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Partial vs. whole trees

Ed Rybicki ED at micro.uct.ac.za
Tue Mar 16 04:38:41 EST 1993

> In article <9303121847.AA05027 at net.bio.net>, preissj at CLVAX1.CL.MSU.EDU ("J Preiss--Seq Anal") writes:
> >
> I just thought it might be worth pointing out that one can hardly grow a
> tree as suggested above when there is a single taxon whose complete genome
> has been sequenced.  The essence of tree building is comparing homologous
> sequences from a variety of taxa.  So perhaps the question should be:
> has anyone tried building a tree of several genome sequences (or several
> sub-genomic sequences) from taxa whose genomic sequences can be align
> ed with confidence.

Yes - again, with viruses, as these are the only organisms whose genomes
are small enough that sufficient have been sequenced to give any sort of
approach to treeing.  For example, there are now a large of number of
complete sequences for picornaviruses, retroviruses, influenza and
paramyxo- and rhabdo- and poty- and geminiviruses, and an even larger
number of partial sequences from relatives of all the above.  I have
played with gemini-, poty- and picornaviruses, and my conclusions are that
using a conserved predicted partial polypeptide sequence from any of these
is sufficient to give the same tree (give or take a branch) as you get
from the entire sequence.  You may argue that virus genomes are so much
smaller than those of cellular organisms that any conclusions reached from
study of whole vs. partial sequences for viruses have no relevance to the
larger beasties - but would you be right?  Viruses represent the limit of
the problem in that they do not normally have any "wasted" sequences
because of informational constriants on small genomes; however, the
largest viruses have the same size genomes as the smallest cells (eg.
poxviruses vs. mycoplasmas), and the entire genomes of several
herpesviruses and poxviruses have already been determined (+/-200 kb each)
- so there is material to test the odd hypothesis.

 | Ed Rybicki, PhD             |     "Emancipate yourselves from      |
 | (ed at micro.uct.ac.za)        |            mental slavery            |
 | Dept Microbiology           |          None but ourselves          |
 | University of Cape Town     |         Can free our minds...."      |
 | Private Bag, Rondebosch     |                                      |
 | 7700, South Africa          |             - Bob Marley             |
 | fax: 27-21-650 4023         |          (Redemption Songs)          |

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