An international research consortium has found that chickens and humans share more than half of their genes, but that their DNA sequences diverge in ways that may explain some of the important differences between birds and mammals. The consortium's analysis is published in the Dec. 9 issue of the journal "Nature."
The International Chicken Genome Sequencing Consortium analyzed the sequence of the Red Jungle Fowl (Gallus gallus), which is the progenitor of domestic chickens. The National Human Genome Research Institute (NHGRI), part of the National Institutes of Health, provided about $13 million in funding for the project, which involved researchers from China, Denmark, France, Germany, Japan, Poland, Singapore, Spain, Sweden, Switzerland, the United Kingdom and the United States.
The chicken is the first bird, as well as the first agricultural animal, to have its genome sequenced and analyzed. The first draft of the chicken genome, which was based on 6.6-fold coverage, was deposited into free public databases for use by researchers around the globe in March 2004. Over the past nine months, the consortium carefully analyzed the genome and compared it with the genomes of organisms that have already been sequenced, including the human, the mouse, the rat and the puffer fish.
"The chicken genome fills a crucial gap in our scientific knowledge. Located between mammals and fish on the tree of life, the chicken is well positioned to provide us with new insights into genome evolution and human biology," NHGRI director Francis S. Collins said adding, "By comparing the genomes of a wide range of animals, we can better understand the structure and function of human genes and, ultimately, develop new strategies to improve human health."
In their paper published in "Nature," members of the International Chicken Genome Sequencing Consortium report that the chicken genome contains significantly less DNA than the human genome, but approximately the same number of genes. Researchers estimate that the chicken has about 20,000-23,000 genes in its 1 billion DNA base pairs, compared with the human count of 20,000-25,000 genes in 2.8 billion DNA base pairs. The difference in total amount of DNA reflects a substantial reduction in DNA repeats and duplications, as well as fewer pseudogenes, in the chicken genome.
About 60 per cent of chicken genes correspond to a similar human gene. However, researchers uncovered more small sequence differences between corresponding pairs of chicken and human genes, which are 75 per cent identical on average, than between rodent and human gene pairs, which are 88 per cent identical on average. Differences between human and chicken genes were not uniform across the board, however. Chicken genes involved in the cell's basic structure and function showed more sequence similarity with human genes than did those implicated in reproduction, immune response and adaptation to the environment.
The analysis also showed that genes conserved between human and chicken often are also conserved in fish. For example, 72 per cent of the corresponding pairs of chicken and human genes also possess a counterpart in the genome of the puffer fish (Takifugu rubripes). According to the researchers, these genes are likely to be present in most vertebrates.
"Genomes of the chicken and other species distant from ourselves have provided us with a powerful tool to resolve key biological processes that have been conserved over millennia," said Richard Wilson of Washington University School of Medicine in St. Louis, the consortium's leader and senior author of the "Nature" article. "Along with the many similarities between the chicken and human genomes, we discovered some fascinating differences that are shedding new light on what distinguishes birds from mammals."
As might be expected, genomic researchers determined that chickens have an expanded gene family coding for a type of keratin protein used to produce scales, claws and feathers, while mammalian genomes possess more genes coding for another type of keratin involved in hair formation. Likewise, chickens are missing the genes involved in the production of milk proteins, tooth enamel and the detection of hormonal substances called pheromones, which researchers say may mirror the evolution of the mammary glands and the nose in mammals and the loss of teeth in birds. But other results of the analysis caught even the researchers by surprise.