Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton

Magwanga, Richard Odongo; Lu, Pu; Kirungu, Joy Nyangasi; Lu, Hejun; Wang, Xingxing; Cai, Xiaoyan; Zhou, Zhongli; Zhang, Zhenmei; Salih, Haron; Wang, Kunbo; Liu, Fang

doi:10.1186/s12863-017-0596-1

Table 4 Gene duplication, Ks, Ka and Ka/Ks values calculated for paralogous LEA gene pairs in cotton genome

From: Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton

GENE FAMILY	Paralogous gene pairs		Length (aa)	K_a	K_s	K_a/K_s	Negative/purifying selection	P-Value (Fisher)
GENE FAMILY	A	B	Length (aa)	K_a	K_s	K_a/K_s	Negative/purifying selection	P-Value (Fisher)
DEHYDRIN	CotAD_66,538	CotAD_74,713	633	0.01677	0.04094	0.409579	YES	0.0891624
DEHYDRIN	CotAD_70,948	CotAD_75,267	996	0.33429	0.42203	0.792098	YES	0.122937
DEHYDRIN	CotAD_53,981	Cotton_A_05444	753	0.00533	0.01072	0.49715	YES	0.365412
DEHYDRIN	CotAD_65,119	Cotton_A_13573	618	0.01516	0.04762	0.318478	YES	0.0332022
DEHYDRIN	CotAD_66,245	Cotton_A_13581	1350	0.01615	0.03716	0.434571	YES	0.0218162
DEHYDRIN	CotAD_64,004	Cotton_A_14354	657	0.02039	0.07908	0.257869	YES	0.00188419
DEHYDRIN	CotAD_66,774	Cotton_A_23172	648	0.0101	0.05547	0.182079	YES	0.0030156
DEHYDRIN	CotAD_66,775	Cotton_A_23173	675	0.02652	0.06314	0.419977	YES	0.0380326
DEHYDRIN	CotAD_60,435	Cotton_A_24371	699	2.87675	2.00242	1.43664	NO	0.319287
DEHYDRIN	CotAD_58,358	Cotton_A_29692	633	0.01197	0.05683	0.210713	YES	0.00684175
DEHYDRIN	CotAD_66,538	Cotton_A_33548	633	0.00417	0.00659	0.63267	YES	0.549017
DEHYDRIN	CotAD_70,948	Cotton_A_40365	996	0.33435	0.4385	0.762473	YES	0.0864744
DEHYDRIN	CotAD_75,267	Cotton_A_40365	996	0.00385	0.0094	0.409167	YES	0.292983
DEHYDRIN	CotAD_65,119	Gorai.008G218500.1	618	0.00214	0.00666	0.321634	YES	0.36944
DEHYDRIN	Cotton_A_13573	Gorai.008G218500.1	618	0.01297	0.0548	0.236675	YES	0.00834018
LEA1	CotAD_01033	CotAD_08181	606	0.05146	0.15416	0.3338	YES	0.000633352
LEA1	CotAD_00275	CotAD_39,719	822	0.01476	0.03476	0.424567	YES	0.130131
LEA1	CotAD_01033	CotAD_46,550	606	0.0493	0.18716	0.263397	YES	1.42E-05
LEA1	CotAD_01298	CotAD_64,120	654	0.0404	0.13464	0.300053	YES	0.000332152
LEA1	CotAD_00275	Cotton_A_14009	822	0.01475	0.04503	0.327622	YES	0.0184625
LEA1	CotAD_01298	Cotton_A_22932	654	0.03303	0.12281	0.268983	YES	0.000202033
LEA1	CotAD_01033	Cotton_A_27543	606	0.05146	0.1456	0.353443	YES	0.00202823
LEA1	CotAD_01298	Gorai.004G155000.1	630	2.63603	3.65804	0.720612	YES	0.753791
LEA1	CotAD_01033	Gorai.009G305100.1	606	0.05153	0.14499	0.355394	YES	0.00205763
LEA2	CotAD_11,658	_Cotton_A_40499	789	0.02309	0.01751	1.3191	NO	0.985982
LEA2	CotAD_01700	CotAD_09578	780	0.01202	0.02634	0.456421	YES	0.151105
LEA2	CotAD_02652	CotAD_14,147	636	0.00835	0.01974	0.422805	YES	0.226532
LEA2	Cotton_A_13471	CotAD_17,103	180.94	2.32397	1.11323	0.778217	YES	837
LEA2	CotAD_13,584	CotAD_20,020	750	0.00878	0.01711	0.513478	YES	0.287642
LEA2	CotAD_17,062	CotAD_21,731	732	0.00719	0.04161	0.17276	YES	0.00506705
LEA2	CotAD_03649	CotAD_31,344	960	0.01103	0.02214	0.497982	YES	0.177084
LEA2	CotAD_17,101	CotAD_31,535	666	0.01576	0.04026	0.391498	YES	0.077316
LEA2	CotAD_17,102	CotAD_31,536	627	0.00422	0.03365	0.125467	YES	0.0107355
LEA2	Cotton_A_31083	CotAD_35,069	939	2.2748	1.83858	1.23726	NO	0.447623
LEA2	CotAD_19,214	CotAD_35,514	543	0.00955	0.02509	0.380645	YES	0.19023
