Different rates of (non-)synonymous mutations in astrovirus genes; correlation with gene function

Table 3 Sites prone to positive selection in astrovirus genes

Bayes Empirical Bayes (BEB) Analysis
BEB positively selected sites in ORF1a
Position in Alignment	Amino acid residue	Position in H1Z25771	Posterior mean value for dN/dS	± SE for dN/dS	Posterior probability (dN/dS > 1)
3	Y	3	0.988	0.576	0.522
109	K	86	1.474	0.225	0.951
110	E	87	1.336	0.407	0.817
812	A	614	1.316	0.421	0.796
813	T	615	1.322	0.416	0.801
821	S	623	1.357	0.385	0.835
822	A	624	1.383	0.351	0.855
1060	V	755	1.436	0.290	0.911
1078	S	790	1.087	0.581	0.623
1102	P	814	1.326	0.410	0.804
1105	P	817	1.036	0.585	0.575
1263	T	932	1.157	0.503	0.646
BEB positively selected sites in ORF1b
Position in Alignment	Amino acid residue	Position in H1Z25771	Posterior mean value for dN/dS	± SE for dN/dS	Posterior probability (dN/dS > 1)
45	L	29	1.068	0.802	0.603
178	N	160	1.384	0.860	0.704
BEB positively selected sites in ORF2 (selection)
Position in Alignment	Amino acid residue	Position in H1Z25771	Posterior mean value for dN/dS	± SE for dN/dS	Posterior probability (dN/dS > 1)
489	A	440	1.231	0.418	0.660
507	D	458	1.182	0.439	0.611
533	V	472	1.123	0.457	0.551
537	L	476	1.282	0.396	0.717
604	S	513	1.122	0.499	0.582
676	G	573	1.441	0.264	0.901
686	T	583	1.094	0.478	0.537
716	K	612	1.078	0.468	0.507
745	S	633	1.182	0.430	0.603
755	S	643	1.183	0.430	0.606
764	H	652	1.172	0.438	0.599
768	S	656	1.350	0.357	0.797
774	N	658	1.269	0.411	0.710
791	T	659	1.389	0.329	0.845
793	Y	661	1.182	0.424	0.603
800	A	668	1.292	0.391	0.729
802	Q	670	1.481	0.205	0.953
803	F	671	1.333	0.366	0.775
804	D	674	1.316	0.394	0.767
814	I	681	1.090	0.470	0.528
882	I	741	1.219	0.431	0.653
919	N	775	1.187	0.442	0.621

The Bayes-Emperical-Bayes (BEB) output of the CODEML NSsites model 8 for nucleotide substitution allows the selection of codon sites (as amino acids) with a posterior mean value for dN/dS ≥ 1 and provides a standard error as well asa value for posterior probability. The position of the selected amino acid in the alignment has been converted into the location in the H1Z25771 polyprotein. "Selection" in the ORF2 panel refers to the limitation of one representative per human serotype in ORF2 analyses.

ISSN: 1743-422X