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AnalyzedGenomes.md

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Genomes for which MGE analyses results are included with this program

Strain Class Size (bp) NCBI Accession Number Reference
Acidobacterium capsulatum ATCC 51196 Acidobacteria 4,127,356 NC_012483 Ward et al., 2009
Aquifex aeolicus VF5 Aquificae 1,551,335 NC_000918 Deckert et al., 1998
Bacillus mycoides ATCC 6462 Bacilli 5,255,868 NZ_CP009692 Johnson et al., 2015
Bordetella pertussis 137 Betaproteobacteria 4,134,593 NZ_CP010323 Akamatsu et al., 2015
Chloroflexus aurantiacus J-10-fl Chloroflexia 5,258,541 NC_010175 Tang et al., 2011
Clostridium beijerinckii NCIMB 8052 Clostridia 6,000,632 NC_009617 Wang et al., 2012
Deinococcus radiodurans R1 Deinococci 3,060,986 NC_001263, NC_001264 White et al., 1999
Escherichia coli O26:H11 11368 Gammaproteobacteria 5,697,240 NC_013361 Ogura et al., 2009
Flavobacterium johnsoniae UW101 Flavobacteriia 6,096,872 NC_009441 McBride et al., 2009
Microcystis aeruginosa NIES-843 Cyanobacteria 5,842,795 NC_010296 Kaneko et al., 2007
Mycobacterium intracellulare ATCC 13950 Actinobacteria 5,402,402 NC_016946 Kim et al., 2012
Nostoc punctiforme PCC 73102 Cyanobacteria 8,234,322 NC_010628 Ekman et al., 2013
Pirellula staleyi DSM 6068 Planctomycetia 6,196,199 NC_013720 Clum et al., 2009
Rhizobium leguminosarum 3841 Alphaproteobacteria 5,057,142 NC_008380 Young et al., 2006
Shigella flexneri 2002017 Gammaproteobacteria 4,650,856 NC_017328 Ye et al., 2010
Simkania negevensis Z Chlamydiae 2,496,337 NC_015713 Collingro et al., 2011
Spirochaeta smaragdinae DSM 11293 Spirochaetes 4,653,970 NC_014364 Mavromatis et al., 2010
Staphylococcus xylosus HKUOPL8 Bacilli 2,836,901 NZ_CP007208 Ma et al., 2014
Streptococcus pneumoniae NT_110_58 Bacilli 2,287,774 NZ_CP007593 Hilty et al., 2014
Sulfolobus solfataricus SULA Thermoprotei 2,727,337 NZ_CP011057 McCarthy et al., 2015
Xyllela fastidiosa 9a5c Gammaproteobacteria 2,679,306 NC_002488 Simpson et al., 2000

References

Akamatsu MA, Nishiyama Jr MY, Morone M (2015) Whole-genome sequence of a Bordetella pertussis Brazilian vaccine strain. Genome Announc 3:e01570-14

Clum A, Tindall BJ, Sikorski J et al (2009) Complete genome sequence of Pirellula staleyi type strain (ATCC 27377). Stand Genomic Sci 1:308-316

Collingro A, Tischler P, Weinmaier T et al (2011) Unity in variety – the pan-genome of the Chlamydiae. Mol Biol Evol 28:3253-3270

Deckert G, Warren PV, Gaasterland T et al (1998) The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 392:353-358

Ekman M, Picossi S, Campbell EL et al (2013) A Nostoc punctiforme sugar transporter necessary to establish a cyanobacterium-plant symbiosis. Plant Physiol 161:1984-1992

Hilty M, Wüthrich D, Salter SJ et al (2014) Global phylogenomic analysis of nonencapsulated Streptococus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages. Genome Biol Evol 6:3281-3294

Johnson SL, Daligault HE, Davenport KW et al (2015) Complete genome sequences for 35 biothreat assay-relevant species. Genome Announc 3:e00151-15

Kaneko T, Nakajima N, Okamoto S et al (2007) Complete genomic structure of the bloom-forming toxic cyanobacterium Microcystis aeruginosa NIES-843. DNA Res 14:247-256

Kim BJ, Choi BS, Lim JS et al (2012) Complete genome sequence of Mycobacterium intracellulare strain ATCC 13950. J Bacteriol 194:2750

Ma APY, Jiang J, Tun HM et al (2014) Complete genome sequence of Staphylococcus xylosus HKUOPL8, a potential oportunistic pathogen of mammals. Genome Announc 2:e00653-14

Mavromatis K, Yasawong M, Chertkov O et al (2010) Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228). Stand Genomic Sci 3:136-144

McBride MJ, Xie G, Martens EC et al (2009) Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Appl Environ Microbiol 75:6864-6875

McCarthy S, Gradnigo J, Johnson T et al (2015) Complete genome sequence of Sulfolobus solfataricus strain 98/2 and evolved derivatives. Genome Announc 3:e00549-15

Ogura Y, Ooka T, Iguchi A et al (2009) Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli. Proc Natl Acad Sci USA 106:17939-17944

Simpson AJG, Reinach FC, Arruda P et al (2000) The genome sequence of the plant pathogen Xyllela fastidiosa. Nature 406:151-159

Tang KH, Barry B, Chertkov O et al (2011) Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus. BMC Genomics 12:334

Wang Y, Li X, Mao Y et al (2012) Genome-wide dynamic transcriptional profiling in Clostridium beijerinckii NCIMB 8052 using single-nucleotide resolution. BMC Genomics 13:102

Ward NL, Challacombe JF, Janssen PH et al (2009) Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl Environ Microbiol 75:2046-2056

White O, Elsen JA, Heidelberg JF et al (1999) Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 286:1571-1577

Ye C, Lan R, Xia S et al (2010) Emergence of a new multidrug-resistant serotype X variant in an epidemic clone of Shigella flexneri. J Clin Microbiol 48:419-426

Young JP, Crossman LC, Johnston AW et al (2006) The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol 7:R34


License

The AnalyzedGenomes dataset is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/.