Abstract
Aneurinibacillus migulanus ATCC 9999T (DSM 2895) is a Gram-positive, round-spore-forming, and gramicidin S-producing bacterium. Here, we report the 6.35-Mb high-quality draft genome sequence of A. migulanus ATCC 9999T, which will provide useful information for the genomic taxonomy and phylogenomics of Bacillus-like bacteria.
GENOME ANNOUNCEMENT
The Bacillus-like strain ATCC 9999T (DSM 2895) was isolated by R. Synge from Moscow, Russia, and initially identified as a member of Bacillus brevis (now Brevibacillus brevi) (1). In 1993, the strain ATCC 9999T was identified as a unique species and named as Bacillus migulanus sp. nov. (1). In 1996, however, Bacillus migulanus was reclassified as Aneurinibacillus migulanus comb. nov. belonging to the family Paenibacillaceae but not the family Bacillaceae (2). It is of great applicable significance that A. migulanus is a promising biocontrol agent against a range of plant-pathogenic bacteria and fungi, due to its ability to produce the antimicrobial peptide gramicidin S (3–5). Given the physiological properties and application prospects of A. migulanus, its type strain ATCC 9999T was selected as one of the research objects in our “genome sequencing project for genomic taxonomy and phylogenomics of Bacillus-like bacteria.” Although two genome sequences of A. migulanus were reported (JYBN01000000 with 82 scaffolds and JYBO01000000 with 89 scaffolds) (4, 5), here, we presented the third draft genome sequence with higher quality (just 28 scaffolds).
The genome sequencing of A. migulanus ATCC 9999T (DSM 2895) was performed via the Illumina Hieseq 2500 system. Two DNA libraries with insert sizes of 500 and 5,000 bp were constructed and sequenced. After filtering of the 1.14-Gb raw data, the 1.10-Gb clean data was obtained, providing approximately 200-fold coverage. The reads were assembled via the SOAPdenovo software version 1.05 (6), using a key parameter K setting at 71. Through the data assembly, 28 scaffolds with total length 6,348,994 bp were obtained, and the scaffold N50 was 4,944,581 bp. The average length of the scaffolds was 226,749 bp, and the longest and shortest scaffolds were 4,944,581 bp and 506 bp, respectively. A total of 91.49% clean reads could be aligned back to the genome, which covered 99.75% of the sequence.
The annotation of the genome was performed using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/) utilizing GeneMark, Glimmer, and tRNAscan-SE tools (7). A total of 6,273 genes were predicted, including 5,673 coding sequences (CDS), 504 pseudo genes, 85 tRNAs, and 12 rRNA genes. There were 3,938 and 2,984 genes assigned to COG and KEGG databases, respectively. The average DNA G+C content was 43.06%, agreeing with the values 43.04% of JYBN01000000 and 43.16% of JYBO01000000 (4, 5) but disagreeing slightly with the value 42.5 mol% acquired by HPLC determination (1).
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. LGUG00000000. The version described in this paper is version LGUG01000000.
ACKNOWLEDGMENTS
This work was supported by the National Natural Science Foundation of China (grant 31370059); the Scientific Research Foundation for Returned Scholars, Fujian Academy of Agricultural Sciences (grant YJRC2014-1); and Fujian Special Fund for Scientific Research Institutes in the Public Interest (grant 2014R1101016-11).
Footnotes
Citation Wang J-P, Liu B, Liu G-H, Ge C-B, Xiao R-F, Zheng X-F, Shi H. 2015. High-quality draft genome sequence of Aneurinibacillus migulanus ATCC 9999T (DSM 2895), a gramicidin S-producing bacterium isolated from garden soil. Genome Announc 3(5):e01227-15. doi:10.1128/genomeA.01227-15.
REFERENCES
- 1.Takagi H, Shida O, Kadowaki K, Komagata K, Udaka S. 1993. Characterization of Bacillus brevis with descriptions of Bacillus migulanus sp. nov., Bacillus choshinensis sp. nov., Bacillus parabrevis sp. nov., and Bacillus galactophilus sp. nov. Int J Syst Bacteriol 43:221–231. doi: 10.1099/00207713-43-2-221. [DOI] [PubMed] [Google Scholar]
- 2.Shida O, Takagi H, Kadowaki K, Komagata K. 1996. Proposal for two new genera, Brevibacillus gen. nov. and Aneurinibacillus gen. nov. Int J Syst Bacteriol 46:939–946. doi: 10.1099/00207713-46-4-939. [DOI] [PubMed] [Google Scholar]
- 3.Berditsch M, Afonin S, Ulrich AS. 2007. The ability of Aneurinibacillus migulanus (Bacillus brevis) to produce the antibiotic gramicidin S is correlated with phenotype variation. Appl Environ Microbiol 73:6620–6628. doi: 10.1128/AEM.00881-07. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Alenezi FN, Weitz HJ, Belbahri L, Ben Rebah H, Luptakova L, Jaspars M, Woodward S. 2015. Draft genome sequence of Aneurinibacillus migulanus strain Nagano. Genome Announc 3(2):e00232-15. doi: 10.1128/genomeA.00232-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Alenezi FN, Weitz HJ, Belbahri L, Nidhal J, Luptakova L, Jaspars M, Woodward S. 2015. Draft genome sequence of Aneurinibacillus migulanus NCTC 7096. Genome Announc 3(2):e00234-15. doi: 10.1128/genomeA.00234-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J. 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272. doi: 10.1101/gr.097261.109. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. doi: 10.1186/1471-2164-9-75. [DOI] [PMC free article] [PubMed] [Google Scholar]