Permanent Draft Genome Sequence of Desulfurococcus amylolyticus Strain Z-533T, a Peptide and Starch Degrader Isolated from Thermal Springs in the Kamchatka Peninsula and Kunashir Island, Russia.

Desulfurococcus amylolyticus Z-533T, a hyperthermophilic crenarcheon, ferments peptide and starch, generating acetate, isobutyrate, isovalerate, CO2, and hydrogen. Unlike D. amylolyticus Z-1312, it cannot use cellulose and is inhibited by hydrogen. The reported draft genome sequence of D. amylolyticus Z-533T will help to understand the molecular basis for these differences.

GENOME ANNOUNCEMENT

Desulfurococcus  amylolyticus Z-533T (DSM 3822T), an inhabitant of thermal springs in the Kamchatka Peninsula and Kunashir Island, Russia, is a hyperthermophilic, anaerobic, sulfur-reducing crenarcheon (1). It is a nonmotile regular coccus of 0.7 to 1.5 μm in diameter (1). In laboratory cultures, D. amylolyticus Z-533T uses peptides such as casein hydrolysates, peptone, and yeast extract and simple carbohydrates that include starch, pectin, and glycogen as energy substrates. Sulfur stimulates growth, and, when it is employed, H2S is produced. The absence of sulfur results in poor growth and H2 production.

The 16S rRNA gene sequences of D. amylolyticus Z-533T differ by 0.1 to 0.3% from those of other D. amylolyticus strains, namely, Z-1312 and 1221n (2–4), which were formerly known as D. fermentans Z-1312 and D. kamchatkensis 1221n, respectively (5). Of these, only D. amylolyticus Z-1312 degrades cellulose (2) and is not inhibited by the presence of hydrogen (6). However, it lacks known cellulose genes and might employ novel mechanisms for cellulose degradation. Thus, a genomic analysis of three desulfurococci will give insight into the mechanisms by which D. amylolyticus Z-1312 degrades cellulose and by which other strains are inhibited by hydrogen.

The permanent draft genome of D. amylolyticus strain Z-533T (DSM 3282T) was generated at the DOE Joint Genome Institute (JGI) (7). The term “permanent” indicates that this genome sequence has been completed at a draft level and submitted to GenBank (8). The sequencing of a standard shotgun library on the Illumina platform generated 28,000,000 reads of 150 bp. These raw sequences were passed through DUK (9), and filtered reads were assembled with Velvet (10) and ALLPATHS-LG (11, 12). The final assembly contained one scaffold and two contigs. Structural and functional annotations were performed using the JGI’s microbial genome annotation pipeline (13). The predicted coding sequences were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant, UniProt, TIGR-Fam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Ribosomal and tRNA genes were identified with HMMER version 3.0rc1 (14) and tRNAscan-SE version 1.23 (15), respectively. Noncoding genes were predicted using Infernal version 1.0.2 (16). Additional annotation was performed within the Integrated Microbial Genomes—Expert Review platform (17). Clustered regularly interspaced short palindromic repeats (CRISPR) elements were detected using CRT (18) and PILER-CR (19).

The draft assembly of D. amylolyticus Z-533T resulted in one scaffold and two contigs with a total sequence size of 1,309,099 bp and a 45.2% G+C content. It encoded 1,394 polypeptides, 59 RNAs (one 5S-, one 16S-, one 23S rRNA, 47 tRNAs, and nine other RNAs), and one putative CRISPR. The analysis predicted a peptide and starch degradation system for D. amylolyticus Z-533T that is present in D. amylolyticus 1221n and Z-1312.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number AZUU00000000. The version described in this paper is the first version, AZUU01000000.