Complete genome sequence of Geodermatophilus obscurus type strain (G-20T)

Geodermatophilus obscurus Luedemann 1968 is the type species of the genus, which is the type genus of the family Geodermatophilaceae. G. obscurus is of interest as it has frequently been isolated from stressful environments such as rock varnish in deserts, and as it exhibits interesting phenotypes such as lytic capability of yeast cell walls, UV-C resistance, strong production of extracellular functional amyloid (FuBA) and manganese oxidation. This is the first completed genome sequence of the family Geodermatophilaceae. The 5,322,497 bp long genome with its 5,161 protein-coding and 58 RNA genes is part of the GenomicEncyclopedia ofBacteria andArchaea project.

[1]  G. Garrity,et al.  The Road Map to the Manual , 2015 .

[2]  Natalia N. Ivanova,et al.  GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes , 2010, Nature Methods.

[3]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[4]  Hans-Peter Klenk,et al.  Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison , 2010, Standards in genomic sciences.

[5]  Hans-Peter Klenk,et al.  Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs , 2010, Standards in genomic sciences.

[6]  Natalia N. Ivanova,et al.  A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea , 2009, Nature.

[7]  I-Min A. Chen,et al.  IMG ER: a system for microbial genome annotation expert review and curation , 2009, Bioinform..

[8]  Lynne A. Goodwin,et al.  Complete genome sequence of Kytococcus sedentarius type strain (541T) , 2009, Standards in genomic sciences.

[9]  Alexandros Stamatakis,et al.  How Many Bootstrap Replicates Are Necessary? , 2009, RECOMB.

[10]  J. Enghild,et al.  Widespread Abundance of Functional Bacterial Amyloid in Mycolata and Other Gram-Positive Bacteria , 2009, Applied and Environmental Microbiology.

[11]  J. Rougemont,et al.  A rapid bootstrap algorithm for the RAxML Web servers. , 2008, Systematic biology.

[12]  Chris F. Taylor,et al.  The minimum information about a genome sequence (MIGS) specification , 2008, Nature Biotechnology.

[13]  I-Min A. Chen,et al.  The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata , 2007, Nucleic Acids Res..

[14]  James R. Cole,et al.  Part 10 - The Bacteria: Phylum Actinobacteria, Class "Actinobacteria" , 2007 .

[15]  Eugene Goltsman,et al.  Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. , 2006, Genome research.

[16]  P. Normand Geodermatophilaceae fam. nov., a formal description. , 2006, International journal of systematic and evolutionary microbiology.

[17]  Ó. Salazar,et al.  Real-Time PCR for the Detection and Quantification of Geodermatophilaceae from Stone Samples and Identification of New Members of the Genus Blastococcus , 2006, Applied and Environmental Microbiology.

[18]  R. Anderson,et al.  Enumeration, isolation, and characterization of ultraviolet (UV-C) resistant bacteria from rock varnish in the Whipple Mountains, California , 2005 .

[19]  O. White,et al.  Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.

[20]  Christopher J. Lee,et al.  Multiple sequence alignment using partial order graphs , 2002, Bioinform..

[21]  R. Wetzel,et al.  Conformational Abs recognizing a generic amyloid fibril epitope , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[22]  C. Sorlini,et al.  Biodiversity of Geodermatophilaceae isolated from altered stones and monuments in the Mediterranean basin. , 2001, Environmental microbiology.

[23]  D. Pataraya,et al.  Study of the Lytic Activities of Actinomycetes Isolated from Different Soils in Georgia , 2001, Applied Biochemistry and Microbiology.

[24]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[25]  Wei Qian,et al.  Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. , 2000, Molecular biology and evolution.

[26]  E. Stackebrandt,et al.  Proposal for a New Hierarchic Classification System, Actinobacteria classis nov. , 1997 .

[27]  James T. Staley,et al.  Morphological, physiological, and molecular characterization of actinomycetes isolated from dry soil, rocks, and monument surfaces , 1996, Archives of Microbiology.

[28]  A. Akkermans,et al.  Identification of atypical Frankia strains by fatty acid analysis , 1991 .

[29]  O. Kandler,et al.  Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[30]  E. Stackebrandt,et al.  Evidence for a Close Phylogenetic Relationship Between Members of the Genera Frankia, Geodermatophilus, and “Blastococcus” and Emdendation of the Family Frankiaceae , 1989 .

[31]  J. T. Staley,et al.  Characterization of manganese-oxidizing (MnII→MnIV) bacteria from Negev Desert rock varnish: implications in desert varnish formation , 1987 .

[32]  E. Stackebrandt,et al.  A phylogenetic analysis of the family Dermatophilaceae. , 1983, Journal of general microbiology.

[33]  E. Ishiguro,et al.  Control of Morphogenesis in Geodermatophilus: Ultrastructural Studies , 1970, Journal of bacteriology.

[34]  H. Lechevalier,et al.  Chemical composition as a criterion in the classification of aerobic actinomycetes , 1970 .

[35]  G. Luedemann Geodermatophilus, a New Genus of the Dermatophilaceae (Actinomycetales) , 1968, Journal of bacteriology.

[36]  M. Gordon THE GENUS DERMATOPHILUS , 1964, Journal of bacteriology.

[37]  G. Garrity Bergey’s Manual® of Systematic Bacteriology , 2012, Springer New York.

[38]  Galina,et al.  Complete genome sequence of Nakamurella multipartita type strain (Y-104) , 2010 .

[39]  Lynne A. Goodwin,et al.  Complete genome sequence of Kytococcus sedentarius type strain (541 T ) , 2009 .

[40]  James R. Cole,et al.  Taxonomic Outline of the Bacteria and Archaea , Release 7 . 7 March 6 , 2007 . Part 9 – The Bacteria : Phylum “ Firmicutes ” : Class “ Bacilli ” , 2007 .

[41]  T. Hansen Bergey's Manual of Systematic Bacteriology , 2005 .

[42]  E. Stackebrandt,et al.  Modestobacter multiseptatus gen. nov., sp. nov., a budding actinomycete from soils of the Asgard Range (Transantarctic Mountains). , 2000, International journal of systematic and evolutionary microbiology.

[43]  P. Normand,et al.  Molecular phylogeny of the genus Frankia and related genera and emendation of the family Frankiaceae. , 1996, International journal of systematic bacteriology.