Info • Acidomyces richmondensis BFW (metagenome-extracted)

Status

December 2011. This is a de novo Velvet assembly of Illumina reads from metagenomic sequencing of a streamer community from the 5-way site in the Richmond Mine at Iron Mountain, CA, USA. The assembly was guided by tetranucleotide binning with Emergent Self-Organizing Maps (Dick et al. 2009) and manually curated for misassemblies and incorrectly binned contigs.  This genome was sequenced by the JGI and assembled in the laboratory of Jillian Banfield at the University of California, Berkeley.

September 2014.  The genome scaffold 5WFSArich_Contig_01615 was found to likely be of Sulfobacillus origin.  We have therefore demoted the 12 models found on this scaffold from the gene catalog.

Dick, G. J., A. F. Andersson, B. J. Baker, S. L. Simmons, B. C. Thomas, A. P. Yelton and J. F. Banfield (2009). "Community-wide analysis of microbial genome sequence signatures." Genome Biol 10(8): R85.

Summary statistics for the Acidomyces richmondensis BFW v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp} 26.82
Sequencing read coverage depth ?
# of contigs 1683
# of scaffolds 1683
# of scaffolds >= 2Kbp 1251
Scaffold N50 166
Scaffold L50 (Mbp) 0.05
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 0.25, 0.20, 0.18


ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests ESTs (RNAseq data assembled using RNNotator) 37087 27797 75.0%


Gene Models FilteredModels1
length (bp) of: average median
gene 1555 1346
transcript 1444 1226
exon 629 361
intron 88 63
description:
protein length (aa) 427 353
exons per gene 2.30 2
# of gene models 10352


Collaborators

Genome Reference(s)

Please cite the following publication(s) if you use the data from this genome in your research:

Mosier AC, Miller CS, Frischkorn KR, Ohm RA, Li Z, LaButti K, Lapidus A, Lipzen A, Chen C, Johnson J, Lindquist EA, Pan C, Hettich RL, Grigoriev IV, Singer SW, Banfield JF
Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage.
Front Microbiol. 2016;7():238. doi: 10.3389/fmicb.2016.00238

Links

Funding

The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.