Species-specific duplications driving the recent expansion of NBS-LRR genes in five Rosaceae species

Zhong, Yan; Yin, Huan; Sargent, Daniel James; Malnoy, Mickael; Cheng, Zong-Ming (Max)

doi:10.1186/s12864-015-1291-0

BMC Genomics

Table 4 Selective pressures of non-TNLs among five Rosaceae species

From: Species-specific duplications driving the recent expansion of NBS-LRR genes in five Rosaceae species

Family no.	Ka / Ks ^a	ω ^b	2Δln	Family no.	Ka / Ks ^a	ω ^b	2Δln
*F. vesca*				*P. bretschneideri*
0	1.01	1.37	244.51^**	12	1.13	1.14	174.51^**
2	0.51	0.51	30.00^**	13	0.67	0.64	309.43^**
3	0.72	0.78	163.67^**	17	0.69	0.72	270.23^**
4	0.52	0.52	26.42^**	19	0.61	0.71	140.67^**
5	0.35	0.39	3.41	21	0.71	0.88	173.72^**
9	0.57	0.57	64.46^**	23	0.62	0.62	69.89^**
10	0.52	0.53	30.72^**	24	0.96	0.96	101.27^**
*M. domestica*				25	0.66	0.67	75.95^**
0	0.34	0.37	20.55^**	26	0.51	0.65	30.17^**
2	0.75	0.65	34.70^**	27	1.70	0.68	38.52^**
3	0.78	0.71	164.45^**	28	0.60	0.67	174.99^**
6	0.55	0.58	47.64^**	29	1.21	1.19	124.18^**
8	0.75	1.38	330.32^**	32	0.62	0.64	40.06^**
9	0.40	0.46	11.37^**	33	0.35	0.40	63.30^**
11	0.64	0.64	26.32^**	38	0.73	0.75	426.85^**
13	0.55	0.58	3.41	40	0.20	0.28	1.27
14	0.88	0.79	53.12^**	42	0.43	0.50	49.36^**
15	0.87	0.45	157.04^**	*P. persica*
16	0.54	0.58	128.15^**	0	0.67	0.72	90.19^**
17	0.65	0.59	45.42^**	1	0.48	0.46	94.92^**
20	1.10	1.08	90.23^**	2	0.58	0.59	64.94^**
22	1.02	1.33	48.89^**	3	0.51	0.57	81.35^**
23	0.59	0.61	123.77^**	4	0.73	0.85	81.38^**
24	0.53	0.65	17.75^**	5	0.56	0.60	53.61^**
25	0.91	0.95	242.51^**	7	0.87	0.77	131.61^**
27	0.55	0.62	236.80^**	10	0.54	0.56	39.07^**
29	0.70	0.84	46.93^**	11	1.01	1.12	35.54^**
30	0.54	0.59	5.43	12	0.53	0.51	161.31^**
32	0.41	0.49	3.81	13	0.33	0.38	0.18
35	0.89	0.62	141.09^**	14	0.59	0.59	68.99^**
36	0.60	0.70	61.85^**	15	0.62	0.77	11.16^**
37	0.65	0.71	30.67^**	16	0.72	0.87	149.36^**
39	0.85	0.95	182.68^**	17	0.64	0.64	94.83^**
41	0.67	0.70	133.44^**	20	0.48	0.53	28.45^**
43	0.93	0.86	158.52^**	22	0.37	0.39	1.92
46	0.76	0.76	88.84^**	23	0.53	0.61	17.38^**
48	0.31	0.47	2.97	24	0.48	0.48	57.74^**
49	0.70	0.91	18.54^**	29	0.62	0.62	156.86^**
51	0.73	0.86	118.63^**	30	0.68	0.69	86.74^**
52	0.84	0.86	88.35^**	*P. mume*
53	0.25	0.32	1.41	0	0.66	0.74	26.03^**
54	-	0.00	0	2	0.73	0.72	118.53^**
56	0.91	1.04	100.03^**	3	0.68	0.73	173.81^**
57	0.81	0.91	230.38^**	5	0.68	0.73	214.41^**
59	0.74	0.70	278.72^**	6	0.67	0.70	49.62^**
60	0.74	0.66	273.76^**	8	0.70	0.69	101.58^**
70	0.82	0.78	208.35^**	10	0.64	0.62	97.65^**
72	0.40	0.34	61.52^**	12	0.59	0.65	103.39^**
75	0.73	0.55	47.28^**	14	0.63	0.69	63.55^**
*P. bretschneideri*				15	0.50	0.48	59.19^**
0	0.60	0.67	312.45^**	17	0.82	0.79	156.79^**
1	0.40	0.47	61.89^**	18	0.58	0.70	179.70^**
2	0.70	0.78	113.38^**	19	0.43	0.49	3.83
4	0.42	0.53	18.57^**	21	0.31	0.34	−2.00E-06
7	0.55	0.63	16.11^**	24	0.92	1.21	38.51^**
9	0.54	0.61	54.18^**	25	0.78	0.89	15.13^**
11	0.74	0.88	58.97^**

^aAverage Ka/Ks ratio of each gene family calculated by MEGA; ^b dN/dS ratio for each gene family using branch model; 2Δln represents the result of LR test for site model; ^** represent highly significant (2Δln > 9.210, p < 0.01) tests for positive selection between model M7 and M8.

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ISSN: 1471-2164

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