Intraspecific sequence variation and differential expression in starch synthase genes of Arabidopsis thaliana

Table 2 Sequence comparison of starch synthases from 30 accessions of A. thaliana

	Domain	Sites	S	η	Nonsyn	Indels	h	Hd	π	GC content
*AtSSI*	gene	3946	126	128	9	26	21	0.966	0.0112	0.396
	exons	1959	30	30	9	-	8	0.584	0.0047	0.467
	introns	1987	96	98	-	26	21	0.966	0.0180	0.321
	promoter	1422	68	71	-	24	22	0.972	0.0151	0.309
	cTP	147	2	2	0	-	2	0.405	0.0055	0.515
	GT5	780	8	8	4	-	4	0.499	0.0024	0.470
	GT1	510	13	13	2	-	3	0.421	0.0097	0.474
*AtSSII*	gene	3226	31	31	13	3	12	0.841	0.0014	0.423
	exons	2379	19	19	13	-	10	0.782	0.0012	0.451
	introns	847	12	12	-	3	7	0.611	0.0019	0.341
	promoter	855	26	26	-	13	14	0.913	0.0063	0.304
	cTP	165	4	4	3	-	3	0.131	0.0016	0.491
	GT5	732	8	8	4	-	8	0.749	0.0025	0.444
	GT1	495	0	0	0	-	1	0.000	0.0000	0.467
*AtSSIII*	gene	4358	105	106	34	11	17	0.929	0.0056	0.403
	exons	3099	63	64	34	1	14	0.899	0.0047	0.422
	introns	1259	42	42	-	10	10	0.811	0.0078	0.357
	promoter	937	8	8	-	4	7	0.676	0.0016	0.356
	cTP	60	0	0	0	-	1	0.000	0.0000	0.517
	GT5	597	15	15	6	-	6	0.680	0.0057	0.406
	GT1	528	11	11	2	-	3	0.297	0.0047	0.444
*AtSSIV*	gene	4874	72	73	17	15	23	0.977	0.0028	0.379
	exons	3123	31	31	17	-	15	0.839	0.0018	0.413
	introns	1751	41	42	-	15	18	0.952	0.0047	0.316
	promoter	547	30	30	-	8	12	0.834	0.0125	0.366
	cTP	126	2	2	2	-	3	0.393	0.0033	0.443
	GT5	726	3	3	2	-	4	0.251	0.0004	0.429
	GT1	525	2	2	1	-	3	0.246	0.0005	0.411
*AtGBSS*	gene	2989	53	53	12	10	17	0.945	0.0045	0.403
	exons	1833	28	28	12	-	14	0.857	0.0042	0.452
	introns	1156	25	25	-	10	16	0.903	0.0050	0.319
	promoter	906	37	38	-	11	15	0.894	0.0078	0.356
	cTP	237	15	15	9	-	5	0.499	0.0223	0.406
	GT5	786	7	7	3	-	8	0.630	0.0017	0.442
	GT1	411	4	4	0	-	5	0.575	0.0019	0.486

Promoter = either the complete intergenic region or about 1 kb upstream the coding region; cTP = chloroplast transit peptide; GT5 domain = starch synthase catalytic domain; GT1 domain = glucosyl transferase group 1; S = polymorphic sites; η = total number of mutations; nonsyn = nonsynonymous sites; indels = number of insertions/deletions; h = number of haplotypes (=alleles); Hd = haplotype diversity; π = nucleotide diversity.