Draft Genome Sequence of the Arsenate-Respiring Bacterium Chrysiogenes arsenatis Strain DSM 11915.

Here we present the draft genome sequence of Chrysiogenes arsenatis strain DSM 11915, only the second genome sequence from the phylum Chrysiogenetes. This strictly anaerobic organism was isolated from arsenic-contaminated gold mine wastewater and respires arsenate or nitrate instead of oxygen. The assembly contains 2,824,977 bp in 22 scaffolds.

GENOME ANNOUNCEMENT

Chrysiogenes arsenatis is a curved, rod-shaped, Gram-negative, strictly anaerobic bacterium that was isolated from arsenic-contaminated mud of a reed bed in the Ballarat Goldfields, Australia (1). Unusually, C. arsenatis uses acetate as the electron donor and carbon source, and arsenate as the preferred electron acceptor, producing CO2 and arsenite (2). Nitrate or nitrite can also be used as electron acceptors, producing NH4. At the time of isolation, this species was the only member of the Chrysiogenetes phylum (3) but has since been joined by members of the genera Desulfurispira and Desulfurispirillum (4, 5). The only other member of this phylum to be sequenced is Desulfurispirillum indicum (6). C. arsenatis was selected in 2002 as part of a project at the Institute for Genomic Research (TIGR) to sequence the genomes of representatives of the seven phyla of bacteria that at the time had cultured representatives but no available genome sequence. Sanger clone-based sequencing of the genome failed to produce a high-quality assembly, and the project was delayed pending additional sequencing with Illumina technology.

DNA from C. arsenatis strain DSM 11915 was extracted at Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) (German Collection of Microorganisms and Cell Cultures) via lysis with lysozyme and proteinase K, phenol and chloroform extraction, and purification with Prep-A-Gene (7). Sanger libraries (small and medium insert and fosmid) were constructed as previously described (8). Illumina paired-end libraries were made from sonicated DNA using standard Illumina protocols and reagents.

A hybrid genome assembly was generated using MIRA (version 3.9.17) (9), with 33,005 Sanger reads (average length, 1,037 bp) and 4,000,000 Illumina reads (average length, 84 bp) that were randomly subsampled from the 41,433,640 total Illumina reads sequenced. The contigs resulting from this assembly were filtered to remove contigs shorter than 500 bp as well as those with >33% of the average coverage for the assembly. This resulted in 51 contigs which, along with 37,362,734 error-corrected/quality-trimmed Illumina reads generated by the A5 assembly pipeline (10), were used to build 22 scaffolds in SSPACE (11). These Illumina reads were then aligned to the scaffolds using Bowtie (12) to eliminate artifacts in the assembly. One such region (~700 bp) was found, which by BLAST (13) analysis appeared to be a vector sequence and was removed from the assembly. During the creation of GenBank submission files, some contigs were merged based on short overlaps and read pair information, yielding a final collection of 23 contigs. The final assembly contains 2,824,977 bp and has a GC content of 50% and coverage estimates of 12× (Sanger) and 120× (Illumina).

Completeness of the genome was assessed using the Phylosift software (A. Darling, G. Jospin, E. Lowe, E. Matsen, H. Bik, and J. Eisen, submitted for publication), which searches for 40 highly conserved, single-copy marker genes (14). All 40 genes were found in this assembly. Automated annotation was performed using the RAST annotation server (15). C. arsenatis DSM 11915 contains 2,592 predicted coding sequences and 43 predicted RNAs.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number AWNK00000000. The version described in this paper is version AWNK01000000. Complete Illumina and Sanger reads are available at http://dx.doi.org/10.6084/m9.figshare.799759.