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Daphnia pulex's genome appears to have 50% to twice as many gene duplications as the duplicate-rich C. elegans genome. See this table of Selected Daphnia duplicate genes with homologs to other organisms.
Gene duplication is widespread in C. elegans, more so than
Drosophila or yeast [1], with about 6,000 genes identified as
paralogous. Around 400 clusters of tandem genes have been found
in this worm.
With over 40 genes for Cytochrome P450,
and large numbers of duplicates for other common gene families,
this organism may be ahead of other eukaryotes, barring polyploid genomes,
for gene duplications.
Duplication clusters (of N >= 3) found in this tandem exon analysis
are Drosophila melanogaster: 168, Dros. mojavensis: 338, C.
elegans: 680, and Daphnia pulex: 919
Protein duplicates :
Protein duplicate analysis is the simplest, and common
way to identify gene paralogs.
This study of Daphnia has shown that gene finding methods often
fail to accurately model tandem duplicate genes, so that
predicted proteins are subject to error for this genome.
With that caveat, this analysis of
predicted proteins also shows a larger number of
duplicates than related genomes, in particular for nearby
duplicate genes.
Tandemgenes, or 'tandy', software has been developed to address a
problem of gene predictions for tandem duplicate genes. Tandem
duplicates can be nearly identical (95+% identity), and very close
(within intron distances of each other), and very interesting biology.
This is described in more detail here.
Supporting data for Daphnia gene duplication is
here.
2. Gorr, T.A., J. D. Cahn, H. Yamagata, and H. F Bunn, 2004.
Hypoxia-induced Synthesis of Hemoglobin in the Crustacean
Daphnia magna Is Hypoxia-inducible Factor-dependent.
J. Biol. Chemistry, 279(34):36038~36047, doi/10.1074/jbc.M403981200
A stunning example is Daphnia's well known hemoglobin (Hb)
genes, which are called into play as Daphnia rapidly turn blood-red
when the oxygen is depleted in their ponds.
Four Hb genes have been described prior to whole genome analysis [2].
We find now a tandem cluster of 8 hemoglobin genes on scaffold_4.
Together with another tandem pair on scaffold 13, provides this
organism with 10 near identical Hb genes.
tRNA clusters :
With 3800 computed tRNAs, this genome has 10 times more
than any other eukaryote genomes. This overabundance of these
appears often in clusters of 1 to 4 types over a span of 1 kb,
with several copies of the same over 10 kb. These also appear to
be repeated 4-5 times in the same scaffold region of 100 kb.
These clusters are often associated with particular stress ESTs
(the same ones map to the same tRNA cluster locations), such as
bacterial infection or titanium nanoparticles, and show some
genome tiling expression. Associates have also located 5 copies
of RNAseP genes that use tRNAs, where 2 are uncommon among other genomes.
Further analysis of this pattern of overabundant tRNAs may give
important clues on Daphnia's general gene duplication mechanisms
and functionality. Are they caused by transposon or other mechanism?
Are they functional, perhaps as part of rapid adaptive responses to
environmental stresses?
Find tRNA data here.
References
1.
Woollard, A. Gene duplications and genetic redundancy in C.
elegans (June 25, 2005), ed. The C. elegans Research
Community, WormBook, doi/10.1895/wormbook.1.2.1,
http://www.wormbook.org.
Don Gilbert, June 2007, gilbertd@indiana.edu