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. 2010 Jul 8;2:584–590. doi: 10.1093/gbe/evq040

Table 1.

Observed (O) and Expected (E) Quantities of Intergenic IS Elements in Fully Sequenced Bacterial Chromosomes, and the χ2 Test Statistic for Each

NGOa
→→ , ←←
 →←
 ←→
O E O E O E χ2b
Actinobacteria
    Corynebacterium efficiens YS-314 36 39.8 21 14.5 16 18.6 3.6
    Corynebacterium glutamicum ATCC 13032 21 20.5 11 7.4 7 11.1 3.3
    Corynebacterium jeikeium K411 38 38.1 18 8.5 12 21.5 14.9***
    Frankia sp. CcI3 88 79.1 27 16.6 21 40.4 16.9***c
    Mycobacterium avium paratuberculosis 29 33.8 14 7.6 14 15.6 6.3*
    Mycobacterium bovis AF2122/97 22 22.7 15 6.6 6 13.7 15.1***
    Mycobacterium smegmatis MC2 33 37.9 24 7.1 11 23.0 47.3***c
    Mycobacterium tuberculosis CDC1551 29 26.6 13 6.7 6 14.7 11.3**
    M. tuberculosis H37Rv 31 27.9 16 8.1 6 17.0 15.2***
    Streptomyces avermitilis MA-4680 36 38.1 25 11.6 8 19.3 22.3***c
    Streptomyces coelicolor A3(2) 19 20.6 9 6.1 11 12.3 1.7
Bacteriodetes
    Bacteroides thetaiotaomicron VPI-5482 22 30.9 24 7.2 6 13.8 45.7***c
    Porphyromonas gingivalis W83 21 27.3 10 8.7 13 8.0 4.7
    Prevotella intermedia 17 26 27.1 14 10.1 9 11.8 2.3
    Salinibacter ruber DSM 13855 24 23.8 4 5.6 11 9.6 0.6
Chlamydiae
    Protochlamydia amoebophila UWE25 26 32.3 14 8.0 17 16.7 5.7
Cyanobacteria
    Anabaena variabilis ATCC 29413 35 31.5 16 8.1 7 18.4 15.0***
    Gloeobacter violaceus PCC7421 41 35.0 18 10.1 6 19.9 17.0***c
    Nostoc sp. PCC 7120 39 37.1 17 8.7 11 21.1 12.8**
    Synechococcus sp. JA-2-3Ba(2-13) 42 37.6 21 27.7 16 13.7 2.5
    Synechococcus sp. JA-3-3Ab 44 40.4 17 29.9 21 11.7 13.2***
    Synechocystis sp. PCC6803 30 30.4 17 6.9 5 14.7 21.0***c
    Thermosynechococcus elongatus BP-1 41 30.5 6 6.6 17 26.9 7.3*
Deinococcus
    Deinococcus radiodurans R1 17 18.1 10 6.0 4 7.0 4.1
Firmicutes
    Bacillus anthracis A0039 28 26.1 8 5.2 6 10.7 3.7
    B. anthracis Ames 26 23.1 6 5.1 6 9.8 2.0
    B. anthracis Ames Ancestor 26 24.3 7 5.4 7 10.3 1.7
    B. anthracis CNEVA-9066 27 24.4 7 5.1 6 10.4 2.8
    B. anthracis USA6153 27 25.3 8 5.2 6 10.5 3.6
    B. anthracis Vollum 27 24.4 7 5.2 6 10.4 2.8
    Bacillus cereus 10987 37 32.3 6 6.6 8 12.2 2.2
    B. cereus ATCC 14579 27 28.6 9 5.0 9 11.4 3.8
    B. cereus Zk 29 25.6 8 5.0 5 11.4 5.8
    Bacillus halodurans C-125 73 74.0 22 13.0 14 22.0 9.1**
    Bacillus thuringiensis konkukian 39 38.6 16 7.7 8 16.6 13.4***
    Clostridium perfringens SM101 39 39.9 9 7.7 12 12.4 0.2
    Desulfitobacterium hafniense Y51 66 60.9 6 11.3 18 17.8 2.9
    Geobacillus kaustophilus HTA426 65 51.4 10 13.7 8 17.9 10.1**
