544
Chicken Genome
(http://hbz.tamu.edu/) are fngerprinting
over 100 000 chicken BAC clones (Fig. 4),
which, when combined with the Wagenin-
genBACdata,willresultinadetailedBAC
map o± the entire chicken genome. This
map will serve to order the whole genome
shotgun (WGS) o± the chicken genome.
6
Genome Sequencing
6.1
Sequence Assembly of the Chicken Genome
Owing to its interest as an important an-
chor species ±or evolutionary studies, there
has been a rapid increase in genome
sequencing o± selected regions o± the
chicken genome. Such e±±orts will end
with a nearly complete genome sequence
in March 2004. Currently, there are 1811
entries in EMBL (June 2003) with in±orma-
tion on gene structure in the chicken. In
addition, there are a number o± sequence
sampling (BAC and cosmid clones) and
BAC-end sequencing e±±orts. O± more in-
terest are sequenced regions larger than
20 kb in length and since June 2003, the
number in the nucleotide database is 133,
o± which 90% represent complete BAC
clones. In general, these pilot genome-
sequencing projects reveal that chicken
genessha
rethesameexon/
in
t
rons
t
ruc
-
ture as their mammalian orthologs. How-
ever, the genes in the chicken are more
compact (2.5-±old), o±ten with smaller in-
trons. Also, the repeat content o± the
chicken is ±ar less (10–15%) compared
to mammals (50%), making WGS a prac-
tical option.
Extensive sequencing o± large segments
in
the
chicken
has
been
limited:
T-
cell receptor beta-chain constant region
(AF110982), T-cell receptor alpha chain
constant
region
(U83833),
beta-globin
gene
cluster
(L17432),
MHC
complex
(AL954802, AL023516), chemokine gene
clusters,
SCL
locus, class II cytokine re-
ceptor gene cluster (AF082667), and to
specifc regions in the chicken orthol-
ogous to human chromosomes 7, 11,
and 14. The general conclusions have
been that the chicken regions tend to
be two to three times smaller and that
gene order is conserved over regions o±
at least 1 cM or 300 kb. The largest se-
quence is ±or a region orthologous to
human
chromosome
7q31.2.
This
se-
quence is 414 kb and covers 5 overlapping
BAC clones. The order o± the genes is
identical (
TES,
CAV1,
MET,
CAPZA2
,
and
ST7
)t
oth
a
oun
dinth
ehum
an
genome, which covers a 1-Mb region.
Another example is the 305-kb IGF2 re-
gion on chicken chromosome 5, also
identical in gene order to its human
counterpart (
IGF2
,INS
,TH
,ASCL2
,and
CD81
).
The chicken genome-sequencing project
will beneft ±rom the experience gained
±rom the human and mouse genome
projects, and will include a mixture o±
targeted and whole genome sequencing.
Currently, a physical map based on a 20-
±old genome coverage o± overlapping BAC
clones is being assembled between labo-
ratories at Washington University, Texas
A&M, Michigan State University, and Wa-
geningen University. This map will be
integrated with other chicken mapping re-
sources, including FISH mapped clones,
genetic maps, and RH panels. Low se-
quence coverage o± selected BAC clones,
and BAC and Fosmid end sequences will
be used to merge the BAC map with
an eight±old whole genome shotgun. Pre-
liminary assemblies based on 2.5 Mb o±
fnished sequence have shown that this as-
sembly approach should be very e±fcient
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