Genome-wide signals of positive selection in strongylocentrotid sea urchins

BMC Genomics

Table 5 Summary of the top 15 ranked positively selected genes (PSGs)

Rank	SPU gene	Name	Protein	Location^a	No of codons	dN	dS	dN/dS	LRT Score^b	No. of positively selected codons^c
1	SPU_003768	Sp-3Apcol	Type IV collagen	ECM	1183	0.159	0.345	0.459	233.04	77
2	SPU_010829	Sp-Ef2	Elongation factor 2	RIB	800	0.153	0.473	0.322	102.62	20
3	SPU_008159	Sp-Kcnk13	Potassium channel	MEM	405	0.079	0.209	0.378	91.68	11
4	SPU_018532	Sp-EgfibL	Fibropellin 1b–like	ECM	439	0.268	0.307	0.873	79.67	38
5	SPU_006534	Sp-Ebr1_5	Egg bindin receptor 1–5	MEM	691	0.174	0.368	0.473	66.79	12
6	SPU_008462	Sp-Hypp_548	Usherin-like	ECM	684	0.212	0.298	0.710	61.85	21
7	SPU_006645	Sp-Gdi1_1	GDP dissociation inhibitor 1	CYT	184	0.254	0.278	0.914	61.38	12
8	SPU_000526	Sp-Ebr1	Egg bindin receptor 1	MEM	1428	0.185	0.518	0.357	59.84	9
9	SPU_009154	Sp-Hypp_42	Unknown protein	UNK	1017	0.217	0.346	0.629	58.28	19
10	SPU_003671	Sp-Lrp12	Low density lipoprotein	ECF	761	0.143	0.453	0.315	55.58	13
11	SPU_018517	Sp-Hypp_915	Fibrosurfin-like	ECM	424	0.282	0.346	0.814	54.02	15
12	SPU_002551	Sp-Egfiii	Fibropellin c	ECM	357	0.194	0.415	0.468	53.88	6
13	SPU_016836	Sp-EMI/Egf	MEGF10-like	MEM	1709	0.110	0.271	0.408	53.41	7
14	SPU_005187	Sp-3Acolf	Type IV collagen	ECM	384	0.116	0.289	0.400	51.59	5
15	SPU_003825	Sp-14-3-3e	14–3-3 epsilon	CYT	152	0.090	0.255	0.354	51.20	4

^aCellular location of protein. ECM extracellular matrix, ECF extracellular fluid, MEM membrane or intrinsic to membrane, CYT cytosolic, RIB ribosome, UNK unknown
^bMean Likelihood Ratio Test Score comparing PAML models M7 and M8
^cNumber of codons with Bayes Emperical Bayes posterior probabilities >0.95

ISSN: 1471-2164