ambystomid protein coding loci

Richard Gordon gordonr at cc.UManitoba.CA
Fri Feb 26 12:02:27 EST 1999


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>We have initiated a project to test for conservation of gene order
>(conserved synteny) between Ambystoma and genomically-well characterized
>vertebrate species.

Dear Randall & David,
This is terrific news for those of us who have had to explain that our
axolotls have the second largest genome, and only 42 known mutations.

I've proposed that one reason gene order is preserved is that genes are
logically arranged in developmental cascades that correspond to steps of
differentiation, and that the genes in these cascades would tend, for
evolutionary reasons (rapid radiation), to stick together. Thus, if we
labelled genes by the earliest tissue in which they are expressed, we might
see the tissue labels clustering together. I call such labelling a GEM
(Gene Expression Map, see book in my signature).

The differentiation cascades are apparently organized in a tree, which we
call the differentiation tree. It is essentially the lineage tree of
embryonic and adult tissues. Now, Ambystoma mexicanum is the only organism
for which a substantial chunk of the differentiation tree has been worked
out*, except for nematodes. Thus we could also determine to what extent the
differentiation tree of an organism can be read right off the genome via
its GEM.

In terms of candidate proteins, then, anything expressed in early
embryogenesis that is known to have homologs would be excellent to try.
Perhaps the work could be coordinated with whole mount staining of embryos
at different stages, to obtain the tissue with earliest expression, and
thus begin to construct the urodele GEM.
Yours, -Dick Gordon

*Gordon, R., N. K. Björklund & P. D. Nieuwkoop (1994). Dialogue on
embryonic induction and differentiation waves. Int. Rev. Cytol. 150,
373-420.

*Björklund, N.K. & R. Gordon (1994). Surface contraction and expansion
waves correlated with differentiation in axolotl embryos. I. Prolegomenon
and differentiation during invagination through the blastopore, as shown by
the fate map. Computers & Chemistry  18(3), 333-345.

Dr. Richard Gordon, Radiology, U. Manitoba, HSC, 820 Sherbrook Street,
Winnipeg R3A 1R9 Canada, Phone: (204) 789-3828, fax: (204)
787-2080/forthcoming book: The Hierarchical Genome & Differentiation Waves:
Novel Unification of Development, Genetics & Evolution:
http://www.wspc.com.sg/books/lifesci/2755.html




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