Draft Genome Sequence of Sinomicrobium sp. Strain PAP.21, Isolated from a Coast Sample of Papua, Indonesia

ABSTRACT Sinomicrobium sp. strain PAP.21 (EXT111902) was isolated from the coast of Cenderawasih Bay National Park in West Papua, Indonesia. Its genome was assembled into 151 contigs with a total size of 5.439 Mbp, enabling the prediction of its specialized metabolite production capacity.

T he phylum Bacteroidetes is a promising, although underexplored, bioresource for natural product discovery (1,2). Bacteroidetes are among the most abundant bacteria within marine ecosystems (3), and their known bioactive natural products represent a remarkable diversity. This diversity is, e.g., exemplified by the lanthipeptide pinensin from Chitinophaga pinensis exhibiting antifungal activity (4). Expecting a positive correlation between the Bacteroidetes diversity and their produced chemical diversity, we aimed at accessing new strains.
In this study, Sinomicrobium sp. PAP.21 was isolated from marine sediment of the upper layer (5 to 10 cm) collected at a coast area of Cenderawasih Bay National Park, Papua, Indonesia (2°23906.80S 134°57953.50E). The strain was deposited in the Fraunhofer strain collection (5) under its identifier EXT111902.
The marine sediment sample was stored in a sterile plastic bag before being plated onto artificial seawater (1.5% agar, 0.01% KBr, 2.3% NaCl, 1.1% MgCl 2 Á 6 H 2 O, 0.1% CaCl 2 Á 2H 2 O, 0.1% KCl, 0.004% SrCl 2 Á 6 H 2 O, 0.4% Na 2 SO 4 , 0.02% NaHCO 3 , and 0.003% H 3 BO 3 in H 2 O), including Escherichia coli prey, and incubated at 30°C. Grown colonies were purified on marine agar (Carl Roth GmbH; product no. CP73.1 1 1.5% agar), and a sequencing sample was prepared by growing EXT111902 aerobically in marine broth (30°C for 24 h; Carl Roth GmbH; product no. CP73.1). The cell pellet was resuspended in ATL buffer (Qiagen) containing RNase A. BashingBead lysis tubes (Zymo Research) were used for cell disruptions. DNA was isolated using QIAmp 96 DNA QIAcube high-throughput (HT) kits with the addition of proteinase K (Qiagen). Libraries for short-read sequencing were prepared using the Illumina DNA prep tagmentation kit with 500 ng DNA input and 5 cycles of indexing PCR. Library quality was evaluated (Agilent 2100 bioanalyzer) and sequenced on an Illumina NovaSeq instrument using a NovaSeq 6000 SP v1 sequencing kit with a 2 Â 150 bp read length and a depth of 4.0 to 5.0 Mio reads. For sequence processing and analysis, software tools were run with default settings unless otherwise stated. The sequencing was demultiplexed (Illumina bcl2fastq, v2. 19 ). An average nucleotide identity (ANI) (13) value of 98.89% supports the affiliation of EXT111902 to the species S. oceani. antiSMASH v6.0 (14) was employed to predict the biosynthetic gene clusters (BGCs). BGC annotation was achieved by their clustering with MIBiG (15) reference clusters into gene cluster families (GCFs) using BiG-SCAPE (16) and setting a cutoff value of 0.6. EXT111902 carries one BGC clustering with BGC0001478, encoding the synthesis of the siderophore desferrioxamine E (17) and another BGC was annotated to BGC0000593, encoding microviridin J (18). The third database annotation refers to pinensin (BGC0001392) (4). Pinensin-like BGCs were detected previously in the genomes of certain Chitinophaga, Chryseobacterium, Elizabethkingia, Pedobacter, and Sinomicrobium strains (19). Variations in the amino acid sequence of the core peptides indicate a yet undiscovered structural diversity within this lantipeptide type. Such alterations toward the known pinensins are also predicted for EXT111902 (Fig. 1).
Data availability. The whole-genome shotgun project has been deposited at DDBJ/ ENA/GenBank under BioProject PRJNA904543 with accession number SAMN31846359. Raw data can be obtained from the Sequence Read Archive (SRP421602). The draft genome sequence has been deposited in GenBank under the accession number JAPPSR000000000.

ACKNOWLEDGMENTS
We   (16) (left) of strain EXT111902 (magenta) (manually curated). EXT111902 carries five ribosomally synthesized and posttranslationally modified peptides (RiPPs; circle), two nonribosomal peptides (NRPSs; arrow), one terpene (diamond), and two other BGCs (rectangle). By networking with the MIBiG reference clusters (brown), a desferrioxamine-like NRPS-independent siderophore BGC (similarity index up to 0.077, BGC0001478), a microviridin-like BGC (similarity index of 0.058, BGC0000593), and a pinensin-like BGC (similarity index of 0.072) were annotated. Alignment of the pinensin-like cluster of EXT11902 to the pinensin BGC0001392 of C. pinensis DSM2588 (right) shows the presence of homologous genes to the biosynthetic core genes pinA to C (light green) and pinT (turquoise), including the split dehydratase genes pinB1 and pinB2. Homologous genes to Cpin5321 to 5324 (dark green) of BGC0001392, suggested to be involved in the perception and import of pinensin, are present. Homologs to Cpin5330 to 5332 (yellow), proposed to be responsible for pinensin export, instead are not detected in the EXT111902 BGC. Alignment of the pinensin core peptide (bottom right) suggests a sequence of 24 amino acids for EXT111902, while the pinensin A peptide contains 22 amino acids.
Sequencing was performed by the Institute for Medical Microbiology (part of the NGS Competence Center NCCT, Tübingen, Germany) while data management, including data storage of raw data for this project, was done by the Quantitative Biology Center (QbiC; Tübingen, Germany). We acknowledge provision of computing resources and technical support by the Bioinformatics Core Facility (BCF) at Justus Liebig University Giessen.