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ASM455v1

Organism name:
Caenorhabditis briggsae (nematodes)
Infraspecific name:
Strain: AF16
BioProject:
PRJNA10731
Submitter:
The C.briggsae Sequencing Consortium
Date:
2008/05/01
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_000004555.1 (replaced)
RefSeq assembly accession:
GCF_000004555.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
CAAC02

IDs: 274198 [UID] 5658 [GenBank] 274198 [RefSeq]

See Genome Information for Caenorhabditis briggsae

History (Show revision history)

Comment

Submitted by: Genome Sequencing Center Department of Genetics, Washington University St. Louis , MO 63110, USA, and Sanger Centre, Hinxton Hall Cambridge CB10 IRQ, England email: stlouis@wormbase.org and sanger@wormbase.org NOTICE: This C. briggsae sequence (version Cb3) 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 (PLoS Biology Vol. 5, No. 7, e167) 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. For a graphical representation of this clone sequence and its analysis see:
http://www.wormbase.org/db/seq/sequence?name=cb25.fpc1402c NOTES: Coding seqences below are the result of integration and manual review of the following data : computer analysis using the programs Genefinder (version 980506; P. Green, unpublished data), FGENESH (Salamov and Solovyev 2000), TWINSCAN (Korf et al. 2001), and the Ensembl annotation pipeline (Clamp et al. 2003); similarity to other proteins from BlastX analyses (http://blast.wustl.edu/); sequence conservation with C. elegans using Jim Kent's WABA alignment program (Genome Research 10:1115-1125, 2000); individual C. briggsae GenBank submissions; and personal communications with C. briggsae researchers. tRNAs are predicted using the program tRNAscan-SE (Lowe, T.M. and Eddy, S.R., 1997, Nucl. Acids. Res., 25, 955-964).  more

Global statistics

Total sequence length108,478,526
Total ungapped length105,439,387
Gaps between scaffolds0
Number of scaffolds12
Scaffold N5014,512,975
Scaffold L504
Number of contigs5,075
Contig N5045,155
Contig L50607
Total number of chromosomes and plasmids6
Number of component sequences (WGS or clone)607

Supplemental Content

PubMed articles for this assembly

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
Assembly Unit: Primary Assembly (GCF_000004565.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome ICU538964.1=NC_013489.11
Chromosome IICU538965.1=NC_013486.11
Chromosome IIICU538966.1=NC_013490.11
Chromosome IVCU538967.1=NC_013487.11
Chromosome VCU538968.1=NC_013488.11
Chromosome XCU538969.1=NC_013491.10
unplacedn/an/an/a1

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule108,478,52612105,439,38714,512,9755,0630
Chromosome IAllAssembled moleculeUnlocalized scaffolds14,783,86411,274,8433,509,02121114,352,31210,937,1833,415,12911,274,84311,274,8433,509,021769549220000
Chromosome IIAllAssembled moleculeUnlocalized scaffolds16,765,88514,512,9752,252,91021116,202,67014,066,1142,136,55614,512,97514,512,9752,252,910750646104000
Chromosome IIIAllAssembled moleculeUnlocalized scaffolds14,409,41813,544,562864,85621113,998,28113,163,382834,89913,544,56213,544,562864,85666661254000
Chromosome IVAllAssembled moleculeUnlocalized scaffolds16,041,35515,290,274751,08121115,529,76714,803,644726,12315,290,27415,290,274751,08175570055000
Chromosome VAllAssembled moleculeUnlocalized scaffolds18,558,28216,004,1012,554,18121118,115,01915,625,6152,489,40416,004,10116,004,1012,554,18169460193000
Chromosome XAssembled molecule20,608,032120,205,70920,608,0324540
unplacedAssembled molecule7,311,69017,035,6297,311,6909750
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