| Researchers Compare Chicken, Human Genomes
Analysis of First Avian Genome Uncovers Differences Between Birds
Bethesda, Maryland 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," said NHGRI Director Francis
S. Collins, M.D., Ph.D. "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
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 percent 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 percent identical on average, than between rodent and human gene
pairs, which are 88 percent 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
The analysis also showed that genes conserved between human and
chicken often are also conserved in fish. For example, 72 percent
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, Ph.D., 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."
Like all birds, chickens are thought to have descended from dinosaurs
in the middle of the Mesozoic period and have evolved separately
from mammals for approximately 310 million years. Chickens were
first domesticated in Asia, perhaps as early as 8000 B.C.
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.
The analysis showed that a group of genes that code for odor receptor
proteins is dramatically expanded in the chicken genome a finding
that appears to contradict the traditional view that birds have
a poor sense of smell. And, as it turns out, birds might not have
such a great sense of taste. When compared with mammals, chickens
have a much smaller family of genes coding for taste receptors,
particularly those involved in detecting bitter sensations.
Other intriguing findings from the Nature paper include:
- Alignment of chicken and human genes indicate that approximately
2,000 human genes may actually start at different sites than scientists
thought. The discovery of these "true" start sites,
which appear to lie inside the previously hypothesized boundaries
of the genes, may have implications for the understanding of human
disease and the design of new therapies.
- Chicken genes that code for eggshell-specific proteins, such
as ovocleidin-116, have mammalian counterparts that play a role
in bone calcification. Previously, such genes were not known outside
of birds. However, the analysis also showed that, in contrast
to chickens, mammals are missing key genes coding for proteins
involved in egg production, such as egg whites and yolk storage.
- Chickens have a gene that codes for interleukin-26 (IL-26),
a protein involved in immune response. Previously, this immune-related
gene was known only in humans. The discovery means that the chicken
may now serve as a model organism in which researchers can investigate
the function of IL-26.
- Chickens possess genes coding for certain light-dependent enzymes,
while mammals have lost those genes. It is thought losses reflect
a period in early mammalian history in which mammals were active
mainly at night.
- The avian genome contains a gene that codes for an enzyme involved
in generating blue color pigments, while mammals are lacking that
Besides providing insights into gene content and evolution of genes,
the consortium's analysis offers new perspectives on the evolution
of portions of the genome that do not code for proteins. Less than
11 percent of the chicken genome consists of interspersed segments
of short, repetitive DNA sequences, compared with 40 to 50 percent
of mammalian genomes. With genes comprising another 4 percent of
the chicken genome, researchers say that leaves them with no explanation
for the function of more than 85 percent of the chicken genome.
They hypothesize this genetic "dark matter" may contain
previously unrecognized regulatory elements, but also may include
ancient DNA repetitive elements that have mutated beyond recognition.
Furthermore, researchers said it appears that the 571 non-coding
RNA "genes" that they identified in the chicken genome
may use different duplication and/or translocation mechanisms than
do regular protein-coding genes, opening the door to a whole new
realm of scientific inquiry.
In addition to its tremendous value as a resource for comparative
genomics, the chicken is widely used in biomedical research. It
serves as an important model for vaccine production and the study
of embryology and development, as well as for research into the
connection between viruses and some types of cancer.
Recent outbreaks of avian flu have accelerated agricultural researchers'
interest in learning more about the chicken genome and how genetic
variation may play a role in susceptibility of different strains
to the disease. The chicken genome sequence will also serve as a
resource for researchers seeking to enhance the nutritional value
of poultry and egg products. Furthermore, as the first of 9,600
species of birds to have its genome fully sequenced and analyzed,
the chicken genome will help to further understanding of avian genomics
and biology in general.
To download a high-resolution photo of the Red Jungle Fowl, go
For more on the rapidly growing field of comparative genomic analysis,
go to: http://www.genome.gov/11509542.
To read the white paper outlining the scientific rationale for sequencing
the chicken genome, go to: www.genome.gov/Pages/Research/Sequencing/SeqProporsals/Chicken_Genome.pdf
NHGRI is one of the 27 institutes and centers at the National Institutes
of Health, which is an agency of the Department of Health and Human
Services. The NHGRI Division of Extramural Research supports grants
for research and for training and career development at sites nationwide.
Additional information about NHGRI can be found at www.genome.gov.