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

Gradnigo, Julien

Huether, Michael J.

Johnson, Craig M.

Kemmy, Richard J.

Moriyama, Etsuko N.

Oliver, Michael G.

Somerville, Greg

English

UNL | Libraries

University of Nebraska - Lincoln
DigitalCommons@University of Nebraska - Lincoln
Faculty Publications in the Biological Sciences Papers in the Biological Sciences
2016
Genome Sequence of Streptomyces aureofaciens
ATCC Strain 10762
Julien Gradnigo
University of Nebraska - Lincoln, jgradnigo@gmail.com
Greg Somerville
University of Nebraska—Lincoln, gsomerville3@unl.edu
Michael J. Huether
Zoetis, Lincoln, Nebraska
Richard J. Kemmy
Zoetis, Lincoln, Nebraska
Craig M. Johnson
Zoetis, Lincoln, Nebraska
See next page for additional authors
Follow this and additional works at: https://digitalcommons.unl.edu/bioscifacpub
Part of the Biology Commons
This Article is brought to you for free and open access by the Papers in the Biological Sciences at DigitalCommons@University of Nebraska - Lincoln.
It has been accepted for inclusion in Faculty Publications in the Biological Sciences by an authorized administrator of DigitalCommons@University of
Nebraska - Lincoln.
Gradnigo, Julien; Somerville, Greg; Huether, Michael J.; Kemmy, Richard J.; Johnson, Craig M.; Oliver, Michael G.; and Moriyama,
Etsuko N., "Genome Sequence of Streptomyces aureofaciens ATCC Strain 10762" (2016). Faculty Publications in the Biological Sciences.
496.
https://digitalcommons.unl.edu/bioscifacpub/496
Authors
Julien Gradnigo, Greg Somerville, Michael J. Huether, Richard J. Kemmy, Craig M. Johnson, Michael G.
Oliver, and Etsuko N. Moriyama
This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/bioscifacpub/496
Genome Sequence of Streptomyces aureofaciens ATCC Strain 10762
Julien S. Gradnigo,a Greg A. Somerville,b Michael J. Huether,c Richard J. Kemmy,c Craig M. Johnson,c Michael G. Oliver,c
Etsuko N. Moriyamaa,d
School of Biological Sciences, University of Nebraska–Lincoln, Lincoln, Nebraska, USAa; School of Veterinary Medicine and Biomedical Sciences, University of Nebraska–
Lincoln, Lincoln, Nebraska, USAb; Zoetis, Lincoln, Nebraska, USAc; Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, Nebraska, USAd
Streptomyces aureofaciens is a Gram-positive actinomycete that produces the antibiotics tetracycline and chlortetracy-
cline. Here, we report the assembly and initial annotation of the draft genome sequence of S. aureofaciens ATCC strain
10762.
Received 9 May 2016 Accepted 11 May 2016 Published 23 June 2016
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.
Copyright © 2016 Gradnigo et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
Address correspondence to Etsuko N. Moriyama, emoriyama2@unl.edu.
Streptomyces aureofaciens was first identified in 1948 (1), fromPlot 23 in Sanborn Field, a timothy hayfield at the Univer-
sity of Missouri (2). Although it has been used for the commer-
cial production of tetracycline antibiotics (1, 3) and has been
the subject of numerous biochemical studies, a genome assem-
bly of S. aureofaciens was not publicly available. Here, we report
the draft assembly of the whole-genome sequence of the S. au-
reofaciens ATCC strain 10762 and its initial annotation.
S. aureofaciens ATCC strain 10762 was cultivated in a chemi-
cally 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 quan-
titation for construction of the DNA library.
Genome sequencing and read quality filtering were done by
Eurofins MWG Operon (Alabama, USA). Illumina MiSeq se-
quencing was done with long-jumping-distance sequencing (3-kb
and 8-kb inserts), generating paired-end 150-bp reads. After re-
moving very short (30 bp) reads, adapter-trimming, and
quality-clipping using Trimmomatic (6), 2.46 Gb of sequence in-
formation 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, re-
sulting 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 GC content was 71.2%.
Genome annotation was done using the NCBI Prokaryotic
Genome Annotation Pipeline version 3.1 (8). In total, 13 con-
tigs 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 assem-
blies. 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 INFORMATION
This work, including the efforts of Julien S. Gradnigo, Greg A.
Somerville, and Etsuko N. Moriyama, was funded by Zoetis.
This research was supported by a contract from Zoetis, Inc.
REFERENCES
1. Duggar BM. 1948. Aureomycin; a product of the continuing search for new
antibiotics. Ann N Y Acad Sci 51:177–181. http://dx.doi.org/10.1111/j.1749
-6632.1948.tb27262.x.
2. Nelson ML, Levy SB. 2011. The history of the tetracyclines. Ann N Y Acad
Sci 1241:17–32. http://dx.doi.org/10.1111/j.1749-6632.2011.06354.x.
3. Darken MA, Berenson H, Shirk RJ, Sjolander NO. 1960. Production of
tetracycline by Streptomyces aureofaciens in synthetic media. Appl Micro-
biol 8:46 –51.
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. http://dx.doi.org/
10.1002/bit.260191210.
5. Tripathi G, Rawal SK. 1998. Simple and efficient protocol for isolation of
crossmark
Genome AnnouncementsMay/June 2016 Volume 4 Issue 3 e00615-16 genomea.asm.org 1
high molecular weight DNA from Streptomyces aureofaciens. Biotechnol
Tech 12:629 – 631. http://dx.doi.org/10.1023/A:1008836214495.
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. http://
dx.doi.org/10.1093/nar/gks540.
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. http://dx.doi.org/10.1089/cmb.2012.0021.
8. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Ciufo S, Li W.
2013. Prokaryotic Genome Annotation Pipeline. The NCBI Handbook [in-
ternet], 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 ge-
nomes. Genome Biol 5:R12. http://dx.doi.org/10.1186/gb-2004-5-2-r12.
Gradnigo et al.
Genome Announcements2 genomea.asm.org May/June 2016 Volume 4 Issue 3 e00615-16


