Chicken Genome
for the chicken. The high repeat content
50%) in mammalian genomes has been
a major problem with the WGS strategy;
however, in the chicken, the repeat content
is only 10 to 15%. This was shown dramati-
cally in the repeat plots of Fnished genome
sequences of human, mouse, and chicken.
Also, more than 75% of WGS sequences
from chicken BAC clones were contained
in a single contig compared to only 25% in
the mouse. The sequence will be based on
a female (the heterogametic sex in chicken)
inbred Jungle ±owl used to create the East
Lansing genetic linkage map.
Comparative Sequencing and Identifcation
oF Conserved Regions
The chicken has often been used as
an outgroup species in many evolution-
ary studies, in particular, in the study
of the evolution of genes and genomes.
Recently, there has been a rise in com-
parative genome analysis between long
sequences in mammals (mostly human
and mouse) and the chicken as a tool
to identify conserved regions with the
potential to function as regulatory se-
quences. This type of analysis began on
a smaller scale in earlier gene sequenc-
ing studies in which conserved sequence
motifs were found in both mammals and
chicken. ±or example, it was identiFed that
tion factor binding sites are associated
with chicken inducible nitric-oxide syn-
thase. It was shown that transcription
binding sites in the 5
-flanking region of
gene are conserved in chick-
ens and humans. It was shown that the
lens-preferred alphaA-crystallin gene con-
tains a conserved stretch in the 5
region of the chicken and mouse genes.
The 5
-half of this region has consensus
binding sites for
and other tran-
scription factors. ±urthermore, the mouse
and chicken alphaA-crystallin genes are
expressed with lens speciFcity using a
similar assortment of transcription factors
but with a different physical arrangement
of their respective cis-elements within the
promoter region.
A detailed study of the
locus com-
pared 36 kb around the chicken locus with
orthologous regions in human and mouse.
In all the three species, the
genes flanked the
gene. A detailed
analysis also conFrmed a number of pre-
viously characterized enhancer sequences
and predicted a new enhancer 23-kb down-
stream of the
promoter start site.
Another example is the comparison of the
gene in a number of species
ning 400 million years of evolution. In this
study, several conserved motifs were iden-
tiFed in all the four species that suggested
a common conserved function. A recent
study on
gene expression in the
chick identiFed Fve functional-enhancer
sequences in a 50-kb region flanking
the chicken gene, after electroporation of
embryos with various constructs. The ex-
citing Fnding was that these functionally
enhancers corresponded
exactly to the extragenic sequence blocks
conspicuously conserved between chicken
and mammals, but which were not de-
tected by sequence comparison among
mammals. These large-scale studies re-
quire new bioinformatic tools such as
. An example of the type of anal-
ysis is shown in ±ig. 5 in which a region
on human chromosome 19p13.1 (contig
011295) is compared with orthologous
regions on chicken and mouse chromo-
somes. The exciting thing about this is that
the chick sequence is so well conserved
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