Abstract
Here, we report the draft genome sequences of the type strains of Demequina aestuarii, Demequina aurantiaca, Demequina flava, Demequina globuliformis, Demequina lutea, Demequina oxidasica, Demequina salsinemoris, and Demequina sediminicola. The genome sequences presented here will facilitate taxonomical, ecological, and functional studies of members of the genus Demequina.
GENOME ANNOUNCEMENT
The genus Demequina, which belongs to the family Demequinaceae within the suborder Micrococcineae, is composed of Gram stain-positive, rod-shaped, and non-endospore-forming actinobacteria (1, 2). At the time of writing, this genus contains 8 species with validly published names: Demequina aestuarii (1), Demequina aurantiaca, Demequina globuliformis, Demequina oxidasica (2), Demequina flava, Demequina sediminicola (3), Demequina lutea (4), and Demequina salsinemoris (5). So far, members of the genus were mainly isolated from samples of marine origin, such as tidal flat and sea sediments. The genus Demequina is characterized by the presence of a discriminative menaquinone, namely, demethylmenaquinone DMK-9(H4). Furthermore, the peptidoglycan type of this genus is of A4β type with ornithine as the diagnostic diamino acid (6), and this feature distinguishes the genus Demequina from the closely related genus Lysinimicrobium within the family Demequinaceae (7). To reveal genomic features of the genus Demequina, we performed whole-genome shotgun sequencing of all type strains of the genus.
Genomic DNAs of D. aestuarii NBRC 106260T, D. aurantiaca NBRC 106265T, D. flava NBRC 105854T, D. globuliformis NBRC 106266T, D. lutea NBRC 106155T, D. oxidasica NBRC 106264T, D. salsinemoris NBRC 105323T, and D. sediminicola NBRC 105855T were extracted and purified from liquid-dried cells in ampules provided from the NBRC culture collection using the EZ1 DNA tissue kit and EZ1 advanced instruments (Qiagen). The whole genomes of these strains were analyzed by using paired-end sequencing with MiSeq (Illumina). These reads were assembled using the Newbler v2.6 software and subsequently finished using the GenoFinisher software (8). The results of the sequencing are summarized in Table 1.
TABLE 1 .
Summary of genome sequencing in the present study
| Organism | Read (Mb) | Fold coverage | No. of scaffolds | Genome size (bp) | G+C content (%) | Accession no. |
|---|---|---|---|---|---|---|
| D. aestuarii NBRC 106260T | 291 | 104 | 3 | 2,790,392 | 69.1 | BBRD00000000 |
| D. aurantiaca NBRC 106265T | 265 | 103 | 4 | 2,565,694 | 64.6 | BBRF00000000 |
| D. flava NBRC 105854T | 215 | 84 | 3 | 2,546,965 | 64.7 | BBRA00000000 |
| D. globuliformis NBRC 106266T | 262 | 100 | 7 | 2,622,354 | 66.3 | BBRG00000000 |
| D. lutea NBRC 106155T | 264 | 100 | 40 | 2,643,741 | 65.9 | BBRC00000000 |
| D. oxidasica NBRC 106264T | 224 | 85 | 5 | 2,623,557 | 64.1 | BBRE00000000 |
| D. salsinemoris NBRC 105323T | 215 | 67 | 14 | 3,209,522 | 70.2 | BBQZ00000000 |
| D. sediminicola NBRC 105855T | 226 | 92 | 8 | 2,460,989 | 62.7 | BBRB00000000 |
The genome sequences reported in this study will provide a foundation for further phylogenetic, taxonomic, comparative genomic, metagenomic, and functional studies of the genus Demequina and related taxa. Recently, we isolated some novel strains which are closely related to the genus Demequina and will perform a taxonomic study for the classification of the isolated strains. In the process of the study, the genome sequences presented here will facilitate phylogenetic analyses, including in silico DNA-DNA hybridization. Detailed reports of these analyses will be included in a future publication.
Nucleotide sequence accession numbers.
The draft genome sequences of D. aestuarii NBRC 106260T, D. aurantiaca NBRC 106265T, D. flava NBRC 105854T, D. globuliformis NBRC 106266T, D. lutea NBRC 106155T, D. oxidasica NBRC 106264T, D. salsinemoris NBRC 105323T, and D. sediminicola NBRC 105855T have been deposited in DDBJ/ENA/GenBank. The accession numbers are listed in Table 1. The versions described in this paper are the first versions.
ACKNOWLEDGMENTS
This work was supported by a fund from the Ministry of Economy, Trade and Industry of Japan.
We are grateful to Yuko Kitahashi, Tomoko Hanamaki, and Yoko Makiyama for excellent technical assistance.
Footnotes
Citation Hamada M, Ichikawa N, Oguchi A, Komaki H, Tamura T, Fujita N. 2015. Draft genome sequences of eight type strains of the genus Demequina. Genome Announc 3(2):e00281-15. doi:10.1128/genomeA.00281-15.
REFERENCES
- 1.Yi H, Schumann P, Chun J. 2007. Demequina aestuarii gen. nov., sp. nov., a novel actinomycete of the suborder Micrococcineae, and reclassification of Cellulomonas fermentans Bagnara et al. 1985 as Actinotalea fermentans gen. nov., comb. nov. Int J Syst Evol Microbiol 57:151–156. doi: 10.1099/ijs.0.64525-0. [DOI] [PubMed] [Google Scholar]
- 2.Ue H, Matsuo Y, Kasai H, Yokota A. 2011. Demequina globuliformis sp. nov., Demequina oxidasica sp. nov. and Demequina aurantiaca sp. nov., Actinobacteria isolated from marine environments, and proposal of Demequinaceae fam. nov. Int J Syst Evol Microbiol 61:1322–1329. doi: 10.1099/ijs.0.024299-0. [DOI] [PubMed] [Google Scholar]
- 3.Hamada M, Tamura T, Yamamura H, Suzuki K, Hayakawa M. 2013. Demequina flava sp. nov. and Demequina sediminicola sp. nov., isolated from sea sediment. Int J Syst Evol Microbiol 63:249–253. doi: 10.1099/ijs.0.039297-0. [DOI] [PubMed] [Google Scholar]
- 4.Finster KW, Herbert RA, Kjeldsen KU, Schumann P, Lomstein BA. 2009. Demequina lutea sp. nov., isolated from a high Arctic permafrost soil. Int J Syst Evol Microbiol 59:649–653. doi: 10.1099/ijs.0.004929-0. [DOI] [PubMed] [Google Scholar]
- 5.Matsumoto A, Nakai K, Morisaki K, Omura S, Takahashi Y. 2010. Demequina salsinemoris sp. nov., isolated on agar media supplemented with ascorbic acid or rutin. Int J Syst Evol Microbiol 60:1206–1209. doi: 10.1099/ijs.0.012617-0. [DOI] [PubMed] [Google Scholar]
- 6.Schleifer KH, Kandler O. 1972. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Hamada M, Tamura T, Yamamura H, Suzuki K, Hayakawa M. 2012. Lysinimicrobium mangrovi gen. nov., sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove. Int J Syst Evol Microbiol 62:1731–1735. doi: 10.1099/ijs.0.035493-0. [DOI] [PubMed] [Google Scholar]
- 8.Ohtsubo Y, Muruyama F, Mitsui H, Nagata Y, Tsuda M. 2012. Complete genome sequence of Acidovorax sp. strain kks102, a polychlorinated-biphenyl degrader. J Bacteriol 194:6970–6971. doi: 10.1128/JB.01848-12. [DOI] [PMC free article] [PubMed] [Google Scholar]