Genome Sequence of \u3ci\u3eStreptomyces aureofaciens\u3c/i\u3e ATCC Strain 10762

DigitalCommons@University of Nebraska

University of Nebraska - LincolnDigitalCommons@University of Nebraska - LincolnFaculty Publications in the Biological Sciences Papers in the Biological Sciences2016Genome Sequence of Streptomyces aureofaciensATCC Strain 10762Julien GradnigoUniversity of Nebraska - Lincoln, jgradnigo@gmail.comGreg SomervilleUniversity of Nebraska—Lincoln, gsomerville3@unl.eduMichael J. HuetherZoetis, Lincoln, NebraskaRichard J. KemmyZoetis, Lincoln, NebraskaCraig M. JohnsonZoetis, Lincoln, NebraskaSee next page for additional authorsFollow this and additional works at: https://digitalcommons.unl.edu/bioscifacpubPart of the Biology CommonsThis Article is brought to you for free and open access by the Papers in the Biological Sciences at DigitalCommons@University of Nebraska - Lincoln.It has been accepted for inclusion in Faculty Publications in the Biological Sciences by an authorized administrator of DigitalCommons@University ofNebraska - Lincoln.Gradnigo, Julien; Somerville, Greg; Huether, Michael J.; Kemmy, Richard J.; Johnson, Craig M.; Oliver, Michael G.; and Moriyama,Etsuko N., "Genome Sequence of Streptomyces aureofaciens ATCC Strain 10762" (2016). Faculty Publications in the Biological Sciences.491.https://digitalcommons.unl.edu/bioscifacpub/491AuthorsJulien Gradnigo, Greg Somerville, Michael J. Huether, Richard J. Kemmy, Craig M. Johnson, Michael G.Oliver, and Etsuko N. MoriyamaThis article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/bioscifacpub/491Genome Sequence of Streptomyces aureofaciens ATCC Strain 10762Julien S. Gradnigo,a Greg A. Somerville,b Michael J. Huether,c Richard J. Kemmy,c Craig M. Johnson,c Michael G. Oliver,cEtsuko N. Moriyamaa,dSchool of Biological Sciences, University of Nebraska–Lincoln, Lincoln, Nebraska, USAa; School of Veterinary Medicine and Biomedical Sciences, University of Nebraska–Lincoln, Lincoln, Nebraska, USAb; Zoetis, Lincoln, Nebraska, USAc; Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, Nebraska, USAdStreptomyces aureofaciens is a Gram-positive actinomycete that produces the antibiotics tetracycline and chlortetracy-cline. Here, we report the assembly and initial annotation of the draft genome sequence of S. aureofaciens ATCC strain10762.Received 9 May 2016 Accepted 11 May 2016 Published 23 June 2016Citation 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.Copyright © 2016 Gradnigo et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.Address correspondence to Etsuko N. Moriyama, emoriyama2@unl.edu.Streptomyces aureofacienswas first identified in 1948 (1), fromPlot 23 in Sanborn Field, a timothy hayfield at the Univer-sity of Missouri (2). Although it has been used for the commer-cial production of tetracycline antibiotics (1, 3) and has beenthe subject of numerous biochemical studies, a genome assem-bly of S. aureofacienswas not publicly available. Here, we reportthe draft assembly of the whole-genome sequence of the S. au-reofaciens ATCC strain 10762 and its initial annotation.S. aureofaciens ATCC strain 10762 was cultivated in a chemi-cally defined medium [4] and grown for 9 days at 30°C with 150-rpm aeration. High-molecular-weight DNA was prepared fromfresh cultures by cetyltrimethylammonium bromide extraction(5). Genomic DNA was evaluated for molecular weight integrityby agarose gel electrophoresis and nucleic acid fluorometric quan-titation for construction of the DNA library.Genome sequencing and read quality filtering were done byEurofins MWG Operon (Alabama, USA). Illumina MiSeq se-quencing was done with long-jumping-distance sequencing (3-kband 8-kb inserts), generating paired-end 150-bp reads. After re-moving very short (30 bp) reads, adapter-trimming, andquality-clipping using Trimmomatic (6), 2.46 Gb of sequence in-formation in 19.42 million reads (3.90 million pairs and 12.84million singletons) were obtained. Shotgun sequencing on theRoche 454Genome Sequencer FLXplatformproduced 132.76Mbof sequence data in 209,530 reads with a mean length of 633 bpafter trimming with Trimmomatic.Genome assembly was done using SPAdes version 3.7.1 withthe “--careful” option (to reducemismatches and short indels) (7)with Illumina (both paired-end and singleton) and 454 reads, re-sulting in 120 contigs (total length: 9,234,994 bp; maximumlength: 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 GC content was 71.2%.Genome annotation was done using the NCBI ProkaryoticGenome Annotation Pipeline version 3.1 (8). In total, 13 con-tigs were removed from the annotation because they were200 bp or were of non–S. aureofaciens origin (e.g., plasmid).From the remaining 107 contigs, a total of 8,083 genes wereannotated. This includes 7,541 protein-coding genes, 22 rRNAgenes (5S, 16S, and 23S), 72 tRNA genes, and 445 potentialpseudogenes.Four related S. aureofaciens strains were recently deposited inthe NCBI Assembly database (ASM71917v1, ASM97851v1,ASM71688v1, and ASM127066v1; these strains were designatedNRRL B-2657, NRRL 2209, NRRL B-1286, and NRRL B-2658,respectively). Our assembled contigs are virtually identical toASM71917v1 (99.75% total aligned bases usingMUMmer version3.23 [9]) and only slightly divergent from ASM97851v1 (99.05%total aligned bases). Our assembly has a greater total length andN50 and a smaller number of contigs compared to these assem-blies. Interestingly, our assembled contigs differ significantly fromASM71688v1 andASM127066v1 (83.69%and 9.92% total alignedbases, respectively).Nucleotide sequence accessionnumbers.Thiswhole-genomeshotgun project of S. aureofaciens ATCC strain 10762 has beendeposited in DDBJ/ENA/GenBank under the accession numberJPRF00000000. The version described in this paper is the secondversion, JPRF02000000.FUNDING INFORMATIONThis work, including the efforts of Julien S. Gradnigo, Greg A.Somerville, and Etsuko N. Moriyama, was funded by Zoetis.This research was supported by a contract from Zoetis, Inc.REFERENCES1. Duggar BM. 1948. Aureomycin; a product of the continuing search for newantibiotics. AnnNYAcad Sci 51:177–181. http://dx.doi.org/10.1111/j.1749-6632.1948.tb27262.x.2. Nelson ML, Levy SB. 2011. The history of the tetracyclines. Ann N Y AcadSci 1241:17–32. http://dx.doi.org/10.1111/j.1749-6632.2011.06354.x.3. Darken MA, Berenson H, Shirk RJ, Sjolander NO. 1960. Production oftetracycline by Streptomyces aureofaciens in synthetic media. Appl Micro-biol 8:46–51.4. Laluce C, Molinari R. 1977. Selection of a chemically defined medium forsubmerged cultivation of Streptomyces aureofaciens with high extracellularcaseinolytic activity. Biotechnol Bioeng 19:1863–1884. http://dx.doi.org/10.1002/bit.260191210.5. Tripathi G, Rawal SK. 1998. Simple and efficient protocol for isolation ofcrossmarkGenome AnnouncementsMay/June 2016 Volume 4 Issue 3 e00615-16 genomea.asm.org 1high molecular weight DNA from Streptomyces aureofaciens. BiotechnolTech 12:629–631. http://dx.doi.org/10.1023/A:1008836214495.6. 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. http://dx.doi.org/10.1093/nar/gks540.7. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS,Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, SirotkinAV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a newgenome assembly algorithm and its applications to single-cell sequencing. JComput Biol 19:455–477. http://dx.doi.org/10.1089/cmb.2012.0021.8. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Ciufo S, Li W.2013. Prokaryotic GenomeAnnotation Pipeline. TheNCBIHandbook [in-ternet], 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 ge-nomes. Genome Biol 5:R12. http://dx.doi.org/10.1186/gb-2004-5-2-r12.Gradnigo et al.Genome Announcements2 genomea.asm.org May/June 2016 Volume 4 Issue 3 e00615-16

