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Announcement
24 October 2019

Draft Genome Sequences of Three Filamentous Cyanobacterial Strains, Dolichospermum planctonicum NIES-80, Planktothrix agardhii NIES-905, and Sphaerospermopsis reniformis NIES-1949

ABSTRACT

Three freshwater planktonic filamentous cyanobacterial strains, Dolichospermum planctonicum NIES-80, Planktothrix agardhii NIES-905, and Sphaerospermopsis reniformis NIES-1949, were sequenced. The genome sizes of NIES-80, NIES-905, and NIES-1949 were 4,571,002 bp, 5,512,454 bp, and 6,025,023 bp, and the number of protein-coding genes in each genome was 4,009, 4,925, and 5,408, respectively.

ANNOUNCEMENT

Water blooms, also called “cyanobacterial blooms” (1), are mainly formed by some planktonic cyanobacterial species in mesotrophic-eutrophic freshwater (2). Among these species, filamentous cyanobacteria have ecological importance. They are the main primary producers and secondary metabolite producers (e.g., cyanotoxins) and are also involved in nitrogen fixation (3). We sequenced the genomes of three bloom-forming filamentous cyanobacterial strains, Dolichospermum planctonicum NIES-80, Planktothrix agardhii NIES-905, and Sphaerospermopsis reniformis NIES-1949.
All three axenic strains were maintained at the National Institute for Environmental Studies (NIES). NIES-80 and NIES-1949 were cultured in 10 ml of CB medium at 22°C and 20°C, respectively. NIES-905 was cultured in 10 ml of CT medium (4) at 20°C. Cyanobacteria were cultured for 3 weeks and harvested using gentle centrifugation. DNA was extracted from NIES-80 and NIES-905 using a DNeasy plant minikit (Qiagen, Düsseldorf, Germany), while NIES-1949 DNA extraction was performed using an Agencourt Chloropure kit (Beckman Coulter, Brea, CA) per the manufacturer’s instructions. DNA was sheared to a fragment size of approximately 550 bp using an M220 focused ultrasonicator (Covaris, Woburn, MA). The DNA libraries were constructed using a NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs, Ipswich, MA). The libraries were sequenced on the MiSeq platform (Illumina, San Diego, CA) using a MiSeq reagent kit v3. We sequenced 587,952,677 bp (NIES-80), 750,851,958 bp (NIES-905), and 125,087,525 bp (NIES-1949) paired-end reads. The raw reads were trimmed using Trimmomatic v0.38 (5) and assembled using SPAdes v3.11.1 (6) and Shovill v1.0.4 (https://github.com/tseemann/shovill). The assemblies were polished using Pilon v1.22 (7). After removal of the short reads (<200 bp), gene model construction and functional annotation were performed using the DFAST legacy server (8) and CyanoBase (9).
The draft genome sizes of NIES-80, NIES-905, and NIES-1949 were 4,571,002 bp (GC content, 37.7%), 5,512,454 bp (GC content, 39.5%), and 6,025,023 bp (GC content, 37.5%), respectively (Table 1). The genome completeness rates were 99.22% (NIES-80), 100.00% (NIES-905), and 98.89% (NIES-1949), respectively, as evaluated by CheckM analysis (10). The number of protein-coding genes in the genomes of NIES-80, NIES-905, and NIES-1949 was 4,009, 4,925, and 5,408, respectively. The genomes of NIES-80, NIES-905, and NIES-1949 were similar to those of Dolichospermum compactum NIES-806, P. agardhii NIES-204, and Sphaerospermopsis kisseleviana NIES-73, respectively, in terms of size and the number of genes. Some strains of Planktothrix agardhii produce a cyanotoxin, microcystin, that is synthesized by the mcy gene cluster (11). The NIES-905 sequence included a conserved mcy gene cluster (mcyJ, mcyC, mcyB, mcyA, mcyH, mcyG, mcyE, and mcyD), suggesting that this strain can probably synthesize microcystin. The three species used in this study are widely present in freshwater. Thus, the genomes can be used for monitoring using quantitative PCR or droplet digital PCR (12) and for metagenomic analyses of cyanobacterial blooms.
TABLE 1
TABLE 1 Genome features of NIES-80, NIES-905, and NIES-1949
SpeciesStrainAssembly size (bp)No. of contigsN50 (kbp)Genome completeness (%)GC content (%)No. of protein-coding genesNo. of tRNAsNo. of rRNAs
Dolichospermum planctonicumNIES-804,571,00220175.299.2237.704,009447
Planktothrix agardhiiNIES-9055,512,45419393.2100.0039.504,925405
Sphaerospermopsis reniformisNIES-19496,025,02368020.098.8937.505,408432

Data availability.

The draft genome sequences of Dolichospermum planctonicum NIES-80, Planktothrix agardhii NIES-905 (= CCAP 1459/11A), and Sphaerospermopsis reniformis NIES-1949 have been deposited in DDBJ/EMBL/GenBank under the accession numbers BJCF01000001 to BJCF01000201, BJCD01000001 to BJCD01000193, and BJCE01000001 to BJCE01000680, respectively. The genomic raw reads are also available in DDBJ/EMBL/GenBank under the accession numbers DRR172254, DRR172255, and DRR172253, respectively.

ACKNOWLEDGMENTS

We thank Nobuyoshi Nakajima (NIES) for the 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.
Hudnell HK, Dortch Q, Zenick H. 2008. An overview of the Interagency, International Symposium on Cyanobacterial Harmful Algal Blooms (ISOC-HAB): advancing the scientific understanding of freshwater harmful algal blooms. Adv Exp Med Biol 619:1–16.
2.
O’Neil JM, Davis TW, Burford MA, Gobler CJ. 2012. The rise of harmful cyanobacteria blooms: the potential roles of eutrophication and climate change. Harmful Algae 14:313–334.
3.
Komárek J, Johansen JR. 2015. Filamentous cyanobacteria, p 135–235. In Wehr JD, Sheath RG, Kociolek JP (ed), Freshwater algae of North America, 2nd ed. Academic Press, London, United Kingdom.
4.
Watanabe MM, Ichimura T. 1977. Fresh- and salt-water forms of Spirulina platensis in axenic cultures. Bull Jpn Soc Phycol 25:371–377.
5.
Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120.
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.
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.
8.
Tanizawa Y, Fujisawa T, Nakamura Y. 2018. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 34:1037–1039.
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.
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.
11.
Christiansen G, Fastner J, Erhard M, Borner T, Dittmann E. 2003. Microcystin biosynthesis in Planktothrix: genes, evolution, and manipulation. J Bacteriol 185:564–572.
12.
Te SH, Chen EY, Gin K-H. 2015. Comparison of quantitative PCR and droplet digital PCR multiplex assays for two genera of bloom-forming cyanobacteria, Cylindrospermopsis and Microcystis. Appl Environ Microbiol 81:5203–5211.

Information & Contributors

Information

Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 8Number 4324 October 2019
eLocator: 10.1128/mra.00605-19
Editor: Julia A. Maresca, University of Delaware

History

Received: 21 May 2019
Accepted: 30 September 2019
Published online: 24 October 2019

Contributors

Authors

Shigekatsu Suzuki
Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Japan
Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Japan
Masanobu Kawachi
Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Japan

Editor

Julia A. Maresca
Editor
University of Delaware

Notes

Address correspondence to Shigekatsu Suzuki, [email protected].

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