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ASM18789v1

Organism name:
Bacteroides plebeius DSM 17135 (CFB group bacteria)
Infraspecific name:
Strain: DSM 17135
BioSample:
SAMN00000028
Submitter:
Washington University Genome Sequencing Center
Date:
2010/09/09
Assembly level:
Scaffold
Genome representation:
full
RefSeq category:
representative genome
Relation to type material:
assembly from type material
GenBank assembly accession:
GCA_000187895.1 (latest)
RefSeq assembly accession:
GCF_000187895.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
ABQC02

IDs: 243158 [UID] 243138 [GenBank] 243158 [RefSeq]

See Genome Information for Bacteroides plebeius

History (Show revision history)

Comment

Bacteroides plebeius (GenBank Accession Number for 16S rDNA gene: AB200217) is a member of the Bacteroidetes division of the domain bacteria and has been isolated from human feces. The sequenced strain was obtained from Deutsche Sammlung von Mikroorganismen und ... Zellkulturen GmbH (DSMZ)(DSM 17135).

We have collected 7.9X coverage in plasmid end reads and 454 reads. We have performed one round of automated sequence improvement(pre-finishing), along with manual improvement that includes breaking apart any mis-assembly, and making manual joins where possible. Manual edits also are made where the consensus appears to be incorrect. All low quality data on the ends of contigs is removed. Contigs are ordered and oriented where possible.

Sequencing/Assembly: The genomic DNA was purified from liquid culture derived from a single bacterial colony. A hybrid sequencing strategy that utilized reads from both 454 GS-20 and ABI 3730xlsequencers was devised and implemented to generate the draft genome sequences. 454 reads were assembled using Newbler (454 Life Sciences) into 454 de novo contigs. These de novo contigs were converted in silico to 800 base paired reads ('superreads') with 400 base overlaps with neighboring superreads. Finally, PCAP (Huang, et al, Genome Research, 13:2164, (2003)) was used to assemble the super-reads and the conventional 3730xl capillary reads.

This sequenced strain is part of a comprehensive, sequence-based survey of members of the normal human gut microbiota. A joint effort of the WU-GSC and the Center for Genome Sciences at Washington University School of Medicine, the purpose of this survey is to provide the general scientific community with a broad view of the gene content of 100 representatives of the major divisions represented in the intestine's microbial community. This information should provide a frame of reference for analyzing metagenomic studies of the human gut microbiome. Further details of this effort are described in a white paper entitled "Extending Our View of Self: the Human Gut Microbiome Initiative (HGMI)" (http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/HGMISeq.pdf). These studies are supported by National Human Genome Research Institute.

Coding sequences were predicted using GeneMark v3.3 and Glimmer2 v2.13. Intergenic regions not spanned by GeneMark and Glimmer2 were blasted against NCBI's non-redundant (NR) database and predictions generated based on protein alignments. tRNA genes were determined using tRNAscan-SE 1.23 and non-coding RNA genes by RNAmmer-1.2 and Rfam v8.0. Gene names are generated at the contig level and may not necessarily reflect any known order or orientation between contigs. 

For answers to your questions regarding this assembly or project, or any other GSC genome project, please visit our Genome Groups web page (http://genome.wustl.edu/genome_group_index.cgi) and email the designated contact person.

Annotation was added to the contigs in September 2008.

This is a reference genome for the Human Microbiome Project. This project is co-owned with the Human Microbiome Project DACC.  more

Global statistics

Total sequence length4,421,924
Total assembly gap length600
Gaps between scaffolds0
Number of scaffolds19
Scaffold N50478,534
Scaffold L504
Number of contigs25
Contig N50478,534
Contig L504
Total number of chromosomes and plasmids0

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Global assembly definition

Download the full sequence report
The primary assembly unit does not have any assembled chromosomes or linkage groups.
Please download the full sequence report for information on the scaffolds.

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
unplaced4,421,924194,421,324478,53460