Complete genome sequence of Intrasporangium calvum type strain (7 KIPT)

Glavina Del Rio, Tijana; Chertkov, Olga; Yasawong, Montri; Lucas, Susan; Deshpande, Shweta; Cheng, Jan-Fang; Detter, Chris; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Rohde, Manfred; Pukall, Rüdiger; Sikorski, Johannes; Göker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Lapidus, Alla

doi:10.4056/sigs.1263355

Complete genome sequence of Intrasporangium calvum type strain (7 KIP^T)

Journal Article · Fri Dec 31 00:00:00 EST 2010 · Standards in Genomic Sciences

DOI:https://doi.org/10.4056/sigs.1263355· OSTI ID:1630544

Glavina Del Rio, Tijana ^[1]; Chertkov, Olga ^[2]; Yasawong, Montri ^[3]; Lucas, Susan ^[1]; Deshpande, Shweta ^[1]; Cheng, Jan-Fang ^[1]; Detter, Chris ^[2]; Tapia, Roxanne ^[2]; Han, Cliff ^[2]; Goodwin, Lynne ^[2]; Pitluck, Sam ^[1]; Liolios, Konstantinos ^[1]; Ivanova, Natalia ^[1]; Mavromatis, Konstantinos ^[1]; Pati, Amrita ^[1]; Chen, Amy ^[4]; Palaniappan, Krishna ^[4]; Land, Miriam ^[5]; Hauser, Loren ^[5]; Chang, Yun-Juan ^[5] more »

USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Helmholtz Centre for Infection Research, Braunschweig (Germany)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Davis, CA (United States)

Intrasporangium calvum Kalakoutskii et al. 1967 is the type species of the genus Intrasporangium, which belongs to the actinobacterial family Intrasporangiaceae. The species is a Gram-positive bacterium that forms a branching mycelium, which tends to break into irregular fragments. The mycelium of this strain may bear intercalary vesicles but does not contain spores. The strain described in this study is an airborne organism that was isolated from a school dining room in 1967. One particularly interesting feature of I. calvum is that the type of its menaquinone is different from all other representatives of the family Intrasporangiaceae. This is the first completed genome sequence from a member of the genus Intrasporangium and also the first sequence from the family Intrasporangiaceae. The 4,024,382 bp long genome with its 3,653 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: German Research Foundation (DFG); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; AC05-00OR22725; AC52-07NA27344

OSTI ID:: 1630544

Alternate ID(s):: OSTI ID: 1029243

Journal Information:: Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Journal Issue: 3 Vol. 3; ISSN 1944-3277

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (31)

