High-quality draft genome sequence of actinobacterium Kibdelosporangium sp. MJ126-NF4, producer of type II polyketide azicemicins, using Illumina and PacBio technologies

Genome Announcements

Volumn 3, Issue 2, 2016, Pages

  Ogasawara, Yasushi ^a,f   Torrez Martinez, Norah ^b   Aragon, Anthony D ^a   Yackley, Benjamin J ^a   Weber, Jessica A ^a   Sundararajan, Anitha ^c   Ramaraj, Thiruvarangan ^c   Edwards, Jeremy S ^a,b,d,e   Melançon, Charles E ^a  

^a UNIVERSITY OF NEW MEXICO   (United States)

^b UNIVERSITY OF NEW MEXICO HEALTH SCIENCES CENTER   (United States)

^c NATIONAL CENTER FOR GENOME RESOURCES   (United States)

^d University of New Mexico   (United States)

^e UNIVERSITY OF NEW MEXICO   (United States)

^f HOKKAIDO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85007426078     PISSN: None     EISSN: 21698287     Source Type: Journal    
DOI: 10.1128/genomeA.00114-15     Document Type: Article

References (17)

1. Walsh CT, Fischbach MA. 2010. Natural products version 2.0: connecting genes to molecules. JAmChem Soc 132:2469-2493. http://dx.doi.org/10.1021/ja909118a.
2. Romero D, Traxler MF, López D, Kolter R. 2011. Antibiotics as signal molecules. Chem Rev 111:5492-5505. http://dx.doi.org/10.1021/cr2000509.
3. Bologa CG, Ursu O, Oprea TI, Melançon CE III, Tegos GP. 2013. Emerging trends in the discovery of natural product antibacterials. Curr Opin Pharmacol 13:678-687. http://dx.doi.org/10.1016/j.coph.2013.07.002.
4. Yamanaka K, Reynolds KA, Kersten RD, Ryan KS, Gonzalez DJ, Nizet V, Dorrestein PC, Moore BS. 2014. Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A. Proc Natl Acad Sci U S A. 111:1957-1962. http://dx.doi.org/10.1073/pnas.1319584111.
5. Gomez-Escribano JP, Bibb MJ. 2011. Engineering Streptomyces coelicolor for heterologous expression of secondary metabolite gene clusters. Microb Biotechnol 4:207-215. http://dx.doi.org/10.1111/j.1751-7915.2010.00219.x.
6. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng J-F, Lucas S, Kerfield C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk H-P, Eisen JA. 2009. A phylogeny-driven genomic encyclopaedia of bacteria and archaea. Nature 462:1056-1060. http://dx.doi.org/10.1038/nature08656.
7. Tiwari K, Gupta RK. 2012. Rare actinomycetes: a potential storehouse for novel antibiotics. Crit Rev Biotechnol 32:108-132. http://dx.doi.org/10.3109/07388551.2011.562482.
8. Tsuchida T, Iinuma H, Kinoshita N, Ikeda T, Sawa R, Takahashi Y, Naganawa H, Sawa T, Hamada M, Takeuchi T. 1993. Azicemicin A, a new antimicrobial antibiotic from Amycolatopsis. J Antibiot 46: 1772-1774.
9. Tsuchida T, Iinuma H, Kinoshita N, Ikeda T, Sawa T, Hamada M, Takeuchi T. 1995. Azicemicins A and B, a new antimicrobial agent produced by Amycolatopsis. I. Taxonomy, fermentation, isolation, characterization and biological activities. J Antibiot 48:217-221.
10. Ogasawara Y, Liu H-W. 2009. Biosynthetic studies of aziridine formation in azicemicins. J Am Chem Soc 131:18066-18068. http://dx.doi.org/10.1021/ja907307h.
11. Chevreux B, Wetter T, Suhai S. 1999. Genome sequence assembly using trace signals and additional sequence information, p 45-56. In Computer science and biology. Proceedings of the German Conference on Bioinformatics, GCB '99. GCB, Hannover, Germany.
12. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013 Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563-569. http://dx.doi.org/10.1038/nmeth.2474.
13. Luo R, Liu B, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu S-M, Peng S, Zhu X, Liu G, Liao X, Li Y, Yang H, Wang J, Lam T-W, Wang J. 2012. SOAPdenovo2: an empirically improved memoryefficient short-read de novo assembler. GigaScience 1:18. http://dx.doi.org/10.1186/2047-217X-1-18.
14. 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. http://dx.doi.org/10.1186/1471-2164-9-75.
15. Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673-679. http://dx.doi.org/10.1093/bioinformatics/btm009.
16. Ogasawara Y, Yackley BJ, Greenberg JA, Rogelj S, Melançon CE, III. Expanding our understanding of sequence-function relationships of type II polyketide biosynthetic gene clusters: bioinformatics-guided identification of Frankiamicin A from Frankia sp. EAN1pec. PLoS One, in press.
17. Blin K, Medema MH, Kazempour D, Fischbach MA, Breitling R, Takano E, Weber T. 2013. antiSMASH 2.0-a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res 41:W204-W212. http://dx.doi.org/10.1093/nar/gkt449.