Sulfitobacter sp. strain AM1-D1, a toxic bacterium of the family Rhodobacteraceae, was isolated from the cultivable phycosphere microbiota of marine toxigenic dinoflagellate Alexandrium minutum amtk4. The complete 4.69-Mb genome comprises one single circular chromosome and five circular plasmids. It has 4,559 coding genes, including those for biosynthesis or degradation of saxitoxin and bioactive exopolysaccharides.
ABSTRACT
Sulfitobacter sp. strain AM1-D1, a toxic bacterium of the family Rhodobacteraceae, was isolated from the cultivable phycosphere microbiota of marine toxigenic dinoflagellate Alexandrium minutum amtk4. The complete 4.69-Mb genome comprises one single circular chromosome and five circular plasmids. It has 4,559 coding genes, including those for biosynthesis or degradation of saxitoxin and bioactive exopolysaccharides.
ANNOUNCEMENT
The phycosphere is a microscopic niche harboring interkingdom exchanges of diverse nutrients, infochemicals, and transferable genetic elements through complex alga-bacterium interactions (ABI) (1). Phycosphere microbiota (PM) inhabiting this microenvironment as a whole bacterial community has been reported in numbers of phytoplanktons in aquatic environments (2, 3). Here, we report the complete genome sequence of Sulfitobacter sp. strain AM1-D1, which was isolated from the cultivable PM of marine toxigenic dinoflagellate Alexandrium minutum amtk4 that produces paralytic shellfish poisoning toxins (PSTs) (4). This genomic information will enable improved mapping of bacterial roles during these dynamic interactions.
The bacterial isolation and extraction of genomic DNA were performed according to our previously described protocols (5). The complete genome sequence of Sulfitobacter sp. strain AM1-D1 was acquired by PacBio RS II single-molecule real time (SMRT) technology performed at Majorbio (Shanghai, China). For PacBio sequencing, genomic DNA was sheared to a standard 10-kb size using g-TUBE (Covaris) and converted into a proprietary SMRTbell library format using the RS DNA template preparation kit (Pacific Biosciences, CA) according to the manufacturer’s instructions. Default parameters were used in this study for all software unless otherwise specified. A quality check of raw sequences was performed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). The genome sequence was de novo assembled from PacBio reads (186,958 reads; average length, 5,769 bp; coverage, 230×) into six contigs using SOAPdenovo2 v2.04 with the Fast Alignment and CONsensus (FALCON) v0.2.1 tools and circularized with Circos v0.64 (http://circos.ca). The 4.69-Mb genome of Sulfitobacter sp. strain AM1-D1 comprises one single circular chromosome (3,840,209 bp) and five circular plasmids (185,176 bp, 95,272 bp, 15,811 bp, 205,668 bp, and 348,874 bp). The G+C contents of these components are 64.9%, 65.6%, 60.3%, 58.7%, 63.7%, and 61.6%, respectively. The genome sequence was annotated by NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v1.2.1 (6). It harbors 43 tRNAs and 3 rRNAs. Of the 4,559 predicted coding genes, the key sxtA genes for starting the biosynthesis of saxitoxin (4) and those for the biosynthesis or degradation of cross-kingdom signals, namely, indole-3-acetic acid (IAA) (2) and bioactive exopolysaccharides (EPS) as promising natural bioflocculants (7), are present in the bacterial chromosome.
Data availability.
The annotated complete genome sequence of Sulfitobacter sp. strain AM1-D1 was deposited in DDBJ/ENA/GenBank under the accession numbers CP018076, CP018077, CP018078, CP018079, CP018080, and CP018081 for the single circular chromosome and five circular plasmids, respectively. The raw reads are available under SRA accession number SRR11216889.
ACKNOWLEDGMENTS
This work was supported by the NSFC (grant number 41876114 to X.-L.Z.), the NSF of Zhejiang Province (grant number LY18D060007 to Q.Y.), the GPM Project (to Q.Y.), the Presidential Foundation of Guangdong Academy of Agricultural Sciences (grant number 201813B to X.Y. and grant number 201918 to L.W.), and the Special Fund for Scientific Innovation Strategy Construction of High Level Academy of Agriculture Science (grant number R2020YJ-LJ001 to X.Y.).
We also acknowledge Hong-Non Chou for kindly providing the dinoflagellate.
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Associated Data
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Data Availability Statement
The annotated complete genome sequence of Sulfitobacter sp. strain AM1-D1 was deposited in DDBJ/ENA/GenBank under the accession numbers CP018076, CP018077, CP018078, CP018079, CP018080, and CP018081 for the single circular chromosome and five circular plasmids, respectively. The raw reads are available under SRA accession number SRR11216889.