Comparative EST sequencing of platyhelminthes - which species to do?

David Johnston daj at nhm.ac.uk
Mon Jul 17 10:57:23 EST 2000


Dear Colleagues,

The Wellcome Trust has recently called for proposals to use the facilities
of the Pathogen Sequencing Unit (PSU) at the Sanger Centre. On behalf of
the Schistosoma Genome Network, I have been in discussion with the PSU and,
as a result of those discussions, we are developing a proposal that would
include generation of a pilot EST dataset of approximately 15,000 expressed
sequence tags for S. haematobium (for which there is virtually no sequence
data available) to compare with S. mansoni and S. japonicum. In addition to
the existing data sets of 16,000 S. mansoni and  2,000 S. japonicum ESTs,
recently announced Brazilian and Chinese large scale projects will generate
many tens of thousands of additional ESTs in the near future. These major
EST initiatives are likely to identify nearly all of the genes expressed in
adult schistosomes, allowing comparison with virtually any EST generated
from adults of another species (like S. haematobium).

In this application we also have the opportunity to generate ESTs from
another, non-schistosome flatworm species in the analysis, to provide a
more distant comparison (again some 15,000 sequences).

The criteria to be applied to any such species would include:

(1) a species of demonstrable medical or veterinary importance
(2) a species with a significant international research community able to
exploit the resulting data
(3) a species for which, high quality cDNA libraries already exist, or,
failing that, a species for which someone on this newsgroup would be
prepared to supply material to us, or construct the necessary libraries
(for which funding would be requested).

Obvious candidates (to my mind) would include Fasciola, Taenia or Echinococcus.

This email is therefore intended to start a discussion on the newsgroup as
to what species (and, if applicable, strain) would be most appropriate to
be included in that application.

If you are involved in an application to the Wellcome Trust Beowulf Scheme
for your own platyhelminth , I would also be grateful to hear from you, so
that I do not  "reinvent the wheel"

Let the debate begin

David.




David A. Johnston,
Secretary to the WHO Schistosoma Genome Network,
Biomedical Parasitology Division,
Dept. of Zoology,
The Natural History Museum,
Cromwell Road, London SW7 5BD, England, UK.

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The  Biomedical Parasitology Division is a WHO Collaborating Centre for the
identification of schistosomes and their snail hosts.



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