Genome sequencing and de novo assembly of Photobacterium arenosum isolate from coastal sediment

TL;DR

This paper reports the genome sequencing of a marine bacterium that can break down chitin, which may have useful industrial and environmental applications.

Contribution

The novel contribution is the genome sequencing and assembly of Photobacterium arenosum, a chitinolytic bacterium from coastal sediment.

Findings

The genome of Photobacterium arenosum was successfully sequenced and assembled.

The bacterium is chitinolytic, suggesting potential applications in biotechnology and environmental processes.

Abstract

Genomic analyses have led to the discovery of novel chitinases with emerging applications as environmentally friendly alternatives to synthetic chemical pesticides and for processing renewable resources in various industries. Here, we report the sequencing and assembly of the chitinolytic marine bacterium Photobacterium arenosum isolated from coastal sediment from Oostende, Belgium.

Tables

TABLE 1. Distribution of CDSs, rRNAs, and tRNAs on scaffolds determined with NCBI Prokaryotic Genome Annotation Pipeline

Scaffold	Protein coding genes	Pseudogene	ncRNA	RNase P RNA	rRNA	tRNA	Other
NZ_JASHHZ010000001.1	2,299	59	1	1	16	71	1
NZ_JASHHZ010000002.1	34	7	0	0	0	0	0
NZ_JASHHZ010000003.1	1,640	34	0	0	0	15	1
NZ_JASHHZ010000004.1	239	11	0	0	7	25	0
NZ_JASHHZ010000005.1	1	0	0	0	0	0	0
Total	4,213	111	1	1	23	111	2

Full text

ANNOUNCEMENT

Genomic and transcriptomic analyses have led to the discovery of novel chitinases with unique characteristics, such as different substrate specificities and enzymatic activities brought about by variations in amino acid sequences (1). Chitinases have gained increasing interest for various applications, including the production of chitin-degradation products and as biological control agents for crop protection against pests and fungal phytopathogens (2). Consequently, chitinases have emerged as an environmentally friendly alternative to synthetic chemical pesticides and hold potential for processing renewable resources in various industries (3, 4). Photobacterium arenosum is a novel gram-negative, aerobic, chitinolytic marine bacterium (5). P. arenosum CAU 1568 was isolated from marine sediment sand sampled at Sido Island in the Republic of Korea (5). In 2022, P. arenosum WH24 was isolated from the gill of the oyster Crassostrea gigas, caught at the Wilhelmshaven Sea in northern Germany (6). In this study, we report the sequencing and de novo assembly of the genome of P. arenosum isolated from coastal sediments in Oostende, Belgium.

A seawater sample was transferred to minimal medium with chitin as the sole carbon source. P. arenosum was selected as a promising strain with high chitinase activity after three consecutive rounds of enrichment culture (7). Tryptic soy complex medium was inoculated with a P. arenosum glycerol stock and cultivated shaking at 28°C for 16 hours. Genomic DNA was isolated from the culture using a NucleoSpin Tissue DNA extraction kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions. The isolated DNA was purified by AMPure bead cleanup (Beckman Coulter, Brea, USA). Subsequently, a 10 kb PacBio SMRTbell library was prepared with Blue Pippin size selection, following the manufacturer’s instructions. No shearing was performed prior to library preparation. The library was sequenced on a PacBio Sequel SMRT HiFi platform. Data quality check and adapter trimming were performed using SMRT Link v.10.1.0 (PacBio), resulting in 978,480 HiFi reads. The reads were assembled using Flye v.2.9 (8) with the parameters “--pacbio-hifi” and “--genome size 5.5 m”, resulting in six contigs. The contigs were BLASTed on the National Center for Biotechnology Information (NCBI) servers using BLAST v.2.2 (9). The best matches included P. arenosum CAU1568 and WH24 and were used for scaffolding using Medusa v.1.6 (10), yielding five scaffolds. The assembly was evaluated using Quast v.5.2.0 (11), polished using BWA-MEM v.0.7.18 (12) and SAMtools v.1.2 (13), for mapping, sorting, and indexing, respectively, and finally corrected by remapping the reads to the assembled genome using Pilon v.1.22 (14). All algorithms were run with default parameters. The draft genome consists of five linear scaffolds with a total size of 4.87 Mbp, mean coverage of 48×, N50 of 2,700,155, and guanine-cytosine content of 48.9%. Quality analysis was performed using CheckM v.1.2.3 (15), indicating 87.49% completeness (50th percentile) and 2.09% contamination. The genome was subsequently annotated using the NCBI Prokaryotic Genome Annotation Pipeline v.6.8 (16), predicting 4,462 genes in total (Table 1).