Draft Genome Sequences of Nine Cyanobacterial Strains from Diverse Habitats

Cyanobacteria are oxygenic photosynthetic prokaryotes that can be found at diverse geographical and ecological locations (1). Based on morphological criteria, cyanobacteria can be divided into five subsections, I to V (2). Initially, a large number of publicly available genome sequences were obtained from subsection I strains, but more recent attempts have been focusing on taxa without representative genome sequences (3). In terms of both fundamental research and biotechnological applications, improved genomic coverage would be advantageous for certain lineages. In this study, nine cyanobacterial strains were sequenced, including three hot spring strains, Chroogloeocystis siderophila NIES-1031 (subsection II, originally collected from bottom mud of LaDuke Hot Springs, MT, USA), Hydrococcus rivularis NIES-593, and Fischerella major NIES-592 (subsections II and V, respectively, originally collected from Yukawa Hot Spring, Japan). Three strains were of terrestrial origin: Nostoc calcicola FACHB-389 (subsection IV, originally collected from soil in Utrecht, The Netherlands), Calothrix sp. NIES-2101, and Scytonema sp. NIES-2130 (both subsection IV and originally collected from the University of Hyogo, Himeji, Japan). Two strains belonging to subsection III were originally collected from freshwater, Leptolyngbya sp. NIES-30 from a paddy field in Akita, Japan, and Phormidium ambiguum NIES-2119 from a pond in northeast Brazil, whereas Oscillatoria rosea NIES-208 (subsection III), a marine isolate, was originally collected from Asaji Bay, Mitsushima, Japan. All strains were cultured in 500-ml flasks containing 300 ml of medium, bubbled with sterile air, and illuminated with 30 to 50 μmol photons m^-2 s^-1 white light in medium BG11 (4), except for Oscillatoria rosea NIES-208, which was cultivated in A⁺ medium (5).

Genomic DNA was extracted from exponential-growth phase cells using the EZ-10 plant genomic DNA purification kit (Sangon Biotech, China). Extracted genomic DNA of Oscillatoria rosea NIES-208, Nostoc calcicola FACHB-389, Fischerella major NIES-592, and Hydrococcus rivularis NIES-593 was sheared to ~500-bp fragments and then sequenced using the paired-end protocol of the Illumina HiSeq 2000 system (2 × 100 bp). The other five strains were sequenced with a fragment size of 300 to 500 bp using the paired-end protocol of Illumina MiSeq (2 × 300 bp). Adapter sequences were removed and low-quality ends trimmed using Trimmomatic version 0.33 (6), with a minimum Phred score of 20 in a sliding window of 4. Reads >20 nucleotides (nt) were used for de novo assembly using SPAdes version 3.9.0 (7) in “--meta” mode with default parameters. Contigs >2 kb were binned using MaxBin version 2.2.1 (8), and the completeness and contamination were assessed using CheckM version 1.0.5 (9). Contigs binned to Cyanobacteria were scaffolded using BESST version 2.2.4 (https://github.com/ksahlin/BESST) and FinishM version 0.0.9 (https://github.com/wwood/finishm) and then polished using Pilon version 1.20 (10). Scaffolds were taxonomically classified using Kaiju (11) and PhyloPythiaS+ (12). Those not assigned to Cyanobacteria were manually checked using BLASTN (13), and contaminants were removed. The final assemblies were annotated using the NCBI PGAAP (14).

This work was supported by the Joint Sino-German Research Project (grant GZ877 to X.L. and W.H.), the National Natural Science Foundation of China (grants 31200001 and 31570068 to T.Z.), the National Science Fund for Distinguished Young Scholars of China (grant 31525002 to X.L.), the Deutsche Forschungsgemeinschaft (grant HE2544/9-1 to W.H.), and the Shandong Taishan Scholarship (to X.L.). The financial support to S. Hou by China Scholarship Council is gratefully acknowledged. The funders had no role in the study design, data collection and interpretation, or decision to submit the work for publication.