Scott,
> Is one of your groups the Osiris gene cluster
No, this one isn't in my short list.
Osiris looks like it is a gene set limited to insects; as I
required Daphnia to be part of the groups, it was left out.
The same computational methods could be applied to finding
insect-specific conserved groupings.
This paper started me looking, with this observation:
"In vertebrates, gene organisation and
synteny is often conserved over long evolutionary distances...
In arthropods few such complexes exist."
Evolution of a genomic regulatory domain: The role of gene
co-option and gene duplication in the Enhancer of Split Complex
Elizabeth J Duncan and Peter K Dearden
doi: 10.1101/gr.104794.109
Given what I found, it is seems accurate that few exist across
arthropods, but also there remain some yet to be found.
The methods I used preclude finding all conserved gene groupings,
based on having adjacent ordered genes for 6 species that also
have reciprocal best matches to that same ortholog in the other species.
Cases where genes diverged enough to drop out of best match status,
but retained their ordered grouping are not included.
Also given the draft nature of some of these genomes, several
orthologous genes have yet to be well defined. This "Enhancer of Split Complex"
is one such case, where the Daphnia gene models are not fully
accurate.
- Don
