Chickens join the genome club
Battery of researchers hatch out full fowl sequence.
The genomic sequence of the chicken has been unveiled. Although several mammalian species and various more primitive organisms have already had their genomes sequenced, the chicken is the first bird to join this prestigious roster.
The data will help to bridge the gap between the genomes already obtained from mammals and other organisms, and help scientists to refine their knowledge of evolution.
The most recent common ancestor for humans and chickens is thought to have been some kind of primitive reptile that lived more than 310 million years ago. The information from the chicken genome should paint a clearer picture of this divergence, and provide information about when mammals lost certain genes, and why.
The International Chicken Genome Sequencing Consortium, which is composed of researchers from around the world, decided on the red jungle fowl (Gallus gallus). This wild ancestor of domestic poultry still lives in parts of southern Asia.
The group sequenced the genome of one individual of this species using the shotgun approach. This involves extracting DNA from the bird, randomly breaking it up, sequencing the small bits, then piecing the sequence back together.
When the process was complete, the researchers found that the chicken genome contains 1 billion base pairs of DNA, which is only one-third as many as humans have. But packed into that are an estimated 20,000-23,000 genes, roughly the same as the human quota. The results are published this week in Nature1.
Analysis of the data is only just beginning, but several surprising results have already emerged from the project. For example, it had been thought that chickens lack a sense of smell, but the large number of olfactory genes in the sequence suggests otherwise.
The gene for keratin, the protein that makes up hair and fingernails in people and beaks and feathers in chickens, also grabbed researchers' attention. According to Christopher Ponting, a functional geneticist at the University of Oxford, UK, and a member of the consortium, keratin is thought to have arisen from a common source in both mammals and birds. Yet the chicken sequence looks very different from the mammal keratin genes known so far, raising the possibility that keratin production might have evolved twice.
Another paper published in Nature this week2 highlights how three domestic breeds differ genetically from the red jungle fowl. In contrast to the idea that domestic animals are more highly inbred than their ancestors, the study detected a startling amount of genetic diversity in broiler, layer and Chinese silkie chickens as compared with their wild relative.
Many researchers may be most intrigued by the non-coding parts of the chicken genome. It is not unusual for different species to share regions of DNA that have a fundamental biological function. Scientists call these areas 'conserved' because any mutations within them disrupt that function and are usually selected against.
But when the group compared the chicken genome with that of other mammal species, including humans, they found a surprising amount of similarity in regions not thought to be involved in protein production.
"I don't think that anyone expected that the conservation would be so non-gene associated," says Ewan Birney of the European Bioinformatics Institute in Cambridge, UK, who was a coordinator of the sequencing consortium. But he and others remain uncertain about exactly what these conserved non-coding regions do.
One possibility is that these mysterious sequences are involved in the regulation of protein production and Birney says he hopes that analysis of the similarities will provide further clues. "It's an open question at the moment," he says.
- International Chicken Genome Sequencing Consortium Nature, 432. 695 - 716 (2004).
- International Chicken Polymorphism Map Consortium Nature, 432. 717 - 722 (2004).