Assembly details (Release Cb3)

This sequence version makes minor modifications to the original Cb1
(cb25.agp8) sequence assembly and uses a genetic map to align the
contigs along chromosomes.  The Cb1 assembly was produced for the
C. briggsae strain AF16 from 2.05 million whole genome shotgun (WGS)
reads, of which 88.2% were in read pairs. The sequence reads were
generated at Washington University School of Medicine's Genome
Sequencing Center and the Sanger Centre (Hinxton, UK).  The Phusion
(Mullikin, J) assembler was used to assemble the WGS reads into
contigs based on overlap information, and then into supercontigs using
read pair information to cross gaps. These supercontigs were assembled
into mapped ultracontigs based on FPC fingerprint mapping (generated
at Washington University School of Medicine's Genome Sequencing
Center), with material from previously finished clones used to bridge
gaps. Using the sequence data to identify SNPs between AF16 and HK104
and to distribute primers along major ultracontigs, a genetic map (Ray
Miller, Washington University School of Medicine) was constructed
using recombinant inbred lines (Scott E. Baird, Wright State
University) which yielded 6 chromosomes.  The genetic mapping data
along with underlying read pairing data were used to break several
misassemblies in ultracontigs and to order and orient the sequences
along the C. briggsae chromosomes to create the Cb3 release.

Of the 108 megabase (Mb) genome, 91Mb of the sequence is ordered along
the chromosomes and of that, 67Mb is confidently oriented.  An
additional 10Mb is localized to a specific chromosome but not ordered
(and thus located in the _random bin) leaving only 7Mb currently
unassigned. The 101 Mb localized to chromosomes is organized into only
139 ultracontigs.

The N50 contig size in this assembly is 41 kb and the N50 supercontig
size is 1.25 Mb. The sequencing centers estimate that this whole
genome shotgun assembly achieved 98% coverage of the genome. We
continue to refine the genetic map and plan to release future updates
to the genomic sequence.


Credits

Sequencing data -  The Genome Sequencing Center at Washington University in St. Louis and the Sanger Institute.
Physical map - The Genome Sequencing Center at Washington University in St. Louis.
Genetic map - The SNP Research Facility at Washington University  in St. Louis
C. briggsae strains and recombinant inbred lines -  Scott E. Baird, Department of Biological Sciences, Wright State University
Chromosomal organization of the data/map integration - Washington University in St. Louis and University of Washington
Initial publication of the C. briggsae genome -  Stein et al., 2003, 
    The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol 1:E45. PMID 14624247
Wormbase - Public repository for C. briggsae sequence and annotation