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cb4 ReadMe

Source: ftp://ftp.wormbase.org/pub/wormbase/species/c_briggsae/assemblies/assembly/cb4/README.briggsae_cb4

Caenorhabditis briggsae nuclear genome assembly cb4


To improve upon the C. briggsae nuclear genome assembly cb3 [Hillier
et al., 2007], 167 AF16/HK104 advanced-intercross recombinant inbred
lines were successfully genotyped at 1,032 single nucleotide
polymorphism (SNP) markers. The resulting data were used to estimate
high-density genetic maps. Sequences were assembled by combining the
physical (cb25 assembly [Stein et al. 2003]) and genetic positions of
the SNPs to inform the process of ordering and orienting the cb25
supercontigs into chromosome assemblies. Detailed methods are
available in the manuscript describing cb4 (see below).


37 of the cb25 fingerprint contigs were split into 100 supercontigs to
resolve discrepancies between the physical and genetic orders of

638 sequence supercontigs comprise the cb4 assembly:

a) 277 supercontigs, comprising 105 Mbp, are ordered along chromosomes
and comprise the chromosome assemblies. 145 of these sctgs, comprising
89 Mbp of sequence, are also genetically-oriented.

b) 8 supercontigs (288 kbp) were genetically mapped to a chromosome
assembly (in cb3 and/or in cb4) but have not been assigned an
unambiguous position within the assembly; these comprise the
Chr*_random assemblies.

c) 353 supercontigs, comprising 2.9 Mbp of sequence (range 1-85 kbp
per sctg), remain unassigned to chromosome assemblies, comprising the
Unassembled (or Unassigned – ChrUn) assembly.

1.8 Mbp of sequence on 15 supercontigs changed chromosomal assignment
from cb3 to cb4.

The total nuclear genome content decreased from cb25 to cb4 because of
the removal of three supercontigs containing mitochondrial genome
sequence (totaling 20.1 kbp).


C. briggsae cb4 will be available in WormBase release WS224, and
revised supercontig sequences and assembly are being submitted to
the International Nucleotide Sequence Database Collaboration (INSDC).


The temporary citation is:
Ross JA, Koboldt DC, Staisch JE, Chamberlin HM, Gupta BP, Miller RD,
Baird SE, Haag ES. “Caenorhabditis briggsae recombinant inbred line
genotypes reveal inter-strain incompatibilities and the evolution of
recombination.” (2011) PLoS Genetics (in review).