Genome-wide evidence for positive selection and recombination in Actinobacillus pleuropneumoniae

Xu, Zhuofei; Chen, Huanchun; Zhou, Rui

doi:10.1186/1471-2148-11-203

BMC Ecology and Evolution

Table 3 Genes that show evidence for positive Darwinian selection

From: Genome-wide evidence for positive selection and recombination in Actinobacillus pleuropneumoniae

Name (Systematic)	Cluster ID ^a	COG ^b	Putative function of coding products	2Δℓ^c	Q-value	p ^d	ω ^e	Positively selected sites ^f
napA	APO_0068	C	Periplasmic nitrate reductase	10.03	0.189	0.000	1.02
glpA	APO_0197	C	Anaerobic glycerol-3-phosphate dehydrogenase subunit A	12.26	0.096	0.009	11.45
fumC	APO_0306	C	Fumarate hydratase	15.63	0.032	0.004	99.56
prlC	APO_0109	E	Oligopeptidase A	14.72	0.042	0.000	607.84
argH	APO_0322	E	Argininosuccinate lyase	13.10	0.071	0.014	10.79	423
gntT	APO_0415	E	Transporter, gluconate/H+ symporter (GntP) family	11.74	0.106	0.008	13.97	190, 193
proA	APO_0424	E	Gamma-glutamyl phosphate reductase	10.02	0.189	0.051	3.29
artP	APO_0998	E	Arginine transport ATP-binding protein	14.75	0.042	0.004	521.75	225
leuD	APO_1132	E	3-isopropylmalate dehydratase small subunit	11.14	0.135	0.032	57.70
cpdB	APO_0120	F	2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase	19.13	0.010	0.032	3.82	9, 99, 554
purD	APO_0394	F	Phosphoribosylamine--glycine ligase	13.44	0.062	0.061	34.74
glgP	APO_00f74	G	Maltodextrin phosphorylase	14.13	0.054	0.019	9.66	13, 27, 392
kdgK	APO_0752	G	2-dehydro-3-deoxygluconokinase	9.98	0.190	0.042	8.28
hemN	APO_0325	H	Oxygen-independent coproporphyrinogen-III oxidase	21.87	0.005	0.015	27.37	38, 136, 428
lipB	APO_1067	H	Octanoyltransferase	10.14	0.189	0.000	1.00
valS	APO_0044	J	Valyl-tRNA synthetase	22.18	0.005	0.016	3.82	47, 792
rumA	APO_0356	J	23S rRNA (uracil-5-)-methyltransferase	26.17	0.002	0.003	47.26	20
trmA2	APO_0540	J	tRNA (uracil-5-)-methyltransferase	10.70	0.160	0.028	4.08	24, 210
yhgF	APO_0081	K	Transcriptional accessory protein	18.60	0.010	0.024	3.78	10, 142
lysR	APO_0797	K	Transcriptional regulatory protein	18.79	0.010	0.012	10.60	284, 287, 292
parC	APO_0090	L	DNA topoisomerase 4 subunit A	13.47	0.062	0.003	10.50	357
mutM	APO_0873	L	Heptosyltransferase family	12.15	0.096	0.077	14.90	270
tatD	APO_0977	L	Deoxyribonuclease	13.73	0.059	0.198	2.42	188, 204, 234
hcsA	APO_0102	M	Capsule polysaccharide modification protein	10.07	0.189	0.027	3.16	483
hcsB	APO_0367	M	Capsule polysaccharide modification protein	18.72	0.010	0.034	18.52	13, 136, 366
ompP2B	APO_0561	M	Outer membrane protein P2-like protein	16.15	0.026	0.095	8.07	306, 317, 320
mscL	APO_1465	M	Large-conductance mechanosensitive channel	12.17	0.096	0.044	103.40	97
ptrA	APO_0039	O	Protease III	17.69	0.013	0.049	6.26	43, 44, 50, 91, 617, 909
glnD	APO_0064	O	uridylyltransferase	17.93	0.013	0.024	12.23	17, 190, 514, 551
