On May 7, 2007 this sequence version replaced gi:123977279.
The Collinsella aerofaciens ATCC 25986 whole genome shotgun (WGS) project has the project accession AAVN00000000. This version of the project (02) has the accession number AAVN02000000, and consists of sequences AAVN02000001-AAVN02000025.
Collinsella aerofaciens (GenBank Accession Number for 16S rRNA gene: AB011816) is a member of the division Actinobacteria. In one comprehensive 16S rDNA sequence-based enumeration of the colonic microbiota of three healthy adult humans, it represents, on average, 0.11% of all 16S rDNA sequences and 59.155% of the sequences in its division (Eckburg et. al. (2005)). The sequenced strain was obtained from ATCC (ATCC 25986) and is part of a 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.
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 3730xl sequencers was devised and implemented to generate the draft genome sequences. At least 15X sequence coverage of 454 reads and at least 4X sequence coverage of 3730 reads were collected. 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 assembly version is a manually improved assembly. The specifications for sequence improvement are similar to those of comparative-grade finished sequence with the exception of providing order and orientation between contigs.
The major specifications for manually improved sequence are
1) detectable, major artifacts resulting from the sequence-assembly process (e.g., misassemblies) must be resolved;
2) suspect, incorrect consensus sequence is manually edited, and irrelevant sequence at ends of contigs trimmed.
3) Joins between contigs, if found, are manually completed.
4) Order and orientations between contigs are provided if possible.
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. RNA genes were determined using tRNAscan-SE 1.23 or Rfam v0.1. Gene names are generated at the contig level and may not necessarily reflect any known order or orientation between contigs.
Annotation was added to the contigs in March 2007.
This is a reference genome for the Human Microbiome Project. This project is co-owned with the Human Microbiome Project DACC.
Product names were updated in August 2012.
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