University of Nebraska - LincolnDigitalCommons@University of Nebraska - LincolnFaculty Publications in the Biological Sciences Papers in the Biological Sciences2016Genome Sequence of Streptomyces aureofaciensATCC Strain 10762Julien GradnigoUniversity of Nebraska - Lincoln, jgradnigo@gmail.comGreg SomervilleUniversity of Nebraska—Lincoln, gsomerville3@unl.eduMichael J. HuetherZoetis, Lincoln, NebraskaRichard J. KemmyZoetis, Lincoln, NebraskaCraig M. JohnsonZoetis, Lincoln, NebraskaSee next page for additional authorsFollow this and additional works at: https://digitalcommons.unl.edu/bioscifacpubPart of the Biology CommonsThis Article is brought to you for free and open access by the Papers in the Biological Sciences at DigitalCommons@University of Nebraska - Lincoln.It has been accepted for inclusion in Faculty Publications in the Biological Sciences by an authorized administrator of DigitalCommons@University ofNebraska - Lincoln.Gradnigo, Julien; Somerville, Greg; Huether, Michael J.; Kemmy, Richard J.; Johnson, Craig M.; Oliver, Michael G.; and Moriyama,Etsuko N., "Genome Sequence of Streptomyces aureofaciens ATCC Strain 10762" (2016). Faculty Publications in the Biological Sciences.496.https://digitalcommons.unl.edu/bioscifacpub/496AuthorsJulien Gradnigo, Greg Somerville, Michael J. Huether, Richard J. Kemmy, Craig M. Johnson, Michael G.Oliver, and Etsuko N. MoriyamaThis article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/bioscifacpub/496Genome Sequence of Streptomyces aureofaciens ATCC Strain 10762Julien S. Gradnigo,a Greg A. Somerville,b Michael J. Huether,c Richard J. Kemmy,c Craig M. Johnson,c Michael G. Oliver,cEtsuko N. Moriyamaa,dSchool of Biological Sciences, University of Nebraska–Lincoln, Lincoln, Nebraska, USAa; School of Veterinary Medicine and Biomedical Sciences, University of Nebraska–Lincoln, Lincoln, Nebraska, USAb; Zoetis, Lincoln, Nebraska, USAc; Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, Nebraska, USAdStreptomyces aureofaciens is a Gram-positive actinomycete that produces the antibiotics tetracycline and chlortetracy-cline. Here, we report the assembly and initial annotation of the draft genome sequence of S. aureofaciens ATCC strain10762.Received 9 May 2016 Accepted 11 May 2016 Published 23 June 2016Citation 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.Copyright © 2016 Gradnigo et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.Address correspondence to Etsuko N. Moriyama, emoriyama2@unl.edu.Streptomyces aureofaciens was first identified in 1948 (1), fromPlot 23 in Sanborn Field, a timothy hayfield at the Univer-sity of Missouri (2). Although it has been used for the commer-cial production of tetracycline antibiotics (1, 3) and has beenthe subject of numerous biochemical studies, a genome assem-bly of S. aureofaciens was not publicly available. Here, we reportthe draft assembly of the whole-genome sequence of the S. au-reofaciens ATCC strain 10762 and its initial annotation.S. aureofaciens ATCC strain 10762 was cultivated in a chemi-cally defined medium [4] and grown for 9 days at 30°C with 150-rpm aeration. High-molecular-weight DNA was prepared fromfresh cultures by cetyltrimethylammonium bromide extraction(5). Genomic DNA was evaluated for molecular weight integrityby agarose gel electrophoresis and nucleic acid fluorometric quan-titation for construction of the DNA library.Genome sequencing and read quality filtering were done byEurofins MWG Operon (Alabama, USA). Illumina MiSeq se-quencing was done with long-jumping-distance sequencing (3-kband 8-kb inserts), generating paired-end 150-bp reads. After re-moving very short (30 bp) reads, adapter-trimming, andquality-clipping using Trimmomatic (6), 2.46 Gb of sequence in-formation in 19.42 million reads (3.90 million pairs and 12.84million singletons) were obtained. Shotgun sequencing on theRoche 454 Genome Sequencer FLX platform produced 132.76 Mbof sequence data in 209,530 reads with a mean length of 633 bpafter trimming with