sppA	APO_0149	O	Protease 4	10.42	0.173	0.030	9.37
lonH	APO_0207	O	Lon protease	15.24	0.035	0.013	106.47	19
nrfG	APO_0983	O	Formate-dependent nitrite reductase complex subunit	12.29	0.096	0.084	27.77
tehA	APO_0711	P	Tellurite resistance protein	11.70	0.106	0.007	70.81	252
cysW	APO_0883	P	Sulfate transport system permease protein	13.80	0.059	0.074	3.68	145
-	APO_0030	R	Helicase	12.14	0.096	0.051	2.56
pqiB	APO_0055	R	Paraquat-inducible protein B	20.31	0.008	0.046	3.62	259, 318, 384
tldD	APO_0268	R	Protease	10.16	0.189	0.009	15.91	377, 379
-	APO_0269	R	Hypothetical protein	10.02	0.189	0.000	1.00	463
pcaK	APO_0359	R	Major facilitator transporter	12.09	0.096	0.022	5.96	195, 238, 416, 417
thiH	APO_0509	R	Thiazole biosynthesis protein	18.32	0.011	0.012	12.98	15, 55
murQ	APO_0754	R	N-acetylmuramic acid 6-phosphate etherase	17.69	0.013	0.059	4.05	54, 99, 293
-	APO_0792	R	Nucleoside-diphosphate sugar epimerase	11.92	0.102	0.060	9.71
rssA	APO_0839	R	Patatin	11.22	0.132	0.019	41.55	225
cof	APO_0888	R	Hydrolases of the HAD superfamily	10.62	0.160	0.000	25.15
smtA	APO_0969	R	Methyltransferase	10.66	0.160	0.045	101.87	134, 204
aphA	APO_1107	R	Membrane protein affecting hemolysin expression	10.83	0.153	0.012	24.96	46
recX	APO_1397	R	Regulatory protein	19.96	0.008	0.008	37.09	47
ytfN	APO_0025	S	Hypothetical protein	14.07	0.054	0.002	239.60	553
-	APO_0098	S	Oligopeptide transporter	20.79	0.007	0.012	15.91	82, 127, 546
glnE	APO_0041	T	Glutamate-ammonia-ligase adenylyltransferase	11.88	0.102	0.023	3.60	53
typA	APO_0150	T	GTP-binding protein	33.59	0.000	0.006	15.43	395, 567, 569
apaA	APO_0772	T	ABC transporter, periplasmic binding protein	13.49	0.062	0.031	7.10	103, 147
-	APO_0051	-	Hypothetical protein	19.00	0.010	0.088	5.16	105
guaB	APO_0259	-	Inosine-5'-monophosphate dehydrogenase	15.25	0.035	0.013	4.98	448
-	APO_0393	-	Hypothetical protein	24.92	0.002	0.027	57.62	97, 104, 134, 355
-	APO_0571	-	Hypothetical protein	12.27	0.096	0.020	28.21	199, 275, 283
wecF	APO_0577	-	TDP-Fuc4NAc:lipid II Fuc4NAc transferase	22.68	0.005	0.035	14.23	70, 92, 182, 183, 289

^a Protein designations were taken from the A. pleuropneumoniae ortholog annotation that was summarized in our recent publication [19].
^b The abbreviations of COG function categories were assigned based on Figure 1.
^c 2Δℓ denote the statistic of likelihood ratio test.
^d The proportion of the amino acid sites under positive selection.
^e ω is equal to the ratio of d_N to d_S (Number of nonsynonymous changes per nonsynonymous sites/Number of synonymous changes per synonymous site) for amino acid sites under positive selection (model M2a).
^f Positively selected sites identified with posterior probability P > 95%.

Back to article page

ISSN: 2730-7182

Contact us

General enquiries: journalsubmissions@springernature.com