Phylogenomic analysis of natural selection pressure in Streptococcus genomes

Table 2 Expanded analyses of ten genes detected to be under positive selection in a genome scan

					P-value of LRT
Gene	Species	N₁	N₂	L_nt	M1a vs M2a	M7 vs M8	p₁in M8	ω in M8
Cell envelope proteinase (prtS);	S. pyogenes	5	28	4947	0.0000	0.0000	0.010	15.0
Lactocepin Dipeptidase (pepD)	S. pyogenes	8	20	1416	0.0002	0.0000	0.016	8.0
	S. agalactiae
	S. mutans
Ftsk/SpoIII family protein^a	S. pyogenes	4	10	756	0.0000	0.0000	0.049	∞
Hypothetical protein	S. pyogenes	4	10	1098	0.0000	0.0000	0.017	27.5
IS1191 transposase (truncated)	S. thermophilus	4	6	372	0.0020	0.0020	0.087	25.0
Hypothetical protein^b	S. pyogenes	3	13	1092	0.0491	0.0004	0.033	12.4
Hypothetical protein^c	S. pyogenes	4	7	402	0.0214	0.0214	0.026	31.2
grab	S. pyogenes	3	11	735	0.0035	0.0034	0.062	15.5
rplS^d	all	11	30	345	0.1254	0.0080	0.010	6.7
Hypothetical protein^e	S. pyogenes	4	13	1023	0.0679	0.0442	0.18	2.6
Homologue of mac/sib38

Notes: N₁ indicates the number of gene sequences in the original gene cluster. N₂ indicates the number of sequences in the expanded dataset. L_nt is the length of the gene sequence in nucleotides. p₁ indicates the proportion of codon sites estimate to be subject to positive selection under model M8.
ω is the parameter in the codon model M8 for the nonsyonymous to synonymous rate ratio (d_N/d_S).
Additional remarks:
^a Best non-GAS blastp hit: gb|AAK79835.1|AE007695_8 (AE007695) FtsK-like DNA segregation ATPase, YDCQ B. subtilis orthologue [Clostridium acetobutylicum];
^b Fibronectin-binding protein (probable antigen);
^c Best non-GAS blastp hit: gb|AAB97959.1| (U96166) ATP-binding cassette lipoprotein [S. cristatus];
^d May play a role in the structure and function of the aminoacyl-tRNA binding site;
^e Novel immunoglobulin binding protein; best blastp hit: sp|P11215|ITAM_human cell surface glycoprotein MAC-1 α subunit precursor (CR-3 α chain) (CD11B) (leukocyte adhesion receptor MO1) (integrin α-M) (neutrophil adherence receptor).

ISSN: 2730-7182