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Figure A shows the number of Daphnia duplicates
increases in medium to larger clusters of similar genes.
Comparing this as percent of total genes (B), the Daphnia excess
in clusters of 8 or more is apparent. Both of these figures
plot the cumulative gene count with increasing gene family size.
Figure C shows that duplicates in larger family sizes (10..80 paralogs)
have a high frequency within 1 to 2 kilobases of each other for Daphnia,
similar to but higher than that for C. elegans. Figure D shows for
small clusters (2..5 paralogs) this nearby tandem effect is not as common,
and shows little species effect.
Figure E below extends Figs. C,D with distant duplicates.
|A. Cumulative Duplicate genes by family size PDF
|B. Cumulative % Duplicates / Total genes by family size PDF
|C. Tandem gene distance, large gene families PDF
|D. Tandem gene distance, small gene families PDF
Figure E extends Figs. C, D with distant duplicates (Far
and Unlinked), as well as shows the portion of inverted
duplicates. Note the high % inverted duplicates in Far
class. There is a suggestion that the nearby tandem
duplicates in Daphnia show a lower inversion rate
than other species, a finding consistent with recent
evolution of these nearby duplicates.
Daphnia shows an excess in Unlinked (across-scaffold) duplicate genes as well as the very near 1-Kb tandem genes. As this draft genome assembly has many thousands of small scaffolds, the unlinked duplicates may be found to be nearby tandems with further assembly refinement. There is a suggestion the small scaffolds failed to assemble in part due to tandem duplicate gene regions.