Microcystis aeruginosa is a bloom-forming cyanobacterium found in freshwater environments. The draft genomes of the M. aeruginosa strains NIES-3787, NIES-3804, NIES-3806, and NIES-3807, which were isolated from Lake Kasumigaura, Japan, were sequenced. The genome sizes of NIES-3787, NIES-3804, NIES-3806, and NIES-3807 were 4,524,637, 4,522,701, 4,370,004, and 4,378,226 bp, respectively.
ABSTRACT
Microcystis aeruginosa is a bloom-forming cyanobacterium found in freshwater environments. The draft genomes of the M. aeruginosa strains NIES-3787, NIES-3804, NIES-3806, and NIES-3807, which were isolated from Lake Kasumigaura, Japan, were sequenced. The genome sizes of NIES-3787, NIES-3804, NIES-3806, and NIES-3807 were 4,524,637, 4,522,701, 4,370,004, and 4,378,226 bp, respectively.
ANNOUNCEMENT
Cyanobacterial blooms occur widely in freshwater environments worldwide (1). Microcystis aeruginosa is the most well-known bloom-forming cyanobacterium, and it is distributed in eutrophic freshwater environments. The most serious problem associated with this species is the production of hepatotoxic cyanotoxins called microcystins (2, 3). M. aeruginosa isolates are genetically divided into at least 12 phylogenetic groups (groups A to K and X) based on multilocus phylogenetic analyses (2, 3). The strains in groups A and X, as well as some B strains, produce microcystins (3, 4). In the current study, we sequenced M. aeruginosa strains NIES-3787, NIES-3804, NIES-3806, and NIES-3807, isolated from Lake Kasumigaura, Japan.
Axenic cultures of M. aeruginosa NIES-3787, NIES-3804, NIES-3806, and NIES-3807 were obtained from the microbial culture collection of the National Institute for Environmental Studies (https://mcc.nies.go.jp/index.html). These strains were established by using a micropipette under an inverted microscope. The strains were cultured in 10 ml of Microcystis aeruginosa medium at 22°C under light at 25 μmol photons m−2 s−1 with a 12:12-h light/dark cycle. Genomic DNA was extracted from 10-ml cultures of these strains using Agencourt Chloropure (Beckman Coulter) following the manufacturer’s protocol. The resultant DNAs were fragmented to approximately 550 bp using an M220 ultrasonicator (Covaris). Genomic libraries of paired-end reads were constructed using a NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs). Next-generation sequencing was performed with the MiSeq platform (Illumina) using a 500-cycle MiSeq reagent kit version 2. The resultant paired-end reads for NIES-3787, NIES-3804, NIES-3806, and NIES-3807 were 151,461,029 bp, 643,439,906 bp, 395,828,445 bp, and 197,435,680 bp, respectively. The raw reads were trimmed using Trimmomatic version 0.38 (5), and then de novo assembly was performed using SPAdes version 3.11.1 (6) in Shovill version 1.0.4 (https://github.com/tseemann/shovill). Next, the assembled scaffolds were polished using Pilon version 1.22 (7). After the removal of short reads (<200 bp), functional annotation was performed using the DFAST legacy server (8) with CyanoBase (9) as a database. We used CheckM version 1.0.11 to estimate genome completeness (10). Default parameters were used for all software. Group identification analysis of each strain was carried out based on ftsZ, one of seven multilocus sequence typing loci (2, 3).
The genome assembly results are detailed in Table 1. As the result of group identification analysis, NIES-3787, NIES-3806, and NIES-3807 were identified as group G, and NIES-3804 was not assigned to any known group. These four strains did not possess a microcystin biosynthetic gene cluster (11). However, some secondary metabolite gene clusters, including aeruginosin (NIES-3787, NIES-3806, and NIES-3807) (12), anabaenopeptin (NIES-3806) (13), microcyclamide (NIES-3804) (14), and micropeptin (NIES-3787 and NIES-3806) (15), were predicted using antiSMASH version 5.0.0 (16). Additional genomic information about M. aeruginosa would be useful for monitoring algal blooms and managing freshwater ecosystems.
TABLE 1.
Characteristics and accession numbers of four Microcystis aeruginosa genomes
| Strain name | Assembly size (bp) | No. of contigs | N50 (bp) | Genome completeness (%) | CheckM contamination (%) | GC content (%) | No. of coding sequences | Accession no. of whole-genome shotgun submissions | SRA accession no. | GenBank assembly accession no. |
|---|---|---|---|---|---|---|---|---|---|---|
| NIES-3787 | 4,378,226 | 214 | 73,037 | 99.89 | 0.66 | 43.0 | 4,126 | BJCH01000001–BJCH01000214 | DRR205020 | GCA_009811815 |
| NIES-3804 | 4,524,637 | 238 | 45,562 | 99.89 | 0.37 | 43.0 | 4,226 | BJCI01000001–BJCI01000238 | DRR205021 | GCA_009811835 |
| NIES-3806 | 4,522,702 | 235 | 67,327 | 99.89 | 0.37 | 43.0 | 4,180 | BJCJ01000001–BJCJ01000235 | DRR205022 | GCA_009811855 |
| NIES-3807 | 4,370,004 | 214 | 46,356 | 99.89 | 0.95 | 43.0 | 4,066 | BJCK01000001–BJCK01000228 | DRR205023 | GCA_009811875 |
Data availability.
