Details
by A. G. Riddle (Author)
From the author of the #1 bestselling The Atlantis Gene comes a new novel in which the world’s past and future rests in the hands of five unwitting strangers in this definitive edition of A. G. Riddle's time-traveling, mind-bending speculative thriller.
En route to London from New York, Flight 305 suddenly loses power and crash-lands in the English countryside, plunging a group of strangers into a mysterious adventure that will have repercussions for all of humankind.
Struggling to stay alive, the survivors soon realize that the world they’ve... View Details
Neanderthal Man: In Search of Lost Genomes
by Svante Pääbo (Author)
"[T]his book is a vibrant testimonial to what might be the greatest creation of modern humans: the scientific method." --Salon
Neanderthal Man tells the story of geneticist Svante Pääbo's mission to answer this question: what can we learn from the genomes of our closest evolutionary relatives? Beginning with the study of DNA in Egyptian mummies in the early 1980s and culminating in the sequencing of the Neanderthal genome in 2010, Neanderthal Man describes the events, intrigues, failures, and triumphs of these scientifically rich years through the lens of... View Details