Markup | Genome Research

Table 2.

Percent G + C Mean and Standard Deviations Determined from All Predicted Protein Coding Regions for Complete Genomes of Pathogenic Bacteria (as of April 2001)

Organism	Approximate host range— “Primary” disease	Intracellular?	Notes regarding clonality and evidence of horizontally transferred regions	No. of protein-coding ORFs	G + C for ORFs > 300 bp[i]
Organism	Approximate host range— “Primary” disease	Intracellular?		No. of protein-coding ORFs	Mean	S.D.
Neisseria meningitidis MC58	humans—meningitis	extracellular	Nonclonal, demonstrated horizontal transfer with other species	2025	52.4	6.9
Neisseria meningitidis Z2491	humans—meningitis	extracellular	Nonclonal, demonstrated horizontal transfer with other species	2121	52.6	6.5
Xylella fastidiosa 9a5c	plants—citrus variegated chlorosis	extracellular	Evidence of phage-mediated horizontal gene transfer	2766	53.4	5.4
Escherichia coli O157:H7	warm-blooded animals, including humans—diarrhea	facultative intracellular	Compared with E coli K12, has higher % G + C S.D. and more predicted horizontally transferred regions	5283	51.0	5.3
Mycoplasma pneumoniae M129	humans— mycoplasmal pneumonia	extracellular		677	40.3	4.9
Vibrio cholerae N16961 chrom. 2 (of 2)	humans, zooplankton, other aquatic life—cholera	extracellular	More genes than chr. 1 that appear to have origins outside alpha-proteobacteria to which Vibrio belongs; proposed megaplasmid origin	1092	46.9	4.3
Treponema pallidum Nichols	humans—syphillis	extracellular		1031	51.4	4.2
Pseudomonas aeruginosa PAO1	humans, a range of other animals— variety of opportunistic mucosal infections	extracellular		5565	67.0	3.8
Ureaplasma urealyticum serovar3	humans—urethritis	extracellular		611	29.3	3.8
Vibrio cholerae N16961 chr. 1 (of 2)	humans, zooplankton, other aquatic life— cholera	extracellular		2736	48.1	3.7
Borrelia burgdorferi B31	humans, rodents, tick vector—Lyme disease	facultative intracellular		850	28.7	3.6
Campylobacter jejuni NCTC11168	humans, fowl, cattle, sheep, dogs, cats—gastroenteritis	extracellular	Noted for lack of insertion sequences or phage-associated sequences	1634	30.6	3.5
Mycoplasma genitalium G37	humans—urethritis (opportunistic)	extracellular		480	31.4	3.5
Pasteurella multocida PM70	range of animals—fowl cholera, cattle septicemia, pig rhinitis	extracellular		2014	40.8	3.3
Helicobacter pylori 266695	humans—peptic ulcers and gastritis	extracellular	Conserved relative to the other H. pylori genome	1553	39.4	3.4
Haemophilus influenzae Rd-KW20	humans—upper respiratory infection and meningitis	extracellular	Evidence of horizontal transfer betweenNeisseria and Haemophilus, but not in this genome sequence	1709	38.5	3.4
Helicobacter pylori J99	humans—peptic ulcers and gastritis	extracellular	Conserved relative to the other H. pylori genome	1491	39.3	3.3
Mycobacterium tuberculosis CSU93	humans—tuberculosis	facultative intracellular		3918	65.6	3.3
Rickettsia prowazekii MadridE	humans, other animals, lice vector—epidemic typhus	obligate intracellular	Highly clonal	834	30.1	3.3
Chlamydophila pneumoniae AR39	humans—chlamydial pneumonia	obligate intracellular	Highly clonal	997	41.1	2.6
Chlamydophila pneumoniae CWL029	humans—chlamydial pneumonia	obligate intracellular	Highly clonal	1052	41.1	2.6
Chlamydophila pneumoniae J138	humans—chlamydia pneumonia	obligate intracellular	Highly clonal	1070	41.1	2.6
Chlamydia trachomatis D	humans—chlamydia	obligate intracellular	Highly clonal	894	41.5	2.3
Chlamydia muridarum MoPn	humans—chlamydia	obligate intracellular	Highly clonal	818	40.8	2.3

[i] The calculation appears to be more accurate when ORFs < 300 bp are omitted from the analysis, as evident from a comparison of two highly similar Chlamydia pneumoniae genomes that suggests there are increased errors in gene prediction for genes > 300 bp in length.

[ii] This table is sorted by percent G + C standard deviation (S.D.) for predicted coding regions (ORFs) > 300 bp. Although the sample size is small, this standard deviation appears to correlate with the clonality of the microbe (two-tailed P-value > 0.005 for a nonparametric/Spearman correlation when condition is ranked). A similar analysis that is continually updated and includes nonpathogens, including archaea, is available athttp://www.pathogenomics.bc.ca/IslandPath.html.