Genome Sequence of Janthinobacterium sp. Strain PAMC 25724, Isolated from Alpine Glacier Cryoconite

Abstract

The draft genome of Janthinobacterium sp. strain PAMC 25724, which is a violacein-producing psychrotolerant bacterium, was determined. The strain was isolated from glacier cryoconite of the Alps mountain permafrost region. The sequence will allow identification and characterization of the genetic determination of its cold-adaptive properties.

GENOME ANNOUNCEMENT

The genus Janthinobacterium includes violacein-producing, Gram-negative, motile, rod-shaped bacteria that are commonly isolated from the microbiota of soils and water of rivers, lakes, and springs, including permafrost regions, such as Antarctic soil (4, 7). Janthinobacterium sp. is one of the most common purple-pigmented species that produces the water-insoluble pigment violacein (6), and it is suggested that the inhibitory effects of the antifungal symbionts are due to secondary bacterial metabolites as opposed to resource competition (2). Janthinobacterium sp. strain PAMC 25724 was isolated from glacier cryoconite of the Alps mountain range, Austria (47°04′N, 12°41′E).

The genome of Janthinobacterium sp. PAMC 25724 was analyzed using a combined approach with the 454 GS FLX Titanium system (Roche Diagnostics, Branford, CT) with an 8-kb paired-end library (111,434 reads) and the Illumina GAIIx (San Diego, CA) with a 500-bp paired-end library (10,757,494 reads). The 454 GS FLX sequencing achieved about 8.7-fold coverage, while 208-fold read coverage was achieved by Illumina paired-end sequencing. The reads generated by the Illumina GAIIx and the 454 GS FLX Titanium were assembled using Celera assembler 6.1 (5). Gene prediction and annotation were carried out using Glimmer3 (3), the rapid annotations using subsystems technology (RAST) server (1), and the NCBI COG database (8). The draft genome sequence of Janthinobacterium sp. PAMC 25724 includes 4,985,247 bases and comprises 4,339 predicted coding sequences. It consists of 48 contigs (N₅₀ contig size was approximately 245 kb), which can be assembled into 4 scaffolds (N₅₀ scaffold size was approximately 4,183 kb). The G+C content was 59.5%. Additionally, 72 tRNA genes, two 5S rRNA genes, one 23S rRNA gene, and one 16S rRNA gene were predicted in the draft genome. Approximately 84.9% of nucleotides were predicted as protein-coding regions, and 73.7% (3,197) of the open reading frames were annotated with known proteins. Comparison with genome sequences available in the RAST server showed that Janthinobacterium sp. Marseille (score, 537), Herminiimonas arsenicoxydans (score, 422), and Oxalobacter formigenes OXCC13 (score, 351) were the closest neighbors of strain PAMC 25724.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number AHHB00000000. The version described in this paper is the first version, AHHB01000000.