Draft C. briggsae genome sequence available

Richard Durbin rd at sanger.ac.uk
Tue Jul 16 09:36:17 EST 2002


         Draft C. briggsae genome sequence available

The C. elegans Sequencing Consortium (Genome Sequencing Center,
Washington University, St. Louis and The Wellcome Trust Sanger
Institute) have released a draft sequence of the C. briggsae genome.

The cb25.agp8 version of the C. briggsae sequence is available from

    ftp://ftp.sanger.ac.uk/pub/wormbase/cbriggsae/cb25.agp8/
    ftp://genome.wustl.edu/pub/cbriggsae/cb25.agp8/

It is also being submitted to the Genomes division of GenBank and
EMBL, and will appear in WormBase.  The main file containing the
sequence is cb25.agp8.fasta.gz.  See the README file in the FTP
directory for a description of the contents of other files available.

IMPORTANT: This is a draft sequence, being made available prior to
publication.  Like any other automatically assembled sequence, it
no doubt contains errors including missassembly errors, and
some sequence will be missing.  We would welcome feedback on any
specific corrections.  We intend to publish an initial paper
describing the collection of the data and primary whole genome
analysis.  We request that anyone undertaking whole genome analysis
prior to this publication contact us at briggsae at sanger.ac.uk
regarding coordination of publication.

BACKGROUND: C. briggsae is a small nematode that diverged from
C. elegans roughly 150 million years ago.  It is expected that the
comparison of the C. briggsae genome with the already-completed
C. elegans genome will reveal new insights into gene function, gene
regulation and the process of genome evolution. 12 Mbp of sequence had
previously been finished by the Genome Sequencing Center, St Louis, on
a clone by clone basis (primarily fosmids).  In the final sequence 270
kb of this finished fosmid data from 155 accessions was incorporated to
bridge gaps.

METHODS: This C. briggsae sequence (version cb25.agp8) was assembled
from 2.05 million whole genome shotgun reads, of which 88.2% are in
read pairs.  Using the Phusion assembler, reads were first assembled
into contigs on the basis of overlap information, and then into
supercontigs using read pair information to cross gaps.  The
supercontigs were then assembled into mapped ultracontigs on the basis
of FPC fingerprint mapping, adding in some material from the
previously finished clones to bridge gaps.  Because of the absence of
dense chromosomal maps for C. briggsae, we can not assign these
ultracontigs to chromosomal locations, and so can not give draft
chromosome sequences.

STATISTICS: In the cb25.agp8 assembly the N50 contig size is 41 kb
(half the sequence is in contigs of this size or greater) and the N50
supercontig (scaffold) size is 1450 kb, so most genes should be
complete.  The size of the assembled and FPC mapped genome is 102 Mb
in 142 pieces, with an additional 6 Mb not placed on the FPC map in
436 pieces (many highly repetitive).  On the basis of comparison to
the 12 Mb of previously finished sequence, we estimate that the whole
genome shotgun assembly achieved 98% coverage of the briggsae genome.
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