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From: Hidemi Watanabe <watanabe@ncbi.nlm.nih.gov>
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Subject: NCBI Seminar (Feb 10, 1998)
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                            CBB Seminar
     (11:00, February 10, Conference Room, 8th Floor, Bldg 38A) 

R E C O N S T R U C T I O N   O F   A N C E S T R A L   G E N O M E S

                  WATANABE, Hidemi (NCBI/NLM/NIH)

One of the objectives of evolutionary studies is to know about
organisms in the past.  In molecular evolutionary studies, some states
of genes in ancestral organisms are inferred.  Since it is difficult
or impossible to obtain the fossil record of most ancient organisms,
molecular evolutionary approaches are crucial for knowing something
about them.  However, it is still difficult for us to know about
ancestral organisms or species with individual molecular evolutionary
studies since organisms are a system of a lot of gene products, which
might be more than a simple collection of gene products.

In order to get more insights into species evolution with molecular
evolutionary studies, we are conducting genome evolutionary studies,
that is, inference of states of ancestral genomes or reconstruction of
ancestral genomes.  In practice, using the complete genome sequence
data of eleven prokaryotes, in which three archaeal species are
included, the gene compositions and gene order in ancestral genomes
are inferred from the results of molecular evolutionary studies.  For
the inference of gene composition, some orthological analyses
including the use of the COG data (Tatusov et al., 1997) were
conducted.  With the data of orthologous gene pairs identified between
different genomes, it is also possible to know the conservation of
gene order in the genomes and infer gene clusters in a common
ancestral genome.

This study is still ongoing, but, so far, about 470 orthologous gene
groups have been identified between Archaea and Bacteria (Eubacteria).
Among them about eighty genes have been found to form gene clusters,
in which gene order is conserved in both archaeal and bacterial
genomes.  This number corresponds to about 1/6 of the genome of
Mycoplasma genitalium.  Since these conserved regions are found in
both archaeal and bacterial genomes, it is very likely that they were
also part of the genome of the common ancestor of Archaea and
Bacteria.  Moreover, if we accept the root position in the Woesian
tree, it is possible to infer that the genome of the last common
ancestor of all the modern species (cenancestor) had very similar
structures to the gene clusters identified.  Based on these results,
backtrack characterizations of ancestral species would be possible
without fossil record.  Several evolutionary tendencies found by
looking at the variations in the conserved regions and the evolution
of some genes in the conserved regions will be discussed.

Acknowledgments: David Lipman, Eugene Koonin and Roman Tatusov

WATANABE, Hidemi

NCBI/NLM/NIH
Bldg 38A, Rm B2N14
Email: watanabe@ncbi.nlm.nih.gov
Phone: (301)435-5896
Fax:   (301)435-2433