*******************
Sorry for second posting of the same message. My previous posting
had a wrong subject line.
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Michael David Baker posted this message to the
bionet.protista group:
======================================================
>From: mike at VOSSBRICKC3.AG.UIUC.EDU> (Michael David Baker)
>Newsgroups: bionet.protista
>Subject: microsporidian spore requests
>Date: 27 Mar 1995 13:48:31 -0800
>Organization: BIOSCI International Newsgroups for
> Molecular Biology
>Lines: 19
>Sender: daemon at net.bio.net>Distribution: world
>Message-lD: <9503272141.AA04137 @
> vossbrinckc3.ag. uiuc.edu
>>Dear Netters,
>I hope that this is the correct medium for the
>following request. I am involved in two major
>research projects; 1. the molecular phylogeny of
>the microsporidia and 2. molecular identification
>of various host strains of Encephalitozoon
>cuniculi. We have developed a moderate database of
>about 45 complete and 15 partial SSU rRNA
>sequences representing about 35 genera of
>microsporidia. The results from which we are just
>starting to publish. We have also given some
>thought to making this database available on the
>internet as a tool for identifying species of this
>diverse group of organisms. I am currently trying
>to obtain more material to sequence and was
>wondering if anybody out there, who may have
>access to microsporidia, would be interested in
>contributing material for these projects.
>Sincerely,
>Michael D. Baker
>mike at vossbrinckc3.ag.uiuc.edu
============================================================
I would like to congratulate your laboratory for this
outstanding achievement. Forty five microsporidian complete
small subunit ribosomal RNA sequences (SSUrRNA) translates
into reading over 350,000 bases with the required redundancy
of six to compensate for Taq polymerase errors. Even if
your lab did direct sequencing (without cloning) of the PCR
product, still over 120,000 bases were read. This
calculation does not include the necessary overlaps nor data
for the fifteen partial sequences you mentioned.
The importance of this accomplishment is immense, both for
the taxonomy of microsporidia, as well as for the search of
reservoirs of human microsporidial infections. In addition,
scientist studying application of microsporidia as
biological insect control agents will be able to use the
data generated in this project to design species-specific
primers to confirm that these microsporidia will not harm
beneficial insects.
You write that your team "(has) given some thought to
making this database available on the internet". In my
opinion, this is an excellent idea. However, I would like
to note that the GenBank database is where data should be
placed to be used "as a tool for identifying species of
this diverse group of organisms". I did a quick search of
GenBank today and found only two entries from your
laboratory of complete microsporidian SSUrRNA coding regions
(loci VNRRNS and VAIRGD). One was submitted in 1987 and the
other in 1989. Uncommonly, both sequences are identical and
are for the same organism, Vairimorpha necatrix. In
addition to this sequence, I found in GenBank data from your
laboratory for partial sequences for both small and large
microsporidian ribosomal RNA. Besides the fact that these
sequences have minimal use for molecular taxonomy, they are
full of unassigned bases (N), which is not the standard
practice in submitting data to this database. Such
unassigned bases can be only tolerated in preliminary
reports.
I find it highly unusual that your laboratory did not send
the 45 complete microsporidial SSUrRNA sequences to GenBank,
especially that in 1993, complete SSUrRNA sequences were
submitted by others to GenBank for 5 species, and in 1994
for nine species of microsporidia. There were up to four
sequences submitted for different isolates of the same
species from different laboratories. This delay may cause
that if your laboratory will not submit "about 45 complete
and 15 partial" sequences to GenBank immediately, other
laboratories may be faster in making their data available to
the scientific community. Please, do not procrastinate any
longer in submitting to the GenBank database the sequences
you mentioned in this posting.
Norman
--
==========================================================================
Norman J. Pieniazek voice: (404) 488-4073
Centers for Disease Control fax: (404) 488-4108
Mailstop F13 e-mail: norman at giardia.pdb.cdc.gov
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Atlanta, GA 30341-3724
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