Report of the Second Meeting
of
the Tetrahymena Genome Project Steering
Committee
Prepared by Eduardo
Orias
The Second Tetrahymena Genome Project Steering
Committee Meeting took place in Chicago, IL
on November 4, 2000. Its purpose was to discuss recent advances in Tetrahymena genomics, priorities
and funding issues. The meeting was attended
by 10 Steering Committee members from the US and Canada.
News from Tetrahymena
research groups. Reports were given by
members of the Steering Committee. Some highlights are:
-
Pilot DNA sequencing of purified small MAC chromosomes is now underway; it should generate the first direct information
about coding density, repeated sequence frequency, functional clustering, annotation issues, etc.
-
A pilot EST (expressed sequence tag) project has yielded, among others, matches to human genes of unknown function;
this reaffirms the potential usefulness of Tetrahymena as a unicellular animal model for the exploration of the
fundamental cell and molecular biology of those genes.
-
A highly inducible promoter system for Tetrahymena, based on the cadmium-induced metallothionein gene, has
been developed. The record-high transformation frequencies that it allows should make cloning by complementation
feasible.
-
A very useful full-length cDNA library from log phase cells is now available; it has been used for antisense mutagenesis
and should also facilitate cloning by complementation.
-
The complete sequence of the linear T. thermophila mitochondrial DNA has now been determined.
-
More than a hundred macronuclear chromosomes are now tagged with STSs (sequenced tag sites).
-
Roughly 10% of the ~300 chromosome breakage junctions that generate the macronuclear chromosomes have now been
characterized and mapped.
-
Construction of deletion maps of germline chromosomes, using >200 deletions, have reached an advanced state.
-
Each of the five germline chromosomes has been genetically purified, allowing the preparation of chromosome- or
chromosome segment-specific probe.
Tetrahymena sequencing proposals for
the Genome Canada initiative.
Ron Pearlman is the PI for the Tetrahymena segment of a Protist EST Project
(PEP) of the Atlantic Regional Center, which was approved subsequent to our meeting. This project will allow the
sequencing and annotation of thousands of Tetrahymena ESTs. His application to the Ontario
Regional Center for 1X coverage's worth of whole-genome shotgun DNA sequencing was positively reviewed but not
approved.
Paramecium Genomic Efforts. The Steering Committee reaffirmed its view that these
efforts, based mainly in Europe, are generating valuable ciliate genomic information, which will complement and
strengthen the Tetrahymena project. Synergy between both efforts should be strongly
encouraged.
NIH Concept paper. Ed
Orias reported that he would meet in the coming week with the co-chairs of the Trans-NIH Non-Mammalian Models Committee
to initiate the NIH application process for funding for sequencing the Tetrahymena genome.
The first step would be to submit a concept paper, describing the reasons why the Tetrahymena genome
should be sequenced. <At that meeting he was encouraged to submit the paper. Dr. Anthony Carter, Director of
the Division of Genetics and Developmental Biology at the National Institute of General Medical Sciences (NIGMS),
was subsequently appointed as the Tetrahymena contact
person.>
The Committee discussed various issues that the concept paper must address and agreed to the following.
- The highest priority for the moment is funding for the sequencing and annotation, and for a public database.
- Funding should be sought on the premise that sequencing and annotation project should proceed as quickly as possible.
-
The minimum first-year funding that would have a significant impact on the whole project would be for 2X shotgun
sequence coverage.
-
Sequences should be made available to the Tetrahymena and scientific-wide communities as quickly and as publicly
as possible at every step to maximize the impact of the project.
-
"Piggy-backing" onto a genomic database center that is already functioning well seems like the wisest
and least expensive way to proceed in the short run.
Strengthening our quest for
funding.
- Two
symposia should be organized in the near future in order to increase awareness of Tetrahymena among NIH officials and other potential funding sources;
one on the state of the art of Tetrahymena genomics and the other to showcase the advantages of Tetrahymena
as an advanced experimental system.
New member of the Steering
Committee. The Committee invited Dr. Laura
F. Landweber, a ciliate molecular biologist with bioinformatics expertise at Princeton University, to join the
Steering Committee.
Clifford F. Brunk, Biology Department,
UCLA, CA
Peter J. Bruns, Cornell University,
Ithaca, NY
Martin A. Gorovsky, University
of Rochester, NY
Carolyn Jahn, Northwestern University,
Evanston, IL
Kathleen M. Karrer, Marquette
University, Milwaukee, WI
Lawrence Klobutcher, University
of Connecticut Health Center, Farmington, CT
Eduardo Orias, University of
California at Santa Barbara, CA
Ronald E. Pearlman, York University,
Toronto, CANADA
Aaron Turkewitz, University of
Chicago, IL
Unable to attend:
Jacek Gaertig, University of
Georgia, Athens, GA
Geoffrey Kapler, Texas A &
M University, College station, TX
Ching Kung, University of Wisconsin,
Madison, WI