Trimmomatic.Genome assembly was done using SPAdes version 3.7.1 withthe “--careful” option (to reduce mismatches and short indels) (7)with Illumina (both paired-end and singleton) and 454 reads, re-sulting in 120 contigs (total length: 9,234,994 bp; maximumlength: 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 GC content was 71.2%.Genome annotation was done using the NCBI ProkaryoticGenome Annotation Pipeline version 3.1 (8). In total, 13 con-tigs were removed from the annotation because they were200 bp or were of non–S. aureofaciens origin (e.g., plasmid).From the remaining 107 contigs, a total of 8,083 genes wereannotated. This includes 7,541 protein-coding genes, 22 rRNAgenes (5S, 16S, and 23S), 72 tRNA genes, and 445 potentialpseudogenes.Four related S. aureofaciens strains were recently deposited inthe NCBI Assembly database (ASM71917v1, ASM97851v1,ASM71688v1, and ASM127066v1; these strains were designatedNRRL B-2657, NRRL 2209, NRRL B-1286, and NRRL B-2658,respectively). Our assembled contigs are virtually identical toASM71917v1 (99.75% total aligned bases using MUMmer version3.23 [9]) and only slightly divergent from ASM97851v1 (99.05%total aligned bases). Our assembly has a greater total length andN50 and a smaller number of contigs compared to these assem-blies. Interestingly, our assembled contigs differ significantly fromASM71688v1 and ASM127066v1 (83.69% and 9.92% total alignedbases, respectively).Nucleotide sequence accession numbers. This whole-genomeshotgun project of S. aureofaciens ATCC strain 10762 has beendeposited in DDBJ/ENA/GenBank under the accession numberJPRF00000000. The version described in this paper is the secondversion, JPRF02000000.FUNDING INFORMATIONThis work, including the efforts of Julien S. Gradnigo, Greg A.Somerville, and Etsuko N. Moriyama, was funded by Zoetis.This research was supported by a contract from Zoetis, Inc.REFERENCES1. Duggar BM. 1948. Aureomycin; a product of the continuing search for newantibiotics. Ann N Y Acad Sci 51:177–181. http://dx.doi.org/10.1111/j.1749-6632.1948.tb27262.x.2. Nelson ML, Levy SB. 2011. The history of the tetracyclines. Ann N Y AcadSci 1241:17–32. http://dx.doi.org/10.1111/j.1749-6632.2011.06354.x.3. Darken MA, Berenson H, Shirk RJ, Sjolander NO. 1960. Production oftetracycline by Streptomyces aureofaciens in synthetic media. Appl Micro-biol 8:46 –51.4. Laluce C, Molinari R. 1977. Selection of a chemically defined medium forsubmerged cultivation of Streptomyces aureofaciens with high extracellularcaseinolytic activity. Biotechnol Bioeng 19:1863–1884. http://dx.doi.org/10.1002/bit.260191210.5. Tripathi G, Rawal SK. 1998. Simple and efficient protocol for isolation ofcrossmarkGenome AnnouncementsMay/June 2016 Volume 4 Issue 3 e00615-16 genomea.asm.org 1high molecular weight DNA from Streptomyces aureofaciens. BiotechnolTech 12:629 – 631. http://dx.doi.org/10.1023/A:1008836214495.6. 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. http://dx.doi.org/10.1093/nar/gks540.7. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS,Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, SirotkinAV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a newgenome assembly algorithm and its applications to single-cell sequencing. JComput Biol 19:455– 477. http://dx.doi.org/10.1089/cmb.2012.0021.8. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Ciufo S, Li W.2013. Prokaryotic Genome Annotation Pipeline. The NCBI Handbook [in-ternet], 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 ge-nomes. Genome Biol 5:R12. http://dx.doi.org/10.1186/gb-2004-5-2-r12.Gradnigo et al.Genome Announcements2 genomea.asm.org May/June 2016 Volume 4 Issue 3 e00615-16

https://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1492&amp;context=bioscifacpub

Genome Sequence of \u3ci\u3eStreptomyces aureofaciens\u3c/i\u3e ATCC Strain 10762

Abstract

Similar works

Full text

Available Versions

UNL | Libraries

DigitalCommons@University of Nebraska

DigitalCommons@University of Nebraska