A Genome Project for Chlamydomonas reinhardtii

John Davies jdavies at exelixis.com
Tue Mar 20 11:31:56 EST 2001

Reposted from the Chlamydomonas newsgroup:

At the Ninth International Conference on the Molecular and Cell
Biology of Chlamydomonas, held in The Netherlands in May 2000, a poll
of participants established that the sequencing of the nuclear genome
of Chlamydomonas reinhardtii is the highest priority for the research
community. To accomplish this goal we have organized a Chlamydomonas
Genome Project Steering Committee.  The committee includes the
following members:

Dr. John Davies, Exelixis, Inc.
Dr. Arthur Grossman, Carnegie Institution of Washington
Dr. George Witman, University of Massachusetts Medical School
Dr. William Snell, University of Texas Southwestern Medical School
Dr. Susan Dutcher, Washington University School of Medicine
Dr. Pete Lefebvre, University of Minnesota
Dr. Carolyn Silflow, University of Minnesota
Dr. Elizabeth Harris, Duke University.

We are sending this message to update you on our efforts to develop a
plan for sequencing the nuclear genome of Chlamydomonas.

In December 2000 members of the steering committee met to discuss the
Genome Project. We decided to apply to the NIH for funding.  As part
of the NIH application process, we are required to submit a concept
paper describing Chlamydomonas and the goals of the genome project to
The Trans-NIH Non-Mammalian Models committee.  This committee must
approve the concept paper before we can submit a formal proposal for
the project.

Over the last several months, we have developed a research plan.
The objective of the Genome Project is to identify all of the genes
in Chlamydomonas, and to unify the physical and genetic maps so
researchers will know the linear arrangement of genes on chromosomes
and be able to obtain clones containing any portion of the genome. To
accomplish the genomic sequencing, we proposed to use a "paired-end,
shot-gun" sequencing strategy.  Clones from BAC, fosmid and small
insert genomic libraries of Chlamydomonas will be end-sequenced.
Enough sequence information needs to be obtained to assemble the BAC
clones into large contigs and to provide most of the sequence
information within the contigs.  Based on modeling experiments using
data from human and mouse sequencing projects, it has been estimated
that 6X coverage of the genome would be sufficient.  The BAC contigs
will be placed on the genetic map using sequence tagged sites (STSs)
from known genetic markers.  Since some of the contigs will not match
the known STSs, we will use sequence information from the unmapped
contig to identify a polymorphism in the S1D2 polymorphic strain and
genetically map the location of the contig.  There are currently ~250
molecular markers on the genetic map and another 250 will soon be
available.  Together these markers should identify roughly 50% of the
genome.  We estimate that approximately 500 contigs will have to be
placed on the genetic map.

We submitted our concept paper on February 23rd and the Non-Mammalian
Models Committee considered it on March 14.  The NIH committee was
convinced of the usefulness of Chlamydomonas as a model system.
However, they still have some questions that must be answered before
approving the concept paper and allowing us to send in a proposal. We
are in the process of answering these questions and will submit them
to the NIH in the near future.  We hope that we will satisfactorily
answer their questions and are working to submit a proposal sometime
this summer.  If you have any questions or comments on the genome
project please submit them to the Chlamy news group, or send them
directly to John Davies (jdavies at exelixis.com).


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