    Staphylococcus epidermidis ATCC 12228 24 34.8 30 9.1 2 12.2 60.3***c
    S. epidermidis RP62A 24 31.7 23 9.6 5 10.7 23.6***c
    Staphylococcus haemolyticus JCSC1435 36 57.0 44 10.6 5 17.4 121.4***c
    Streptococcus pneumoniae G54 39 40.2 11 8.3 8 9.6 1.2
    S. pneumoniae R6 30 39.0 15 7.2 9 7.8 10.7**
    S. pneumoniae TIGR4 37 43.7 22 11.7 6 9.7 11.6**
    Thermoanaerobacter tengcongensis MB4(T) 39 37.5 7 5.8 7 9.8 1.1
Spirochaetes
    Leptospira interrogans lai 56601 34 35.4 17 16.9 15 13.7 0.2
Unclassified proteobacteria
    Magnetococcus sp. MC-1 41 38.4 16 18.1 15 15.5 0.4
Alphaproteobacteria
    Bradyrhizobium japonicum USDA 110 58 65.3 31 21.7 28 30.0 5.0
    Caulobacter crescentus CB15 12 15.7 14 5.0 2 7.4 21.2***c
    Gluconobacter oxydans 621H 28 28.7 12 5.8 10 15.5 8.4*
    Magnetospirillum magneticum AMB-1 33 24.0 9 8.6 4 13.4 9.9**
    Mesorhizobium loti MAFF303099 31 29.9 13 7.1 11 17.9 7.6*
    Nitrobacter winogradskyi Nb-255 50 51.4 34 13.8 11 29.7 41.2***c
    Rhodopseudomonas palustris BisB18 15 23.4 19 7.7 8 10.9 20.7***c
    Rickettsia bellii RML369-C 24 24.0 6 6.5 10 9.5 0.1
    Sinorhizobium meliloti 1021 28 32.4 22 10.9 7 13.8 15.3***
    Wolbachia pipientis wMel 23 24.7 15 6.6 3 9.7 15.4***
Betaproteobacteria
    Azoarcus sp. EbN1 63 61.4 29 16.8 11 24.8 16.7***c
    Bordetella pertussis Tohama I 68 79.9 52 13.1 15 42.0 134.2***c
    Burkholderia cenocepacia AU 1054 30 40.5 23 9.3 18 21.2 23.3***c
    Burkholderia mallei ATCC 23344 46 56.6 39 20.7 15 22.7 20.8***c
    Burkholderia pseudomallei 1710b 31 33.9 22 15.4 9 12.7 4.1
    B. pseudomallei K96243 26 29.8 22 10.2 6 13.9 18.6***c
    Burkholderia thailandensis E264 40 38.8 21 13.6 9 17.6 8.2*
    Burkholderia sp. 383 20 20.0 10 5.6 7 11.4 5.2
    Neisseria meningitidis MC58 21 29.3 21 10.2 8 10.5 14.2***
    N. meningitidis Z2491 14 22.3 17 8.1 8 8.6 12.8**
    Nitrosomonas europaea ATCC 19718 37 52.6 30 9.7 19 23.7 48.4***c
    Nitrosospira multiformis ATCC 25196 32 32.1 15 7.8 7 14.0 10.1**
    Ralstonia solanacearum GMI1000 21 24.0 11 5.2 8 10.8 7.7*
Deltaproteobacteria
    Desulfovibrio desulfuricans G20 33 28.7 12 10.8 5 10.5 3.6
    Geobacter metallireducens GS-15 48 50.0 16 8.9 14 19.0 7.0*
    Myxococcus xanthus DK 1622 23 21.8 10 5.5 7 12.7 6.2*
    Pelobacter carbinolicus DSM 2380 20 26.5 12 5.5 10 10.0 9.4**
Gammaproteobacteria
    Acidithiobacillus ferrooxidans ATCC 23270 33 34.4 14 8.0 8 12.6 6.3*
    Coxiella burnetii RSA 493 17 16.9 3 5.0 10 8.1 1.2
    Escherichia coli CFT073 44 44.1 26 12.5 11 24.4 22.0***c
    E. coli K12 MG1655 33 34.1 18 8.0 9 17.9 17.0***c
    E. coli O157:H7 EDL933 24 28.6 16 5.7 6 11.7 22.3***c