The draft genomic sequences of Microcystis aeruginosa NIES-3787, NIES-3804, NIES-3806, and NIES-3807 have been deposited in DDBJ/EMBL/GenBank under the accession numbers BJCH01000001 to BJCH01000214, BJCI01000001 to BJCI01000238, BJCJ01000001 to BJCJ01000235, and BJCK01000001 to BJCK01000228, respectively. The raw genomic reads of the strains are available in DDBJ/EMBL/GenBank under the accession numbers DRR205020, DRR205021, DRR205022, and DRR205023, respectively.
ACKNOWLEDGMENTS
We thank Nobuyoshi Nakajima (National Institute for Environmental Studies) for genome sequencing.
This work was partially supported by the National BioResource Project for Algae under grant number 17km0210116j0001, which was funded by the Japan Agency for Medical Research and Development (AMED).
REFERENCES
- 1.Carmichael WW. 1996. Toxic Microcystis and the environment, p 1–11. In Watanabe MF, Harada K, Carmichael WW, Fujiki H (ed), Toxic Microcystis. CRC Press, Boca Raton, FL. [Google Scholar]
- 2.Tanabe Y, Kasai F, Watanabe MM. 2007. Multilocus sequence typing (MLST) reveals high genetic diversity and clonal population structure of the toxic cyanobacterium Microcystis aeruginosa. Microbiology 153:3695–3703. doi: 10.1099/mic.0.2007/010645-0. [DOI] [PubMed] [Google Scholar]
- 3.Tanabe Y, Hodoki Y, Sano T, Tada K, Watanabe MM. 2018. Adaptation of the freshwater bloom-forming cyanobacterium Microcystis aeruginosa to brackish water is driven by recent horizontal transfer of sucrose genes. Front Microbiol 9:1150. doi: 10.3389/fmicb.2018.01150. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Tanabe Y, Watanabe MM. 2011. Local expansion of a panmictic lineage of water bloom-forming cyanobacterium Microcystis aeruginosa. PLoS One 6:e17085. doi: 10.1371/journal.pone.0017085. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi: 10.1093/bioinformatics/btu170. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi: 10.1089/cmb.2012.0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963. doi: 10.1371/journal.pone.0112963. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Tanizawa Y, Fujisawa T, Nakamura Y. 2018. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 34:1037–1039. doi: 10.1093/bioinformatics/btx713. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Fujisawa T, Narikawa R, Maeda S, Watanabe S, Kanesaki Y, Kobayashi K, Nomata J, Hanaoka M, Watanabe M, Ehira S, Suzuki E, Awai K, Nakamura Y. 2017. CyanoBase: a large-scale update on its 20th anniversary. Nucleic Acids Res 45:D551–D554. doi: 10.1093/nar/gkw1131. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. doi: 10.1101/gr.186072.114. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Tillett D, Dittmann E, Erhard M, Döhren H, Börner T, Neilan BA. 2000. Structural organization of microcystin biosynthesis in Microcystis aeruginosa PCC7806: an integrated peptide–polyketide synthetase system. Chem Biol 7:753–764. doi: 10.1016/S1074-5521(00)00021-1. [DOI] [PubMed] [Google Scholar]
- 12.Ishida K, Welker M, Christiansen G, Cadel-Six S, Bouchier C, Dittmann E, Hertweck C, De Marsac NT. 2009. Plasticity and evolution of aeruginosin biosynthesis in cyanobacteria. Appl Environ Microbiol 75:2017–2026. doi: 10.1128/AEM.02258-08. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Harada KI, Fujii K, Shimada T, Suzuki M, Sano H, Adachi K, Carmichael WW. 1995. Two cyclic peptides, anabaenopeptins, a third group of bioactive compounds from the cyanobacterium Anabaena flos-aquae NRC 525–17. Tetrahedron Lett 36:1511–1514. doi: 10.1016/0040-4039(95)00073-L. [DOI] [Google Scholar]
- 14.Ishida K, Nakagawa H, Murakami M. 2000. Microcyclamide, a cytotoxic cyclic hexapeptide from the cyanobacterium Microcystis aeruginosa. J Nat Prod 63:1315–1317. doi: 10.1021/np000159p. [DOI] [PubMed] [Google Scholar]
- 15.Nishizawa T, Ueda A, Nakano T, Nishizawa A, Miura T, Asayama M, Fujii K, Harada KI, Shirai M. 2011. Characterization of the locus of genes encoding enzymes producing heptadepsipeptide micropeptin in the unicellular cyanobacterium Microcystis. J Biochem 149:475–485. doi: 10.1093/jb/mvq150. [DOI] [PubMed] [Google Scholar]
- 16.Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, Medema MH, Weber T. 2019. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 47:W81–W87. doi: 10.1093/nar/gkz310. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The draft genomic sequences of Microcystis aeruginosa NIES-3787, NIES-3804, NIES-3806, and NIES-3807 have been deposited in DDBJ/EMBL/GenBank under the accession numbers BJCH01000001 to BJCH01000214, BJCI01000001 to BJCI01000238, BJCJ01000001 to BJCJ01000235, and BJCK01000001 to BJCK01000228, respectively. The raw genomic reads of the strains are available in DDBJ/EMBL/GenBank under the accession numbers DRR205020, DRR205021, DRR205022, and DRR205023, respectively.