Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus)

BMC Microbiology

Table 3 Summary of nucleotide sequence variation between the MC/Mars Bar koala C. pecorum type strain and non-koala C. pecorum strains in sampled regions of the C. pecorum genome

Group and locus	N	Size (bp)	AlleleNo.	Δnt	%nt	π	Δrep	%rep	Δnon-rep	%non-rep	dN/dS	D	Pars	D.I.
Housekeeping Genes
16S rRNA	2	1549	2	2	0.130	0.001	N/A	N/A	N/A	N/A	N/A	N/A	0	N/A
16S/23S intergenic spacer	2	225	1	0	0.000	0	N/A	N/A	N/A	N/A	N/A	N/A	0	N/A
Membrane Proteins
ompA	20	1170	13	122	10.430	0.162	72	59.020	21	17.210	0.170	1.734	111	0.910
omcB	2	1675	2	8	0.420	0.004	7	87.500	1	12.500	2.150	N/A	0	N/A
pmpD	2	4145	2	20	0.480	0.005	13	65.000	5	25.000	0.670	N/A	0	N/A
incA	20	984	17	116	11.790	0.656	78	67.240	19	16.380	1.540	0.703	59	0.980
copN	20	1191	9	9	0.760	0.008	9	55.560	5	44.440	0.550	1.163	7	0.880
Potential Virulence Genes
tarP	2	2604	2	56	2.150	0.029	37	66.070	19	33.903	0.660	N/A	0	N/A
MACPF	2	2346	2	7	0.300	0.003	5	71.430	2	28.570	0.730	N/A	0	N/A
ORF663	20	552	18	66	11.960	0.741	29	43.940	23	34.850	1.350	0.381	48	0.980

N: no. of C. pecorum sequences analysed; Allele no.: no. of unique sequences according to gene; Δnt: number of polymorphic nucleotide sites; %nt: percent nucleotide sites polymorphic; π: average p-distance at all sites; Δrep: number of polymorphic sites resulting in an amino acid replacement; %rep: percent sites with replacement; Δnon-rep: number of polymorphic sites not resulting in an amino acid replacement (synonymous changes); %non-rep: percent sites with non-replacement; dN/dS: ratio of the number of non-synonymous (dN) to synonymous (dS) substitutions per site; D: Tajima's test for neutrality; Pars: parsimony-informative sites; D.I.: discrimination index; D: Tajima's test for neutrality.

ISSN: 1471-2180