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Castoe, Fujita assist in turtle genome research project
     
Two UT Arlington assistant professors of biology have recently completed work on an international effort to sequence the genome of a western painted turtle, only the second reptile species to have its genetic information fully mapped.

Matthew Fujita and Todd Castoe, both of whom joined the UT Arlington College of Science in 2012, were among 30 co-authors on a recent Genome Biology publication that described the work. Researchers found that some of the western painted turtle's extraordinary abilities - like being able to withstand oxygen deprivation and near total freezing of its tissue - may be linked to sets of genes that are common to all vertebrates, but used uniquely in the turtle. It also showed that the turtle genome has evolved extremely slowly.

Learning more about how common gene networks work in different vertebrates such as the turtle could someday lead to better understanding of human disease, scientists say. The scientists also looked to the genome for information about the turtle's lack of teeth, as well as its immune function, longevity and determination of whether offspring are male or female.

"Despite the fact that they make up so much of the vertebrate tree of life, we know very little about the genes and genomes of reptiles," Castoe said. "To know more about them will help us understand how mammals, including humans, are different from other vertebrates and how we're the same."

Jonathan Campbell, chairman of the biology department at UT Arlington, said the team's work adds to our understanding of how genetic diversity comes about.

"Matthew and Todd are among a new generation of biologist that is using the very latest in technology to unlock genomic mysteries and open up new avenues for exploration," Campbell said.

Fujita said understanding how the turtle's body form has been so successful for the past 220 million years is important, especially in light of the extinction danger faced by numerous turtle species today. "One of the challenges scientists face worldwide is trying to protect and preserve these species so that we can learn from them," Fujita said.

The name of the Genome Biology paper is, "The Western Painted Turtle Genome, A Model for the Evolution of Extreme Physiological Adaptations in a Slowly Evolving Lineage." It is available online at http://genomebiology.com/content/pdf/gb-2013-14-3-r28.pdf.

 
Western painted turtle
Castoe Fujita
The research team was led by Dr. Brad Schaffer from the University of California at Los Angeles UCLA, and involved scientists from the Washington University School of Medicine in St. Louis, Iowa State University, and several others. The work also was featured in the Los Angeles Times.

Fujita studies evolutionary genetic and genomic processes affecting diversification in reptiles and amphibians, including isochore evolution. Isochores are large-scale regions of the genome characterized by distinct nucleotide compositions, such as high guanine and cytosine content. Scientists believe they can yield clues about evolutionary changes in vertebrates.

Previous theories assumed that isochore structures would be similar for many vertebrates. But, Fujita's work showed that, when it comes to isochore structure, the turtle's genome resembled an intermediate between birds or mammals and the lizard genome.

Castoe studies snake genomics, including the genetic basis of extreme snake phenotypes and adaptations. He used his snake genome information to provide a set of snake genes to compare to those of the western painted turtle. These comparisons determined that the turtle had a comparatively slow rate of molecular evolution.

Fujita and Castoe also are members of a project called the Genome 10K, an effort to sequence the DNA of 10,000 vertebrate species.

Posted May 15, 2013

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