Complete Genome Sequence of Phenylobacterium Strain NIBR 498073, Isolated from the Sediment of a Tidal Flat

ABSTRACT We report the complete genome sequence of Phenylobacterium sp. strain NIBR 498073. The sample was isolated from sediment from a tidal flat in Incheon, South Korea. The whole genome consists of one circular chromosome of 4,289,989 bp, and annotation using PGAP predicted 4,160 protein coding genes, 47 tRNAs, 6 rRNAs, and 3 noncoding RNAs.

P henylobacterium sp. strain NIBR 498073, which is Gram negative, flagellar, and rod shaped, was isolated from tidal flat sediments in Incheon, South Korea (1,2). Phenylobacterium not only plays a role in maintaining the environment by participating in various metabolism processes in nutrient-poor environments but also has important roles in biodegradation (3)(4)(5). However, only 17 valid descriptions of Phenylobacterium species have been published so far (https://lpsn.dsmz.de/genus/phenylobacterium) (6).
A sediment sample taken from a depth of less than 5 cm at a tidal flat in Incheon, South Korea (37°39902.00N, 126°31910.00E), was diluted in 0.85% (wt/vol) saline, spread onto marine agar 2216 (BD), and then incubated at 25°C for 3 days. Cells from a single colony were collected in a 5-mL Eppendorf tube for DNA extraction. Genomic DNA was extracted using the RBC DNA extraction kit (Taiwan), and a Covaris g-TUBE device was used to shear the genomic DNA according to the manufacturer's instructions. The DNA was sheared to a target size of 15 kb, purified using AMPure XP magnetic beads (Beckman Coulter, Inc.), and measured using a bioanalyzer (Agilent, USA). A library was constructed using the PacBio SMRTbell library preparation kit version 1.0 (Pacific Biosciences, Menlo Park, CA, USA). DNA damage repair and end repair were performed using the SMRTbell damage repair kit (Pacific Biosciences), and then the SMRTbell enzyme cleanup kit (Pacific Biosciences) was added to the library. The genome library size was measured using the Blue Pippin size selection system (Sage Science, Beverly, MA, USA) to ensure that all reads were over 15 kb, and the library was sequenced on the PacBio RS II platform.
To preprocess the raw sequence reads (N 50 , 9,998 bp), the SeqKit v2.3.0 was used to evaluate quality and filter reads less than 1,000 bp long (7). This step yielded 1,535,346 filtered sequence reads, with 13,303,322,204 bp. The bacterium formed a high-quality sequence, with a coverage of over 2,892Â. As a result of assembly using the Flye version 2.9.1 pipeline (8), 1 complete circular genome sequence of 4,289,989 bp was constructed. After annotation based on the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) version 6.5 (9), strain NIBR 498073 was found to contain 4,160 protein coding genes, 47 tRNAs, 6 rRNAs, and 3 noncoding RNAs (ncRNAs). All genomic sequence data are summarized in Table 1.
The complete genome of strain NIBR 498073 will provide insight into isolating novel Phenylobacterium species and contribute to a deeper understanding of the biological properties of bacteria.
Data availability. The accession numbers are listed in Table 1. The assembled genome was deposited at GenBank under the accession number CP114599 and the BioProject accession number PRJNA913615. The raw sequence reads have been submitted to the Sequence Read Archive (SRA) under the accession number SRR22805297.