Open access
Announcement
19 March 2015

Whole Genome Sequence of the Non-Microcystin-Producing Microcystis aeruginosa Strain NIES-44

ABSTRACT

Microcystis aeruginosa is a typical algal bloom-forming cyanobacterium. This report describes the whole-genome sequence of a non-microcystin-producing strain of Microcystis aeruginosa, NIES-44, which was isolated from a Japanese lake.

GENOME ANNOUNCEMENT

Microcystis aeruginosa is a typical algal bloom-forming cyanobacteria, one of several cyanobacteria known to produce the potent hepatotoxin microcystin (1, 2). Harmful algal blooms (HABs) caused by these toxic cyanobacteria have become a problem in many developed countries. In Japan, adopting appropriate measures to combat these blooms is also an urgent issue. Recent studies have indicated a correlation between the seasonal prevalence of blue-green algae and genotypes of the genus Microcystis (3), and, as such, the genetic analysis of microcystin-producing and nonproducing strains is of prime importance. We report the whole-genome sequence of the non-microcystin-producing Microcystis aeruginosa strain NIES-44 (4).
Whole-genome sequencing was carried out using an Illumina HiSeq1000 system (Illumina, San Diego, CA, USA) with a paired-end library (400 bp) and a Roche/454 PE genome sequencer FLX (454 Life Sciences, Branford, CT, USA) with a mate-paired library (8 kb). HiSeq reads were assembled de novo using Velvet version 1.2.08 (https://www.ebi.ac.uk/~zerbino/velvet) and combined into a hybrid assembly with the 454 reads using GS de novo assembler version 2.8 (454 Life Sciences). Gaps between the resultant 375 contigs were closed using NESONI version 0.118 (http://www.vicbioinformatics.com/software.nesoni.shtml) and Platanus version 1.2.1 (http://platanus.bio.titech.ac.jp/platanus-assembler). The draft genome was annotated using the RAST server (http://rast.nmpdr.org/rast.cgi), which predicted protein-coding sequences (CDSs). Whole-genome homology mapping of various strains, including M. aeruginosa NIES-44, was performed using Gegenees version 2.2.1 (5).
The M. aeruginosa NIES-44 genome comprised 80 contigs (six scaffolds) and had a total length of 4,565,330 bp and a G+C content of 43.19%. It included 4,790 protein-coding sequences and 47 RNA-coding genes (i.e., two sets of rRNA genes and 41 tRNA genes). The annotation revealed that 2,614 CDSs exhibited homology to genes with known functions, and the remaining 2,176 genes were identified as encoding hypothetical proteins of unknown function.
The 16S rRNA sequences of M. aeruginosa NIES-44 were 99.73% homologous (1,489 bp) to those of M. aeruginosa strain NIES-843 (6). However, homology across the whole genome was only 70.04%, owing to deficits in microcystin synthetase (mcy) and nonribosomal peptide synthetase gene clusters. Since M. aeruginosa NIES-44 showed 64.69% homology to M. aeruginosa TAIHU98, in which mcy gene cluster deficits have been previously reported (7), these results support a high genetic diversity among non-microcystin-producing strains. Furthermore, only 37 of the numerous copies of the transposase gene identified in M. aeruginosa NIES-843 (6) and TAIHU98 (7) were found in NIES-44; it is therefore predicted that M. aeruginosa NIES-44 has a characteristic gene structure.

Nucleotide sequence accession number.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number BBPA00000000 and refers to the first version that is described in this paper.

ACKNOWLEDGMENT

This work was supported by the President Project of Akita Prefectural University.

REFERENCES

1.
Watanabe MF, Oishi S, Harda K, Matsuura K, Kawai H, Suzuki M. 1988. Toxins contained in Microcystis species of cyanobacteria (blue-green algae). Toxicon 26:1017–1025.
2.
Welker M, Von Döhren VH. 2006. Cyanobacterial peptides—nature's own combinatorial biosynthesis. FEMS Microbiol Rev 30:530–563.
3.
Kardinaal W, Janse I, Kamst-van Agterveld M, Meima M, Snoek J, Mur L, Huisman J, Zwart G, Visser P. 2007. Microcystis genotype succession in relation to microcystin concentrations in freshwater lakes. Aquat Microb Ecol 48:1–12.
4.
Otsuka S, Suda S, Li R, Watanabe M, Oyaizu H, Matsumoto S, Watanabe MM. 1999. Phylogenetic relationships between toxic and non-toxic strains of the genus Microcystis based on 16S to 23S internal transcribed spacer sequence. FEMS Microbiol Lett 172:15–21.
5.
Ågren J, Sundström A, Håfström T, Segerman B. 2012. Gegenees: fragmented alignment of multiple genomes for determining phylogenomic distances and genetic signatures unique for specified target groups. PLoS One 7:e39107.
6.
Kaneko T, Nakajima N, Okamoto S, Suzuki I, Tanabe Y, Tamaoki M, Nakamura Y, Kasai F, Watanabe A, Kawashima K, Kishida Y, Ono A, Shimizu Y, Takahashi C, Minami C, Fujishiro T, Kohara M, Katoh M, Nakazaki N, Nakayama S, Yamada M, Tabata S, Watanabe MM. 2007. Complete genomic structure of the bloom-forming toxic cyanobacterium Microcystis aeruginosa NIES-843. DNA Res 14:247–256.
7.
Yang C, Zhang W, Ren M, Song L, Li T, Zhao J. 2013. Whole-genome sequence of Microcystis aeruginosa TAIHU98, a nontoxic bloom-forming strain isolated from Taihu Lake, China. Genome Announc 1(3):e00333-13.

Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 3Number 230 April 2015
eLocator: 10.1128/genomea.00135-15

History

Received: 4 February 2015
Accepted: 5 February 2015
Published online: 19 March 2015

Contributors

Authors

Department of Biological Environment, Faculty of Bioresource Sciences, Akita Prefectural University, Akita City, Akita, Japan
Naoyuki Miyata
Department of Biological Environment, Faculty of Bioresource Sciences, Akita Prefectural University, Akita City, Akita, Japan
Yasuo Ozaki
Department of Biological Environment, Faculty of Bioresource Sciences, Akita Prefectural University, Akita City, Akita, Japan

Notes

Address correspondence to Kunihiro Okano, [email protected].

Metrics & Citations

Metrics

Note:

  • For recently published articles, the TOTAL download count will appear as zero until a new month starts.
  • There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.
  • Citation counts come from the Crossref Cited by service.

Citations

If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. For an editable text file, please select Medlars format which will download as a .txt file. Simply select your manager software from the list below and click Download.

View Options

Figures and Media

Figures

Media

Tables

Share

Share

Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy