Divergence in cis-regulatory sequences surrounding the opsin gene arrays of African cichlid fishes

Table 3 Comparison of sequence similarity and TFBS/miRNA target site divergence for putative cis-regulatory regions surrounding the opsin arrays of O. niloticus and M. zebra

Region		Identity	D_xy¹	Length	Length	TFBS	TFBS	Est.	p-value³
		(%)	(%)	On(bp)	Mz(bp)	Divt.	Shrd	P_div² (%)
CNE⁴	1	96.84	3.23	158	158	0	2	0.0	1.000
	2	96.22	3.88	240	239	2	6	25.0	0.130
	3	94.74	4.53	349	359	7	1	87.5	< 0.001*
	4	98.31	1.70	240	241	2	0	100.0	0.006
	5	96.14	3.97	207	207	1	0	100.0	0.080
	6	-	-	300	-	-	-	-	-
	7	97.16	2.89	882	885	1	8	11.1	0.528
	8	88.46	4.86	779	799	3	9	25.0	0.065
	9	93.93	6.33	313	313	1	3	25.0	0.283
	10	97.64	2.40	127	127	0	0	-	-
	11	95.97	4.14	124	124	1	1	50.0	0.154
	12	95.53	4.61	246	249	1	3	25.0	0.284
	13	97.66	2.37	214	214	1	9	10.0	0.566
	14	88.97	4.71	999	1404	1	9	10.0	0.566
	15	95.32	4.84	428	428	3	6	33.3	0.030
	16	91.21	9.35	182	191	0	2	0.0	1.000
	17	96.14	3.96	311	313	2	3	40.0	0.054
	18	93.25	7.07	1087	976	5	13	27.8	0.012
	19	-	-	69	-	-	-	-	-
	20	98.88	1.13	358	38	1	13	7.1	1.000
Proximal Promoter⁵	LWS	97.56	2.48	1000	1000	1	16	5.9	1.000
	RH2Aα	94.80	5.38	1000	1000	10	11	47.6	< 0.001*
	RH2Aβ	91.77	8.60	1000	1000	14	19	42.4	< 0.001*
	RH2B	61.35	9.40	1000	1000	15	7	68.1	< 0.001*
	SWS1	71.49	26.37	1000	1000	18	10	64.3	< 0.001*
	SWS2A	97.19	2.87	1000	1000	11	12	47.8	< 0.001*
	SWS2B	81.96	16.31	1000	1000	4	10	28.6	0.021
3'-UTR⁶	LWS	93.39	6.92	189	189	1	4	20.0	0.341
	RH2Aα	94.04	6.21	438	442	4	9	30.8	0.016
	RH2Aβ	93.26	7.06	465	460	4	11	26.7	0.027
	RH2B	93.15	7.18	310	319	4	4	50.0	0.002*
	SWS1	96.74	3.33	217	242	1	3	25.0	0.284
	SWS2A	98.37	1.64	123	123	0	1	0.0	1.000
	SWS2B	95.90	4.21	124	137	4	1	80.0	< 0.001*

¹ Pairwise sequence divergence between O. niloticus and M. zebra, corrected for multiple hits.
² Actual proportion of divergent TFBSs observed for O. niloticus and M. zebra.
³ P-values for the Exact binomial test at a null proportion divergence = 8%. Tests marked with an asterisk (*) are significant after Bonferroni correction for multiple comparisons.
⁴ See Additional file 6 for individual counts of each TFBS identified for the CNEs.
⁵ See Figure 3 for individual counts of each TFBS identified for the proximal promoters.
⁶ See Additional file 7 for individual counts of each microRNA target site identified for the 3'-UTRs.

ISSN: 2730-7182