Whole-Genome Sequence of Filimonas lacunae, a Bacterium of the Family Chitinophagaceae Characterized by Marked Colony Growth under a High-CO2 Atmosphere.

We report here the genome sequence of Filimonas lacunae, a bacterium of the family Chitinophagaceae characterized by high-CO2-dependent growth. The 7.81-Mb circular genome harbors many genes involved in carbohydrate degradation and related genetic regulation, suggesting the role of the bacterium as a carbohydrate degrader in diverse environments.

GENOME ANNOUNCEMENT

The Gram-negative bacterial genus Filimonas was established based on the identification of Filimonas lacunae NBRC 104114, whose colony growth depends on high atmospheric CO2 and humidity (1–3). The genus currently consists of three species, F. lacunae, Filimonas endophytica (4), and Filimonas zeae (5). While F. lacunae was isolated from freshwater, the other two were originated from plant root. Filimonas constitutes a novel taxonomic group within the family Chitinophagaceae (6). At the time of this writing, genome sequence information from eight genera of this family is available at the NCBI database (http://www.ncbi.nlm.nih.gov/genome/). Here, we report the whole-genome sequence of F. lacunae, the first genome information from Filimonas.

Genomic DNA isolated from F. lacunae, as described previously (1), was checked for quality using a NanoDrop spectrophotometer (Thermo Scientific, USA) and a Qubit fluorometer (Invitrogen, USA). The genomic DNA was sheared to an average size of 10 kb using g-Tubes (Covaris, USA). A genomic library was generated using a DNA template prep kit 1.0 and DNA/polymerase binding kit P6 (Pacific Biosciences [PacBio]). Size selection and quality checking of the genome library were carried out with a BluePippin system (Nippon Genetics, Japan) and an Agilent 2100 Bioanalyzer (Agilent, USA), respectively. A PacBio RSII sequencer was used to sequence the 10-kb library of the F. lacunae genome using P4-C2 chemistry. Coverage of 176-fold was achieved, and the reads were assembled using the Hierarchical Genome Assembly Process version 2 (PacBio) (7). The genome sequences were successfully assembled to closure to yield a single contig. The assembled genome was then circularized prior to annotation with Rapid Annotations using Subsystems Technology (RAST) (8). The annotation was manually checked, modified, and submitted to DDBJ.

A single contig of 7,814,405 bp with 44.05% G+C content was generated from the assembly. The GC-skew profile resembled that of Chitinophaga pinensis (9), the close taxon of the family Chitinophagaceae. The genome did not contain any plasmids. RAST predicted 6,363 genes for protein-coding sequences, 15 rRNA (5 rrn operons), and 70 tRNA genes. The total length of these coding regions was 7,082,902 bp (90.6% of the total genome size). The majority (62.5%) of the coding regions were assigned a putative function, while those remaining were annotated as hypothetical proteins.

A whole-genome survey using the SEED viewer (10) showed the presence of a large number of genes encoding proteins involved in carbohydrate metabolism and related genetic control. Sugar-degrading enzymes affiliated with glucosidase (20 copies) and galactosidase (33 copies) and transcriptional regulators of AraC (107 copies) and cAMP receptor protein (CRP)/fumarate and nitrate reduction regulatory protein (FNR) family (45 copies) were identified. Many signal transducers, such as extracytoplasmic function (ECF)-type RNA polymerase sigma factors (86 copies), anti-sigma factors (68 copies), two-component regulatory systems (124 components), and TonB-dependent receptors (106 copies), were also identified. The genome information implies the feature of the organism as a carbohydrate degrader adapting to diverse environments.

Nucleotide sequence accession number.

The genome sequence of Filimonas lacunae is available in DDBJ under the accession no. AP017422. The version described in this paper is the first version.