International research team maps evolutionary history of an amphibian
Huntsville, Ala. — Researchers at the HudsonAlpha Institute for Biotechnology, in collaboration with a group of scientists affiliated with 46 institutions around the world, have sequenced an African clawed frog genome and used it to better understand the evolutionary history of the clawed frog. Their research was published today in Nature.
“The most exciting finding in our analysis of the genome of Xenopus laevis is that we could find distinct transposable element relicts that proved the whole-genome duplication to be the result of two extinct progenitor species,” said Adam Session,PhD. “While this has been shown in manygrasses, this is the first time this has been experimentally shown without extant progenitors.”Session is a lead author of the paper and a researcher at the Department of Energy Joint Genome Institute.
The newly sequenced genome of X. laevis (on top) is compared to the X. tropicalis (two frogs on bottom) genome to understand evolution of clawed frogs in a Nature paper published this week. Image credit: Atsushi Suzuki, PhD, of the Institute for Amphibian Biology, at Hiroshima University in Japan.
For its role in the project, the HudsonAlpha Genome Sequencing Center (GSC) contributed to the sequencing and improvement of the Xenopus laevis genome, commonly called the African clawed frog. The sequencing at HudsonAlpha was led by Jeremy Schmutz and Jane Grimwood, PhD, both faculty investigators and co-directors of the center, and Jerry Jenkins, PhD, genome analysis group leader in the GSC. Schmutz is also the plant program lead at the Department of Energy Joint Genome Institute.
The African clawed frog has a complex tetraploid genome. Humans have a diploid genome, meaning each person’s cells usually contain a pair of chromosomes – one from each biological parent. Tetraploid genomes have four pairs of chromosomes, which is fairly common in plants but rare in animals.
The clawed frog genome is important for scientific research because the amphibian is often used as a model to discover the molecular mechanisms fundamental to life, providing a shortcut to understanding human biology.
“Xenopus has become a major vertebrate model supporting cellular and developmental biology research important to major drivers of medical research like the National Institutes of Health,” said GSC co-director Schmutz. “We are pleased to continue to provide high-quality genome sequencing that can be used for new discoveries in the scientific community.”
Once the X. laevis genome was sequenced, researchers in the United States and Japan compared that newly sequenced genome to a related frog genome, X. tropicalis, commonly called the Western clawed frog. In contrast to the tetraploid African clawed frog, the Western clawed frog has a diploid genome.
The GSC also sequenced the X. tropicalis genome, which was published in Science in 2010.
“While we typically work on plant genomes, this was a fantastic opportunity to continue our work with the Xenopus project,” said Jenkins, the genome analysis group leader. “We’re excited about what was learned from comparing the two genomes.”
With the two genomes sequenced, the team of scientists was able to take a closer look at the evolutionary relationship between the two frogs. The paper in Nature describes how two now-extinct frog species, each with a diploid genome, combined about 17 million years ago to form a frog with a tetraploid genome.
“With current funding from NIH, we are continuing to improve the completeness and accuracy of these two paired frog genomes in order to enable functional genomics with these developmental models,” said Jane Grimwood, PhD.
The Nature paper was authored by 74 scientists affiliated with institutions in seven countries.
About the Genome Sequencing Center: The Genome Sequencing Center (GSC) produces, analyzes and interprets genomic data on economically important species to improve crop breeding and other agricultural practices. Co-directed by Jane Grimwood, PhD, and Jeremy Schmutz, the GSC is one of the few centers in the world performing de novo sequencing of complex plant genomes. The center has sequenced over 100 species and is focused on genomes related to food production and renewable biofuel research. Research at the GSC in the field of bioenergy supports initiatives related to clean energy generation, improving biomass yield and the efficiencies of processes used to convert plant materials into liquid fuels. To learn more about the Genome Sequencing Center, visit: http://www.hagsc.org/.
About HudsonAlpha: HudsonAlpha Institute for Biotechnology is a nonprofit institute dedicated to innovating in the field of genomic technology and sciences across a spectrum of biological challenges. Founded in 2008, its mission is four-fold: sparking scientific discoveries that can impact human health and well-being; bringing genomic medicine into clinical care; fostering life sciences entrepreneurship and business growth; and encouraging the creation of a genomics-literate workforce and society. The HudsonAlpha biotechnology campus consists of 152 acres nestled within Cummings Research Park, the nation’s second largest research park. Designed to be a hothouse of biotech economic development, HudsonAlpha’s state-of-the-art facilities co-locate nonprofit scientific researchers with entrepreneurs and educators. The relationships formed on the HudsonAlpha campus encourage collaborations that produce advances in medicine and agriculture. Under the leadership of Dr. Richard M. Myers, a key collaborator on the Human Genome Project, HudsonAlpha has become a national and international leader in genetics and genomics research and biotech education, and includes 30 diverse biotech companies on campus. To learn more about HudsonAlpha, visit: http://hudsonalpha.org/.
About the U.S. Department of Energy Joint Genome Institute: The U.S. Department of Energy Joint Genome Institute, User Facility of Lawrence Berkeley National Laboratory 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. 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.
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Margetta Thomas
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