Open access
2 March 2017

Draft Genome Sequences of Nine Cyanobacterial Strains from Diverse Habitats


Here, we report the annotated draft genome sequences of nine different cyanobacteria, which were originally collected from different habitats, including hot springs, terrestrial, freshwater, and marine environments, and cover four of the five morphological subsections of cyanobacteria.


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 ( and FinishM version 0.0.9 ( 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).

Accession number(s).

The draft genome sequences of the nine cyanobacterial strains have been deposited as NCBI whole-genome shotgun (WGS) projects at DDBJ/EMBL/GenBank under the accession numbers listed in Table 1; the versions described in this paper are the first versions.
TABLE 1 Genome features and GenBank accession numbers of the strains
StrainHabitatBiosample no.Accession no.Genome size (Mb)Coverage (×)
Oscillatoria rosea NIES-208MarineSAMN05890674MRBY000000004.0102
Nostoc calcicola FACHB-389TerrestrialSAMN05890684MRBZ000000008.845
Fischerella major NIES-592Hot springSAMN05890685MRCA000000005.5156
Hydrococcus rivularis NIES-593Hot springSAMN05890686MRCB000000005.0136
Chroogloeocystissiderophila NIES-1031Hot springSAMN05890687MRCC000000004.956
Calothrix sp. NIES-2101TerrestrialSAMN05890688MRCD000000009.713
Phormidium ambiguum NIES-2119FreshwaterSAMN05890689MRCE000000007.2117
Scytonema sp. NIES-2130TerrestrialSAMN05890690MRCF000000009.344
Phormidium tenue NIES-30FreshwaterSAMN05890691MRCG000000005.784


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.


Tomitani A, Knoll AH, Cavanaugh CM, and Ohno T. 2006. The evolutionary diversification of cyanobacteria: molecular-phylogenetic and paleontological perspectives. Proc Natl Acad Sci U S A103:5442–5447.
Stanier RY, Deruelles J, Rippka R, Herdman M, and Waterbury JB. 1979. Generic assignments, strain histories and properties of pure cultures of cyanobacteria. Microbiology111:1–61.
Shih PM, Wu D, Latifi A, Axen SD, Fewer DP, Talla E, Calteau A, Cai F, de Tandeau de Marsac NT, Rippka R, Herdman M, Sivonen K, Coursin T, Laurent T, Goodwin L, Nolan M, Davenport KW, Han CS, Rubin EM, Eisen JA, Woyke T, Gugger M, and Kerfeld CA. 2013. Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc Natl Acad Sci U S A110:1053–1058.
Stanier RY, Kunisawa R, Mandel M, and Cohen-Bazire G. 1971. Purification and properties of unicellular blue-green algae (order Chroococcales). Bacteriol Rev35:171–205.
Stevens SE and Porter RD. 1980. Transformation in Agmenellumquadruplicatum. Proc Natl Acad Sci U S A77:6052–6056.
Bolger AM, Lohse M, and Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics30:2114–2120.
Nurk S, Meleshko D, Korobeynikov A, and Pevzner P. 2016. metaSPAdes: a new versatile denovo metagenomics assembler. arXivarXiv:1604.03071.
Wu Y-W, Simmons BA, and Singer SW. 2015. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics32:605–607.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, and Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res25:1043–1055.
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, and Earl AM. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One9:e112963.
Menzel P, Ng KL, and Krogh A. 2016. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat Commun7:11257.
Gregor I, Dröge J, Schirmer M, Quince C, and McHardy AC. 2014. PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes. PeerJ4:1603.
Altschul SF, Gish W, Miller W, Myers EW, and Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol215:403–410.
Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, and Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res44:6614–6624.

Information & Contributors


Published In

cover image Genome Announcements
Genome Announcements
Volume 5Number 92 March 2017
eLocator: e01676-16
PubMed: 28254973


Received: 12 December 2016
Accepted: 5 January 2017
Published online: 2 March 2017



Tao Zhu
Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Beijing, China
Shengwei Hou
Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
Xuefeng Lu
Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Beijing, China
Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany


Address correspondence to Xuefeng Lu, [email protected], or Wolfgang R. Hess, [email protected].
T.Z. and S.H. contributed equally to this work.

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