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Whole-Genome Shotgun Assembly and Analysis
of the Fugu rubripes Genome
The genome of the pufferfish Fugu rubripes is unusually
small for a vertebrate, at about one-eighth the length of
the human genome, but it contains a comparable complement
of protein-coding genes. When sequencing of the Fugu genome
was proposed a decade ago, it was expected that direct comparison
of the two genomes would be useful for identifying human genes.
The analysis performed by Aparicio et al. shows that this
expectation has been fulfilled.
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2 Distribution of protein similarities
between Fugu and human proteomes. |
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The similar numbers of gene loci in both Fugu and
human (between 30,000 and 40,000) led the researchers to conclude
that the core set of vertebrate gene loci is unlikely to exceed
40,000. Examination of the similarities and differences between
the human and Fugu proteomes (Figure 2) revealed
two features: first, the majority of peptides have some degree
of match in Fugu; second, ~25% of predicted human
proteins (8,109) do not appear to have homologs in the Fugu
genome.
The comparison of the two genomes enabled researchers to
discover almost 1,000 human putative genes that have so far
not been described in public annotation databases. Examination
of the conservation of synteny (location of genes on the same
chromosome, whether or not there is demonstrable linkage between
them) reveals that about one-eighth of the Fugu genome—more
than 900 segments of two or more genes—shows conserved
linkages of two or more genes with the human genome. Enumeration
of conserved segments between Fugu and human may
be an important starting point for detecting conserved regulatory
elements. Tracing the fate of such segments in other species
may allow us to reconstruct some of the evolutionary history
of vertebrate chromosomes.
INVESTIGATORS
D. Rokhsar, J. Chapman, N. Putnam, P. Dehal, S. Rash, M. D.
S. Gelpke, I. Y. Ho, C. Detter, P. Predki, S. Lucas, P. Richardson,
and T. Hawkins, DOE Joint Genome Institute; S. Aparicio, Cambridge
University; E. Stupka, J.-M. Chia, A. Christoffels, S. Hoon,
T. Oh, M. Wong, F. Verhoef, A. Tay, Y. H. Tan, B. Venkatesh,
and S. Brenner, Institute of Molecular and Cell Biology, Singapore;
A. Smit, J. Roach, G. Glusman, L. Rowen, and L. Hood, Institute
for Systems Biology, Seattle; S. F. Smith, M. S. Clark, Y.
J. K. Edwards, and G. Elgar, UK Human Genome Mapping Project
Resource Centre; N. Doggett, Los Alamos National Laboratory;
A. Zharkikh, S. V. Tavtigian, and D. Pruss, Myriad Genetics
Inc.; M. Barnstead, C. Evans, and H. Baden, Celera Genomics;
J. Powell, Paradigm Therapeutics Ltd.
PUBLICATION
S. Aparicio, J. Chapman, E. Stupka, N. Putnam, J.-M. Chia,
P. Dehal, A. Christoffels, S. Rash, S. Hoon, A. Smit, M. D.
S. Gelpke, J. Roach, T. Oh, I. Y. Ho, M. Wong, C. Detter,
F. Verhoef, P. Predki, A. Tay, S. Lucas, P. Richardson, S.
F. Smith, M. S. Clark, Y. J. K. Edwards, N. Doggett, A. Zharkikh,
S. V. Tavtigian, D. Pruss, M. Barnstead, C. Evans, H. Baden,
J. Powell, G. Glusman, L. Rowen, L. Hood, Y. H. Tan, G. Elgar,
T. Hawkins, B. Venkatesh, D. Rokhsar, and S. Brenner, “Whole-genome
shotgun assembly and analysis of the genome of Fugu rubripes,”
Science 297, 1301 (2002).
URL
http://www.jgi.doe.gov/
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