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs Zerbino, D. R.; Birney, E. Genome Research, Vol. 18, Issue 5 https://doi.org/10.1101/gr.074492.107	journal	February 2008
How Many Bootstrap Replicates Are Necessary? Pattengale, Nicholas D.; Alipour, Masoud; Bininda-Emonds, Olaf R. P. Lecture Notes in Computer Science https://doi.org/10.1007/978-3-642-02008-7_13	book	January 2009
The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains Yarza, Pablo; Richter, Michael; Peplies, Jörg Systematic and Applied Microbiology, Vol. 31, Issue 4 https://doi.org/10.1016/j.syapm.2008.07.001	journal	September 2008
En route to a genome-based classification of Archaea and Bacteria? Klenk, H. -P.; Göker, M. Systematic and Applied Microbiology, Vol. 33, Issue 4 https://doi.org/10.1016/j.syapm.2010.03.003	journal	June 2010
Gene Ontology: tool for the unification of biology Ashburner, Michael; Ball, Catherine A.; Blake, Judith A. Nature Genetics, Vol. 25, Issue 1 https://doi.org/10.1038/75556	journal	May 2000
The use of stable isotope probing to identify key iron-reducing microorganisms involved in anaerobic benzene degradation Kunapuli, Umakanth; Lueders, Tillmann; Meckenstock, Rainer U. The ISME Journal, Vol. 1, Issue 7 https://doi.org/10.1038/ismej.2007.73	journal	September 2007
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos Nature, Vol. 462, Issue 7276 https://doi.org/10.1038/nature08656	journal	December 2009
The minimum information about a genome sequence (MIGS) specification Field, Dawn; Garrity, George; Gray, Tanya Nature Biotechnology, Vol. 26, Issue 5 https://doi.org/10.1038/nbt1360	journal	May 2008
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia Nature Methods, Vol. 7, Issue 6 https://doi.org/10.1038/nmeth.1457	journal	May 2010
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Woese, C. R.; Kandler, O.; Wheelis, M. L. Proceedings of the National Academy of Sciences, Vol. 87, Issue 12 https://doi.org/10.1073/pnas.87.12.4576	journal	June 1990
A Rapid Bootstrap Algorithm for the RAxML Web Servers Stamatakis, Alexandros; Hoover, Paul; Rougemont, Jacques Systematic Biology, Vol. 57, Issue 5 https://doi.org/10.1080/10635150802429642	journal	October 2008
Multiple sequence alignment using partial order graphs Lee, C.; Grasso, C.; Sharlow, M. F. Bioinformatics, Vol. 18, Issue 3 https://doi.org/10.1093/bioinformatics/18.3.452	journal	March 2002
IMG ER: a system for microbial genome annotation expert review and curation Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N. Bioinformatics, Vol. 25, Issue 17 https://doi.org/10.1093/bioinformatics/btp393	journal	June 2009
GenBank Benson, D. A.; Karsch-Mizrachi, I.; Lipman, D. J. Nucleic Acids Research, Vol. 37, Issue Database https://doi.org/10.1093/nar/gkn723	journal	January 2009
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata Liolios, Konstantinos; Chen, I-Min A.; Mavromatis, Konstantinos Nucleic Acids Research, Vol. 38, Issue suppl_1 https://doi.org/10.1093/nar/gkp848	journal	November 2009
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis Castresana, J. Molecular Biology and Evolution, Vol. 17, Issue 4 https://doi.org/10.1093/oxfordjournals.molbev.a026334	journal	April 2000
Approved Lists of Bacterial Names Sneath, P. H. A.; McGOWAN, Vicki; Skerman, V. B. D. International Journal of Systematic and Evolutionary Microbiology, Vol. 30, Issue 1 https://doi.org/10.1099/00207713-30-1-225	journal	January 1980
Friedmanniella antarctica gen. nov., sp. nov., an LL-Diaminopimelic Acid-Containing Actinomycete from Antarctic Sandstone Schumann, P.; Prauser, H.; Rainey, F. A. International Journal of Systematic Bacteriology, Vol. 47, Issue 2 https://doi.org/10.1099/00207713-47-2-278	journal	April 1997
Proposal for a New Hierarchic Classification System, Actinobacteria classis nov. Stackebrandt, E.; Rainey, F. A.; Ward-Rainey, N. L. International Journal of Systematic Bacteriology, Vol. 47, Issue 2 https://doi.org/10.1099/00207713-47-2-479	journal	April 1997
Polyamine profiles within genera of the class Actinobacteria with ll-diaminopimelic acid in the peptidoglycan Busse, Hans-Jürgen; Schumann, Peter International Journal of Systematic and Evolutionary Microbiology, Vol. 49, Issue 1 https://doi.org/10.1099/00207713-49-1-179	journal	January 1999
Description of Bogoriellaceae fam. nov., Dermacoccaceae fam. nov., Rarobacteraceae fam. nov. and Sanguibacteraceae fam. nov. and emendation of some families of the suborder Micrococcineae. Stackebrandt, E.; Schumann, P. International Journal of Systematic and Evolutionary Microbiology, Vol. 50, Issue 3 https://doi.org/10.1099/00207713-50-3-1279	journal	May 2000
Nomenclatural type of orders: corrections necessary according to Rules 15 and 21a of the Bacteriological Code (1990 Revision), and designation of appropriate nomenclatural types of classes and subclasses. Request for an opinion. Euzéby, J. P.; Tindall, B. J. International Journal of Systematic and Evolutionary Microbiology, Vol. 51, Issue 2 https://doi.org/10.1099/00207713-51-2-725	journal	March 2001
A New Genus of the Actinomycetales--Intrasporangium gen.nov. Kalakoutskii, L. V.; Kirillova, I. P.; Krassilnikov, N. A. Journal of General Microbiology, Vol. 48, Issue 1 https://doi.org/10.1099/00221287-48-1-79	journal	July 1967
EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences Kim, Byung Kwon; Lim, Young-Woon; Kim, Myungjin International Journal of Systematic and Evolutionary Microbiology, Vol. 57, Issue 10 https://doi.org/10.1099/ijs.0.64915-0	journal	October 2007
An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa Zhi, X. -Y.; Li, W. -J.; Stackebrandt, E. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 3 https://doi.org/10.1099/ijs.0.65780-0	journal	March 2009
Application of a High-Density Oligonucleotide Microarray Approach To Study Bacterial Population Dynamics during Uranium Reduction and Reoxidation Brodie, E. L.; DeSantis, T. Z.; Joyner, D. C. Applied and Environmental Microbiology, Vol. 72, Issue 9 https://doi.org/10.1128/AEM.00246-06	journal	September 2006
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB DeSantis, T. Z.; Hugenholtz, P.; Larsen, N. Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072 https://doi.org/10.1128/AEM.03006-05	journal	July 2006
Ultramicroscopic Structure of Intrasporangium calvum (Actinomycetales) Lechevalier, Hubert; Lechevalier, Mary P. Journal of Bacteriology, Vol. 100, Issue 1 https://doi.org/10.1128/JB.100.1.522-525.1969	journal	January 1969
Studies in the Nomenclature and Classification of the Bacteria ii. the Primary Subdivisions of the Schizomycetes Buchanan, R. E. Journal of Bacteriology, Vol. 2, Issue 2 https://doi.org/10.1128/JB.2.2.155-164.1917	journal	January 1917
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
Complete genome sequence of Kytococcus sedentarius type strain (541T) Sims, David; Brettin, Thomas; Detter, John C. Standards in Genomic Sciences, Vol. 1, Issue 1 https://doi.org/10.4056/sigs.761	journal	July 2009

Cited By (3)

A real-time multiplexed microbial growth intervalometer for capturing high resolution growth curves Vuono, David C.; Lipp, Bruce; Staub, Carl Frontiers in Microbiology https://doi.org/10.1101/533356	posted_content	January 2019
Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria Gao, B.; Gupta, R. S. Microbiology and Molecular Biology Reviews, Vol. 76, Issue 1 https://doi.org/10.1128/mmbr.05011-11	journal	March 2012
Resource Concentration Modulates the Fate of Dissimilated Nitrogen in a Dual-Pathway Actinobacterium Vuono, David C.; Read, Robert W.; Hemp, James Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00003	journal	January 2019