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Innovative software tools help thrust rock pigeons into the spotlight

Boston Common. Image courtesy Brent Danley.

Researchers at the University of Utah, US, have decoded the genome of the rock pigeon (Columba livia), discovering surprising insights into its traits and origins. Using innovative software developed by study co-author Mark Yandell, a University of Utah professor of human genetics, the scientists found a single gene mutation responsible for how the bird's neck feathers grow.

Rock pigeons are not, as the name suggests, birds that sleep all day and play all night. Instead they prefer crowding public squares and sidewalks looking for scraps of food and pestering onlookers. Though a common sight in large cities, surprisingly little is known about the bird's genetics.

"There are more than 10,000 species of birds, yet we know very little about what makes them so diverse genetically and developmentally, especially when compared to what we know about mammals and fish," says Michael D. Shapiro, assistant professor of biology at the University of Utah. Shapiro led the study with Jun Wang of China's BGI-Shenzhen (formerly Beijing Genomics Institute).

Old Dutch Capuchin. Image courtesy Sydney Stringham.

There are around 350 breeds of rock pigeon - each with different shapes, sizes, color patterns, and feather arrangements on the feet and around the neck and head. Shapiro says his team's study is the first to pinpoint a gene mutation responsible for a specific pigeon trait - head crests. "A head crest is a series of feathers on the back of the head and neck that point up instead of down," Shapiro says. "Some are small and pointed. Others look like a shell behind the head; some people think they look like mullets. They can be as extreme as an Elizabethan collar."

At work behind these discoveries were some innovative software tools. First, the scientists assembled 1.1 billion base pairs of DNA in the rock pigeon genome. Then they used MAKER, an annotation pipeline developed by Yandell, to attach biological information to the sequences. MAKER is a multi-threaded, parallelized application and can produce accurate annotations of novel genomes, even where training-data is limited.

"After you sequence and assemble a new genome you've got several million locations and functions of genes to describe. The compute time to do this may be anywhere from 24 to 36 hours running constantly on thousands of nodes," says Yandell. His lab utilizes compute resources at the Center for High Performance Computing at the University of Utah, as well as the Texas Advanced Computing Center at the University of Texas at Austin, US.

Following annotation, the researchers used the well-known Variant Annotation, Analysis & Search Tool (VAAST), also created by Yandell, to identify variants, and ultimately, EphB2 - the gene responsible for the polarity of the neck feathers resulting in head crests. VAAST is a probabilistic search tool, and although used in second-generation genome projects like that of the rock pigeon, it is widely accepted and successfully used for identifying both common and rare genetic variants in humans and their associated diseases.

DNA double helix. Image courtesy iStock.

Sequenced genomes and annotations, however, are still far from providing the foundation for experimental work. As Yandell sees it, second-generation genome projects - projects without the benefit of pre-existing published gene models - continue to require novel approaches in technology and computer science. Excelling at the intersection of both domains, his lab is up for the challenge. The University of Utah freely licenses both MAKER and VAAST for academic research with the goal of providing research communities the means to independently annotate their genomes and distribute important results to the larger biomedical community.

The research is supported by the National Science Foundation and published online in the journal Science.You can see a photo, taken by Sydney Stringham, of an Old Dutch Capuchin on the March 1 cover of Science. Stringham is a graduate student from the lab of Michael Shapiro at the University of Utah.

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