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Sequence Set Browser

 

AADL00000000.1 mine drainage metagenome

Master
# of Contigs: 2,534 (109 are dead)
# of Proteins: 2,543
# of Scaffolds/Chrs: 908
Total length: 12,979,231 bp
BioProject: PRJNA13696
BioSample: SAMN02954273
Keywords: WGS
Annotation: Scaffolds
Organism: mine drainage metagenomeshow lineagehide lineage
Biosource:
/country = USA: Richmond Mine at Iron Mountain 5-way site, CA
/environmental_sample
/isolation_source = pink biofilm microbial community collected from flowing acid mine drainage (pH 0.8, 42C)
/lat_lon = 40.68 N 122.2 W
/metagenomic
/mol_type = genomic genomic
WGS: AADL01000110:AADL01002534
Scaffolds: CH003545:CH003921, CH003922:CH004070, CH004071:CH004104, CH004105:CH004435, DS995259:DS995275
908 scaffolds, 2,543 proteins, total length is 9,768,579 bases
Reference:
Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation : PLoS Biol. 6 (7), E177 (2008) – show 6 authorshide authors
Simmons,S.L., Dibartolo,G., Denef,V.J., Goltsman,D.S., Thelen,M.P., Banfield,J.F.
Reference:
Community structure and metabolism through reconstruction of microbial genomes from the environment : Nature 428 (6978), 37-43 (2004) – show 10 authorshide authors
Tyson,G.W., Chapman,J., Hugenholtz,P., Allen,E.E., Ram,R.J., Richardson,P.M., Solovyev,V.V., Rubin,E.M., Rokhsar,D.S., Banfield,J.F.
Reference:
Genome dynamics in a natural archaeal population : Proc. Natl. Acad. Sci. U.S.A. 104 (6), 1883-1888 (2007) – show 6 authorshide authors
Allen,E.E., Tyson,G.W., Whitaker,R.J., Detter,J.C., Richardson,P.M., Banfield,J.F.
Submission:
Submitted (27-JAN-2004) DOE Joint Genome Institute, 2800 Mitchell Drive - B100, Walnut Creek, CA 94598-1698, USA – DOE Joint Genome Institute
Submission:
Submitted (11-JUL-2008) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA – show 14 authorshide authors
DiBartolo,G., Denef,V.J., Aliaga Goltsman,D.S., Simmons,S.L., Banfield,J.F., Lucas,S.L., Copeland,A., Glavina del Rio,T., Dalin,E., Tice,H., Bruce,D., Goodwin,L., Pitluck,S., US DOE Joint Genome Institute (JGI-PGF)

The mine drainage metagenome whole genome shotgun (WGS) project has the project accession AADL00000000. This version of the project (01) has the accession number AADL01000000, and consists of sequences AADL01000110-AADL01002534.

URL -- http://www.jgi.doe.gov Contact: Paul Richardson microbes@cuba.jgi-psf.org An environmental sample consisting of an acid mine drainage microbial biofilm was obtained and sequenced. This has resulted in the culture-independent recovery of two near-complete microbial genomes and partial recovery of three other genomes. The scaffolds of these five genomes are: DS995259-DS995275 (Leptospirillum sp. Group II '5-way CG') CH003545-CH003921 (Leptospirillum sp. Group III) CH003922-CH004070 (Ferroplasma acidarmanus Type I) CH004071-CH004104 (Ferroplasma sp. Type II) CH004105-CH004435 (Thermoplasmatales archaeon Gpl) Additional Leptospirillum sp. Group II '5-way CG' sequences were identified and that genome was updated, as discussed in PubMed 18651792. Thus, contigs AADL01000001-AADL01000109 were replaced by contigs AADL01002456-AADL01002534 in August 2008, and scaffolds CH003520-CH003544 were replaced by scaffolds DS995259-DS995275 in September 2008. Scaffolds DS995259-DS995275 are annotated.

Contigs
Download
GenBank:AADL01.1.gbff.gz 4.7 Mb
FASTA:AADL01.1.fsa_nt.gz 3.2 Mb
ASN.1:AADL01.1.bbs.gz 2.7 Mb