    E. coli O157:H7 VT2-Sakai 38 44.1 26 9.0 8 18.9 39.0***c
    E. coli UTI89 19 23.5 17 5.6 5 11.9 27.8***c
    Francisella tularensis holarctica 60 56.5 22 11.2 16 30.3 17.2***c
    F. tularensis tularensis 28 25.6 14 5.8 5 15.6 18.9***c
    Hahella chejuensis KCTC 2396 25 22.0 5 5.4 8 10.6 1.1
    Legionella pneumophila Paris 19 22.5 12 6.4 12 14.1 5.8
    Methylococcus capsulatus Bath 16 17.2 10 5.7 6 9.1 4.3
    Nitrosococcus oceani ATCC 19707 48 52.3 17 11.5 23 24.2 3.0
    Photobacterium profundum SS9 121 109.1 38 30.3 35 54.6 10.3**
    Photorhabdus luminescens TTO1 79 71.0 28 16.7 14 33.3 19.7***c
    Pseudomonas putida KT2440 29 31.6 19 10.4 9 15.1 9.8**
    Pseudomonas syringae DC3000 61 66.7 36 18.0 24 36.2 22.5***c
    P. syringae pv B728a 16 21.2 15 6.5 8 11.3 13.6***
    P. syringae pv phaseolicola 58 57.6 28 16.7 19 30.7 12.1**
    Psychrobacter arcticum 273-4 20 28.7 16 5.9 12 13.3 19.9***c
    Salmonella enterica Choleraesuis 18 28.4 19 7.7 13 13.9 20.4***c
    Shewanella oneidensis MR-1 68 73.9 33 21.9 33 38.2 6.7*
    Shigella boydii Sb227 100 114.6 55 24.0 48 64.4 46.1***c
    Shigella dysenteriae Sd197 156 177.4 72 33.0 78 95.6 51.9***c
    Shigella flexneri 2a 301 116 113.9 51 38.3 34 48.9 8.8*
    S. flexneri 2a 2457T 60 61.1 27 11.1 20 34.8 28.9***c
    Shigella sonnei Ss046 103 100.8 37 23.1 36 52.1 13.3***
    Sodalis glossinidius morsitans 12 18.3 7 6.8 14 7.9 6.9*
    Vibrio cholerae El Tor N16961 15 12.7 6 5.0 3 6.3 2.3
    Vibrio vulnificus YJ016 24 25.2 15 6.9 6 13.0 13.4***
    Xanthomonas axonopodis pv. citri 306 28 28.2 11 8.9 8 9.9 0.9
    Xanthomonas campestris 8004 25 28.5 16 10.8 9 10.7 3.3
    X. campestris ATCC 33913 37 36.4 16 13.6 10 13.0 1.1
    X. campestris pv. armoraciae 756C 24 22.6 14 12.5 4 6.9 1.5
    X. campestris pv. vesicatoria 85-10 33 34.4 12 11.5 14 13.1 0.1
    Xanthomonas oryzae KACC10331 179 189.6 93 77.2 44 49.2 4.3
    X. oryzae pv. oryzae MAFF 311018 155 170.2 91 58.5 45 62.3 24.2***c
    X. oryzae pv. oryzicola BLS256 98 95.9 62 57.2 23 29.9 2.0
    Yersinia pestis biovar Medievalis 91001 37 38.4 29 10.3 2 19.3 49.3***c
    Y. pestis CO92 44 48.7 35 13.0 7 24.3 50.0***c
    Y. pestis KIM 57 62.7 45 19.9 11 30.3 44.4***c
    Yersinia pseudotuberculosis IP32593 17 19.4 12 5.0 5 9.6 12.3**
a

NGOs in bold contribute a significant excess of observed ISs to significant χ2 deviations, and those in gray contribute a significant deficit of observed ISs.

b

Asterisks indicate significant P values: *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001.

c

P value is significant following a sequential Bonferroni (Rice 1989).