Genomic analysis of Leptospira interrogans serovar Paidjan and Dadas isolates from carrier dogs and comparative genomic analysis to detect genes under positive selection

Table 2 Statistical summary of 18 virulence-associated genes under positive selection in 13 representative L. interorgan strains

Gene	COG categories^a	Gene annotation	ω^b	2Δℓ^c	q-value
Adhesion
kdsD	M	Arabinose 5-phosphate isomerase	15.32026	10.347320	0.011652800
ompA	M	Outer membrane protein A	17.12571	20.820944	0.000130800
yiaD	M	Outer membrane protein A	18.64214	23.296514	0.000046900
rfaF	M	Glycosyl transferase, family 9	20.83838	13.943466	0.002602300
la_2410	M	Glycerol-3-phosphate cytidylyltransferase	20.63787	11.376946	0.007541200
sunS	M	Glycosyl transferase, family 2	77.84603	23.733642	0.000039100
patA	M	Membrane bound O-acyltransferase (MBOAT) family protein	33.76757	34.295972	0.000000426
Anti-phagocytosis
rmd	M	NAD-dependent epimerase dehydratase	15.67082	13.845838	0.002710400
capB	M	Capsule biosynthesis protein	10.13343	16.584998	0.000831400
capA	M	Capsule biosynthesis protein	26.72717	7.6514580	0.037726700
Iron uptake system
fecA	M	TonB-dependent receptor plug domain	14.34022	31.619632	0.000001330
hbpA	P	TonB-dependent receptor	8.341820	10.766942	0.009678900
modF	P	ABC transporter	10.62873	8.1123800	0.030958000
LPS biosynthesis
lpxD1	M	UDP-3-O-(3-hydroxymyristoryl) glucosamine N-acyltransferase	65.82909	9.594336	0.016131033
Exotoxin
tlyA^d	J	Hemolysin A	61.51328	30.989188	0.000001670
Motility
fliN2	N	Flagella motor switch protein	31.01218	35.57534	0.000000249
flgK	N	Flagella hook-associated protein	16.72326	15.544766	0.001312461
flhB	N	Polar flagella protein	999.0000^e	22.055182	0.000076800

^aThe abbreviations for COG categories are defined as: M (Cell wall/membrane/envelope biogenesis), P (Inorganic ion transport and metabolism), J (Translation, ribosomal structure and biogenesis) and N (Cell motility)
^bω is the ratio of dN/dS under positive selection (model M2a)
^C2Δℓ is likelihood ratio test (LRT) statistic
^dtlyA is not found in VFDB database but this gene has been shown to be a virulence factor in pathogenic Leptospira [24]
^eAll substitutions of flhB are non-synonymous and dS = 0; therefore the ω value is undefined and represented as 999 in the table. According to CODEML developer, LRT is not affected by dS in this analysis as shown by a significant q-value result

ISSN: 1471-2164