Gene Duplications and Genome Evolution:
Gene duplication is considered one of the most important steps for the emergence of genetic novelties (Haldane 1932; Ohno 1970).
A substantial portion of the eukaryotic genomes is composed of multigene families, which evolved from duplication events.
Duplications can involve parts of genes, a complete single gene, part of a chromosome (called block duplication), an
entire chromosome, or the whole genome (Li 1997). According to Ohno (1970), whole-genome duplications have been more important
in evolution than regional duplications; in regional duplications only parts of the regulatory system of structural
genes may be duplicated causing an imbalance that can disrupt the normal function of the duplicated regions. Lynch and Conery (2000) proposed that duplication of a single gene, even if it conserves an intact regulatory region, might disrupt the stoichiometric relationships between the gene and its interacting partners and it would be advantageous to eliminate one of the redundant copies. This is not the case for duplications by polyplidization which maintains the stoichiometric relations between gene products, and stabilizing selection would now tend to maintain the two copies of the duplicated genes. With the availability of complete genome sequences, it has become possible to study the extent of gene duplication on a
Patterns of Gene Duplication in Eukaryotic Genomes:
In Gu et al (2002), Li et al (2003) and Cavalcanti et al (2003) we studied the patterns of duplications in the genomes of
yeast, C. elegans, and Drosophila. We showed that Drosophila appears to have much fewer young
duplicate genes than do yeast and nematode and has much fewer gene families than C. elegans. Our results also support the idea
of a recent whole genome duplication in yeast, as proposed by Wolfe and Shields (2000). We also showed that block duplication
is a common phenomenon in both yeast and C. elegans. The patterns of block duplication in the two species are, however, markedly
diferent. The yeast genome shows much more extensive block duplication than the nematode, with some chromosomes having more than 40% of
the duplications derived from block duplications. Moreover, in yeast the majority of block duplications occurred between chromosomes,
while in the nematode most block duplications occurred within chromosomes.
Paucity of Gene Duplication in C. elegans Operons:
Spliced leader (SL) trans-splicing is a mRNA maturation process found to date only in a small number of metazoan phyla and in euglenid and
trypanosomatid protists. During SL addition, a short exon from the 5' end of a small nuclear RNA, the SL RNA, is trans-spliced to a site in
the 5' UTR of a pre-mRNA. The region of the pre-mRNA upstream of the splice site is lost, and is replaced by the SL sequence, which includes
a methylated guanosine cap at the 5' end. SL addition thereby allows cells to cap otherwise uncapped RNAs, provided they contain a 3' splice
site and the requisite splicing signals. In the nematode Caenorhabditis elegans, as well as in a number of other well-characterized SL trans-splicing capable species (trypanosomes and flatworm), this process is used to cap the downstream genes of operons following
the 3' mRNA cleavage of the gene immediately upstream. The addition of the SL and its attached cap allows for the proper transport and translation
of these messages. A large number of operons have been identified in the C. elegans genome: a total of 1,052 operons, comprised of 2,727 genes,
or about 15% of the genome (Blumenthal et al 2002; Blumenthal and Gleason 2003).
Recently Lercher et al (2003) showed that genes in C. elegans operons have duplicated copies in the genome less often than
expected. We are writing a paper that analyzes the effect of operons in the patterns of duplications of the C. elegans
genome and proposes an explanation as to why genes in operons seem to duplicate less often than genes outside operons in this organism.
Blumenthal T, Evans D, Link CD, Guffanti A, Lawson D, Thierry-Mieg J, Thierry-Mieg D, Chiu WL, Duke K, Kiraly M, Kim SK (2002) A global analysis of Caenorhabditis elegans operons. Nature 417 (6891): 851-4.
Blumenthal T, Gleason KS (2003) Caenorhabditis elegans operons: form and function. Nat Rev Genet 4 (2): 112-120.
Cavalcanti A.R.O. , Gu Z., Ferreira R., W.H. Li. Patterns of Gene Duplication in Yeast and Worm (2003) J. Mol. Evol.56 (1): 28- 37.
Gu Z., Cavalcanti A.R.O., Chen F.C., Bouman P., Li W.H. ( 2002) Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol. Biol. Evol.19(3): 256-62
Haldane JBS (1932) The causes of evolution. Longsmans and Green, London.
Lercher MJ, Blumenthal T, Hurst LD (2003) Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes. Genome Res 13: 238-243.
Li WH (1997) Molecular evolution. Sinauer, Sunderland, MA.
Li W.H., Gu Z., Cavalcanti A.R.O., Nekrutenko A. (2003) Detection of gene duplications and block duplications in eukaryotic genomes. J. Struct. Funct. Genomics. 3(1-4): 27- 34.
Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
Ohno S (1970) Evolution by gene duplication. Springer-Verlag, Berlin.
Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713.