Complete Genome Sequence of Flavobacterium sediminilitoris YSM-43T, Isolated from Tidal Sediment in Yeosu.

Here, we report the complete genome sequence of Flavobacterium sediminilitoris YSM-43T, isolated from a tidal flat in Yeosu, Republic of Korea. The whole genome consists of one circular chromosome of 3,913,692 bp. A total of 3,599 genes were predicted, comprising 3,537 coding DNA sequences (CDSs), 50 tRNAs, 9 rRNAs, and 3 noncoding RNAs (ncRNAs).

ANNOUNCEMENT

The genus Flavobacterium, the type genus of the family Flavobacteriaceae in the phylum Bacteroidetes, is a Gram-negative, yellow-pigmented, and rod-shaped bacterium. Commonly, Flavobacterium thrives in various habitats, including both terrestrial and marine ecosystems (1). At the time of writing, 268 valid descriptions of Flavobacterium species have been published (https://lpsn.dsmz.de/genus/flavobacterium) (2). According to BacDive (3), two Flavobacterium spp. have been isolated from tidal flats, Flavobacterium sediminis and Flavobacterium sediminilitoris (4, 5). F. sediminilitoris YSM-43T was isolated from a tidal flat in the Republic of Korea in 2018, but its genomic properties are still unknown (5). Therefore, in this study, whole-genome sequencing of F. sediminilitoris YSM-43T was conducted, which will provide insight into the adaptation of YSM-43T to the tidal flats and promote future comparative genomic studies of bacteria in tidal flats.

YSM-43T was cultivated on marine agar 2216 (BD). The cells were collected in a 5-mL Eppendorf tube for DNA extraction. Extraction of genomic DNA was performed using a genomic DNA extraction kit (RBC), following the manufacturer’s instructions. A spin column (QIAquick PCR purification kit; Qiagen) was utilized for DNA cleanup. The NanoDrop 2000 UV-visible (UV-vis) spectrometer was used for measuring the ratio of absorbance at 260/280 nm and 260/230 nm. The genomic DNA (gDNA) concentration was measured using a Qubit double-stranded DNA (dsDNA) high-sensitivity (HS) assay kit (Invitrogen) with a Qubit 2.0 fluorometer. The quantity and size distribution of the purified gDNA were calculated using Agilent 2200 TapeStation software (A.01.05) (6). A Covaris g-TUBE device was used to shear the genomic DNA according to the manufacturer’s specifications. Between 1 and 5 μg DNA was normalized for library construction using the PacBio SMRTbell 20-kb library preparation kit and sequenced on the PacBio Sequel platform (7). For bioinformatics analysis, default parameters were applied unless otherwise noted. In all, 558,605 PacBio raw reads (read length N50, 7,594 bp) were assembled de novo using Flye version 2.8.3 with the parameter “asm-coverage 100” (8). The resulting circular contig was polished using pbmm2 version 1.4.0 and GCpp version 2.0.2 until a highly accurate consensus for the final assembly was derived (https://github.com/PacificBiosciences/pbbioconda). Then, the genome was rotated using the fixstart method in Circlator version 1.5.5 (9). Finally, we verified that the genome of YSM-43T was complete, with a circular form of 3,913,692 bp and a GC content of 29.38%. No plasmids were detected. The completeness of the genome assembly was assessed using BUSCO version 5.2.2 with the lineage flavobacteriales_odb10 data set (10). It showed that 732 of the 733 BUSCO groups were found to be complete, and 1 was fragmented. Subsequently, genomic annotation was conducted using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) version 6.1 (11). As a result, 3,537 coding sequences, 50 tRNAs, 9 rRNAs, and 3 noncoding RNAs (ncRNAs) out of a total of 3,599 genes were predicted. The complete circular genome map of F. sediminilitoris YSM-43T was built using the Proksee server (https://proksee.ca/) (Fig. 1). To assign the Clusters of Orthologous Groups (COGs) functional categories in accordance with biological systems (12), eggNOG-mapper version 2.1.6 was used with the eggNOG v5 database (13, 14) (Table 1).

FIG 1

Circular genome map of the Flavobacterium sediminilitoris YSM-43T chromosome: (outer to inner) CDSs on the forward strand, CDSs on the reverse strand, positive (red) and negative (yellow) GC skew, GC content (black). CDSs, coding DNA sequences; ncRNA, noncoding RNA; tmRNA, transfer-messenger RNA.

TABLE 1

General features of the complete genome sequence of Flavobacterium sediminilitoris YSM-43T

Genomic feature	Value	% of total	Description
Genome size (bp)	3,913,692
DNA GC (%)	29.38
No. of DNA scaffolds	1
Total no. of genes	3,599
No of CDSs	3,537
No of rRNAs	9
No of 16S rRNAs	3
No of 23S rRNAs	3
No of 5S rRNAs	3
No of tRNAs	50
No of ncRNAs	3
No. of genes assigned to COGs
Total	2,694
M	275	8.94	Cell wall/membrane/envelope biogenesis
E	190	6.18	Amino acid transport and metabolism
J	176	5.72	Translation, ribosomal structure, and biogenesis
K	162	5.27	Transcription
H	141	4.58	Coenzyme transport and metabolism
L	141	4.58	Replication, recombination, and repair
O	138	4.49	Posttranslational modification, protein turnover, and chaperones
C	131	4.26	Energy production and conversion
T	120	3.9	Signal transduction mechanisms
P	107	3.48	Inorganic ion transport and metabolism
I	86	2.8	Lipid transport and metabolism
G	74	2.41	Carbohydrate transport and metabolism
F	68	2.21	Nucleotide transport and metabolism
V	55	1.79	Defense mechanisms
Q	45	1.46	Secondary metabolite biosynthesis, transport, and catabolism
U	43	1.4	Intracellular trafficking, secretion, and vesicular transport
D	27	0.88	Cell cycle control, cell division, and chromosome partitioning
N	17	0.55	Cell motility
W	3	0.1	Extracellular structures
A	1	0.03	RNA processing and modification
B	1	0.03	Chromatin structure and dynamics
Z	1	0.03	Cytoskeleton
S	692	22.5	Function unknown
UCa	382	12.42	Not in COGs

UC, uncharacterized.

Data availability.

The complete genome sequence of F. sediminilitoris YSM-43T has been deposited at GenBank under the accession number CP090145. The raw data have been deposited in the SRA under the accession number SRR17867805.