PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of genannJournal InfoAuthorsPermissionsJournals.ASM.orggenomeA ArticleGenome Announcements
 
Genome Announc. 2016 May-Jun; 4(3): e00615-16.
Published online 2016 June 23. doi:  10.1128/genomeA.00615-16
PMCID: PMC4919415

Genome Sequence of Streptomyces aureofaciens ATCC Strain 10762

Abstract

Streptomyces aureofaciens is a Gram-positive actinomycete that produces the antibiotics tetracycline and chlortetracycline. Here, we report the assembly and initial annotation of the draft genome sequence of S. aureofaciens ATCC strain 10762.

GENOME ANNOUNCEMENT

Streptomyces aureofaciens was first identified in 1948 (1), from Plot 23 in Sanborn Field, a timothy hayfield at the University of Missouri (2). Although it has been used for the commercial production of tetracycline antibiotics (1, 3) and has been the subject of numerous biochemical studies, a genome assembly of S. aureofaciens was not publicly available. Here, we report the draft assembly of the whole-genome sequence of the S. aureofaciens ATCC strain 10762 and its initial annotation.

S. aureofaciens ATCC strain 10762 was cultivated in a chemically defined medium [4] and grown for 9 days at 30°C with 150-rpm aeration. High-molecular-weight DNA was prepared from fresh cultures by cetyltrimethylammonium bromide extraction (5). Genomic DNA was evaluated for molecular weight integrity by agarose gel electrophoresis and nucleic acid fluorometric quantitation for construction of the DNA library.

Genome sequencing and read quality filtering were done by Eurofins MWG Operon (Alabama, USA). Illumina MiSeq sequencing was done with long-jumping-distance sequencing (3-kb and 8-kb inserts), generating paired-end 150-bp reads. After removing very short (<30 bp) reads, adapter-trimming, and quality-clipping using Trimmomatic (6), 2.46 Gb of sequence information in 19.42 million reads (3.90 million pairs and 12.84 million singletons) were obtained. Shotgun sequencing on the Roche 454 Genome Sequencer FLX platform produced 132.76 Mb of sequence data in 209,530 reads with a mean length of 633 bp after trimming with Trimmomatic.

Genome assembly was done using SPAdes version 3.7.1 with the “--careful” option (to reduce mismatches and short indels) (7) with Illumina (both paired-end and singleton) and 454 reads, resulting in 120 contigs (total length: 9,234,994 bp; maximum length: 881,164 bp; N50: 228,235 bp) in 60 scaffolds (total length: 9,244,380 bp; maximum length: 1,746,076 bp; N50: 660,648 bp). The average G+C content was 71.2%.

Genome annotation was done using the NCBI Prokaryotic Genome Annotation Pipeline version 3.1 (8). In total, 13 contigs were removed from the annotation because they were <200 bp or were of non–S. aureofaciens origin (e.g., plasmid). From the remaining 107 contigs, a total of 8,083 genes were annotated. This includes 7,541 protein-coding genes, 22 rRNA genes (5S, 16S, and 23S), 72 tRNA genes, and 445 potential pseudogenes.

Four related S. aureofaciens strains were recently deposited in the NCBI Assembly database (ASM71917v1, ASM97851v1, ASM71688v1, and ASM127066v1; these strains were designated NRRL B-2657, NRRL 2209, NRRL B-1286, and NRRL B-2658, respectively). Our assembled contigs are virtually identical to ASM71917v1 (99.75% total aligned bases using MUMmer version 3.23 [9]) and only slightly divergent from ASM97851v1 (99.05% total aligned bases). Our assembly has a greater total length and N50 and a smaller number of contigs compared to these assemblies. Interestingly, our assembled contigs differ significantly from ASM71688v1 and ASM127066v1 (83.69% and 9.92% total aligned bases, respectively).

Nucleotide sequence accession numbers.

This whole-genome shotgun project of S. aureofaciens ATCC strain 10762 has been deposited in DDBJ/ENA/GenBank under the accession number JPRF00000000. The version described in this paper is the second version, JPRF02000000.

Funding Statement

This research was supported by a contract from Zoetis, Inc.

Footnotes

Citation Gradnigo JS, Somerville GA, Huether MJ, Kemmy RJ, Johnson CM, Oliver MG, Moriyama EN. 2016. Genome sequence of Streptomyces aureofaciens ATCC strain 10762. Genome Announc 4(3):e00615-16. doi:10.1128/genomeA.00615-16.

REFERENCES

1. Duggar BM. 1948. Aureomycin; a product of the continuing search for new antibiotics. Ann N Y Acad Sci 51:177–181. doi:.10.1111/j.1749-6632.1948.tb27262.x [PubMed] [Cross Ref]
2. Nelson ML, Levy SB 2011. The history of the tetracyclines. Ann N Y Acad Sci 1241:17–32. doi:.10.1111/j.1749-6632.2011.06354.x [PubMed] [Cross Ref]
3. Darken MA, Berenson H, Shirk RJ, Sjolander NO 1960. Production of tetracycline by Streptomyces aureofaciens in synthetic media. Appl Microbiol 8:46–51. [PMC free article] [PubMed]
4. Laluce C, Molinari R 1977. Selection of a chemically defined medium for submerged cultivation of Streptomyces aureofaciens with high extracellular caseinolytic activity. Biotechnol Bioeng 19:1863–1884. doi:.10.1002/bit.260191210 [PubMed] [Cross Ref]
5. Tripathi G, Rawal SK 1998. Simple and efficient protocol for isolation of high molecular weight DNA from Streptomyces aureofaciens. Biotechnol Tech 12:629–631. doi:.10.1023/A:1008836214495 [Cross Ref]
6. Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B 2012. RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res 40:W622–W627. doi:.10.1093/nar/gks540 [PMC free article] [PubMed] [Cross Ref]
7. 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 [PMC free article] [PubMed] [Cross Ref]
8. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Ciufo S, Li W 2013. Prokaryotic Genome Annotation Pipeline. The NCBI Handbook [internet], 2nd ed. NCBI, Bethesda, MD: http://www.ncbi.nlm.nih.gov/books/NBK174280.
9. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL 2004. Versatile and open software for comparing large genomes. Genome Biol 5:R12. doi:.10.1186/gb-2004-5-2-r12 [PMC free article] [PubMed] [Cross Ref]

Articles from Genome Announcements are provided here courtesy of American Society for Microbiology (ASM)