Lineage specific recombination rates and microevolution in Listeria monocytogenes

Table 1 Descriptive analysis of nucleotide sequence data

All Isolates (n = 195)	Length of sequenced region (in bp)	No. of Poly-morphisms	No. of Mutations	No. of Alleles	GC content	π/site^b	k^c	Tajima's D^d	Syn.^e	Nonsyn.^e	dN/dS ^f
actA	561	138	156	46	38.40	0.0593	33.26	0.78	59	70	0.32
gap	569	16	16	18	40.00	0.0044	2.50	-0.22	13	3	0.02
inlA	771	105	109	50	40.90	0.0264	18.90	0.04	64	44	0.10
prs	633	57	58	21	40.90	0.0209	13.25	1.01	58	0	n/a
purM	714	161	185	49	42.00	0.0669	47.74	1.61	133	26	0.05
ribC	639	121	131	34	39.60	0.0632	40.41	2.51	117	14	0.02
sigB	666	75	82	22	38.70	0.0251	16.63	0.57	76	3	0.02
Lineage I (n = 87)
actA	561	15	15	15	38.90	0.0058	3.24	0.25	6	9	1.06
gap	569	2	2	3	40.10	0.0009	0.54	0.55	2	0	n/a
inlA	771	17	17	12	41.00	0.0043	3.07	-0.26	6	11	0.32
prs	633	8	8	5	40.70	0.0018	1.14	-0.70	8	0	n/a
purM	714	10	10	13	42.40	0.0034	2.41	0.56	7	3	0.02
ribC	639	18	18	8	39.00	0.0061	3.91	0.27	15	3	0.06
sigB	666	9	9	8	38.60	0.0035	2.30	0.73	9	0	n/a
Lineage II (n = 93)
actA	561	19	20	17	37.90	0.0064	3.58	-0.25	11	9	0.42
gap	569	11	11	12	39.80	0.0050	2.85	0.85	8	3	0.04
inlA	771	54	54	25	41.30	0.0227	17.72	2.04	34	20	0.12
prs	633	18	18	4	41.10	0.0017	1.05	-2.02	18	0	n/a
purM	714	128	140	22	41.60	0.0603	43.05	1.91	108	26	0.08
ribC	639	86	88	16	40.20	0.0417	26.66	1.80	80	8	0.02
sigB	666	27	27	4	38.60	0.0035	2.35	-1.69	26	1	0.01

^a The total of 195 includes 15 lineage III isolates, which were not analyzed separately.
^b Average pairwise nucleotide difference per site.
^c Average pairwise nucleotide differences per sequence.
^d Tajima's D values significantly different from 0 (indicating deviation from standard neutral model) are marked in bold type.
^e Syn., number of synonymous mutations; Nonsyn., number of nonsynonymous mutations.
^f The dN/dS ratio was determined only when some nonsynonymous mutations were observed.

ISSN: 2730-7182