Complete Genome Sequence of Pseudomonas sp. UK4, a Model Organism for Studies of Functional Amyloids in Pseudomonas.

Here, we present the complete genome of Pseudomonas sp. UK4. This bacterium was the first Pseudomonas strain shown to produce functional amyloids, and it represents a model organism for studies of functional amyloids in Pseudomonas (Fap).

GENOME ANNOUNCEMENT

Members of the gammaproteobacterial genus Pseudomonas are Gram-negative, rod shaped, bacteria renowned for their incredible metabolic capacity, physiologic versatility, and ability to form biofilms, which allows them to occupy a wide range of environmental niches (1). Pseudomonas sp. UK4 was originally isolated from a biofilm formed in a drinking water reservoir in a random search for bacteria producing functional amyloids (2, 3). UK4 was taxonomically assigned to the P. fluorescens group based on 16S rRNA gene nucleotide sequence analysis, as well as physiological and biochemical features (4). UK4 was shown to produce functional amyloid fimbriae, which were distinct from the previously known curli fimbriae of E. coli (5–7). Pseudomonas sp. UK4 represents an important model organism for studies of functional amyloids in Pseudomonas (Fap).

Genomic DNA was isolated using the PowerMicrobial Maxi DNA isolation kit (MoBIO, Carlsbad, CA). Paired-end and mate-pair libraries were prepared with the TruSeq DNA PCR-Free and mate-pair (v2) sample preparation kits (Illumina, Germany), respectively. The mate-pair library was prepared without any size selection. All procedures were carried out as recommended by the manufacturer. Sequencing of the libraries was performed using a MiSeq sequencer (Illumina, Germany). The paired-end reads were trimmed for adapters and quality using the build-in tool of CLC Genomics Workbench v7.0 (CLC bio, USA). The mate-pair reads were trimmed for adapters and quality using the NextClip tool v0.8 (8). The genome was de novo assembled from the paired-end and mate-pair data using SPAdes genome assembler v3.1.0 (9) with k-mers of 55, 77, 99, and 127 bp. Manual scaffolding of contigs was carried out based on paired-end and mate-pair information. Cytoscape v2.8.3 (10) was used for visualization and manual inspection of the assemblies as described elsewhere (11). Gaps were closed and subsequent validated by manual read mapping in CLC Genomics Workbench. The average coverage of the assembly was 150×. Annotation was done using the NCBI prokaryotic genome automatic annotation pipeline (PGAAP) (12).

The complete genome of Pseudomonas sp. UK4 is composed of a circular chromosome of 6,064,456 bp. The overall G+C content is 60.1%. The strain is most closely related to Pseudomonas sp. strain TKP, with which it shares 84.8% average nucleotide identity (ANIb) (13, 14). Annotation by the NCBI PGAAP identified 5,178 coding sequences (CDS) as well as 19 rRNA (5S, 16S, or 23S) and 68 tRNA genes.

Nucleotide sequence accession number.

This whole-genome sequencing project has been deposited at GenBank under the accession no. CP008896.