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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

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