LEA2	CotAD_19,623	CotAD_36,999	282	0.03296	0.04771	0.69081	YES	0.631725
LEA2	CotAD_18,546	CotAD_37,776	519	0.01016	0.04195	0.242116	YES	0.0375368
LEA2	CotAD_03649	CotAD_37,888	960	0.04522	0.54142	0.08352	YES	9.32E-36
LEA2	CotAD_40,972	CotAD_38,978	591	0.96025	2.04193	0.470264	YES	0.00125135
LEA2	CotAD_32,847	CotAD_39,064	612	0.01106	0.0461	0.239936	YES	0.0153075
LEA2	CotAD_12,375	CotAD_42,408	597	2.42062	1.68288	1.43838	NO	0.288342
LEA2	CotAD_28,872	CotAD_44,941	720	0.0141	0.01369	1.03042	NO	0.900519
LEA2	CotAD_08181	CotAD_46,550	606	0.00654	0.04975	0.131503	YES	0.00250188
LEA2	CotAD_25,271	CotAD_48,769	405	0.00647	0.01063	0.609395	YES	0.539117
LEA2	CotAD_28,252	CotAD_53,263	492	0.01356	0.04285	0.31656	YES	0.069282
LEA2	CotAD_09685	CotAD_53,981	753	0.00711	0.04386	0.162112	YES	0.00252472
LEA2	CotAD_35,091	CotAD_60,435	753	0.03016	0.07689	0.392211	YES	0.0144267
LEA2	CotAD_46,873	CotAD_60,617	630	0.00835	0.03452	0.241852	YES	0.0372109
LEA2	CotAD_46,888	CotAD_61,391	573	0.01387	0.05313	0.261111	YES	0.0175133
LEA2	CotAD_35,069	CotAD_62,996	954	0.00551	0.03643	0.151164	YES	0.0017334
LEA2	CotAD_17,045	CotAD_64,004	657	0.02247	0.06523	0.344452	YES	0.0157104
LEA2	CotAD_36,328	CotAD_64,346	630	0.01777	0.07564	0.23489	YES	0.000973496
LEA2	CotAD_21,924	CotAD_64,657	786	0.01373	0.04693	0.292471	YES	0.0120925
LEA2	CotAD_50,359	CotAD_66,538	633	0.01677	0.04094	0.409579	YES	0.0891624
LEA2	CotAD_19,078	CotAD_66,774	648	0.01009	0.04842	0.208435	YES	0.00834864
LEA2	CotAD_53,438	CotAD_68,189	618	0.02341	0.02898	0.80786	YES	0.519399
LEA2	CotAD_20,308	CotAD_70,003	573	0.00915	0.02291	0.399181	YES	0.206152
LEA2	CotAD_03649	CotAD_73,966	960	0.04597	0.527	0.087231	YES	4.70E-35
LEA2	CotAD_37,888	CotAD_73,966	960	0.01528	0.0442	0.345761	YES	0.0157353
LEA2	CotAD_23,118	CotAD_74,061	1215	0.01611	0.06882	0.234049	YES	5.00E-05
LEA2	CotAD_59,405	CotAD_76,129	627	0	0.00654	0	YES	0
LEA2	CotAD_13,584	Cotton_A_01845	750	0.00878	0.02294	0.382644	YES	0.139381
LEA2	CotAD_20,020	Cotton_A_01845	750	0	0.00568	0	YES	0
LEA2	CotAD_01700	Cotton_A_02196	780	0.09992	0.58986	0.169389	YES	8.68E-22
LEA2	CotAD_09578	Cotton_A_02196	780	0.0903	0.59944	0.150635	YES	7.07E-24
LEA2	Gorai.007G048400.1	Cotton_A_02294	576	2.54671	1.77281	1.43654	NO	0.3084
LEA2	CotAD_02652	Cotton_A_02370	636	0.01256	0.03311	0.379343	YES	0.101339
LEA2	CotAD_14,147	Cotton_A_02370	636	0.00416	0.01312	0.316903	YES	0.244174
LEA2	CotAD_09685	Cotton_A_05444	753	0.0089	0.04387	0.202818	YES	0.00516244
LEA2	CotAD_10,376	Cotton_A_05625	831	0.00645	0.03444	0.187227	YES	0.00723285
LEA2	CotAD_19,375	Cotton_A_06435	675	0.01345	0.05541	0.242679	YES	0.00759106
LEA2	CotAD_01700	Cotton_A_07036	780	0.01551	0.03701	0.419158	YES	0.0752732
LEA2	CotAD_09578	Cotton_A_07036	780	0.00342	0.01037	0.33004	YES	0.256013
LEA2	Cotton_A_02196	Cotton_A_07036	780	0.09428	0.60765	0.155148	YES	1.27E-23
LEA2	CotAD_12,681	Cotton_A_08212	432	0.03121	0.04928	0.633189	YES	0.35887
LEA2	Gorai.005G043200.1	Cotton_A_08334	792	0.00507	0.01526	0.332323	YES	0.16956
LEA2	CotAD_03649	Cotton_A_08663	960	0.00549	0.00437	1.25606	NO	0.744588
LEA2	CotAD_37,888	Cotton_A_08663	960	0.04378	0.55839	0.07841	YES	1.73E-37
LEA2	CotAD_10,044	Cotton_A_09473	1902	0.00274	0.00228	1.20458	NO	0.731531
LEA2	CotAD_46,888	Cotton_A_09596	573	0.00922	0.0453	0.203506	YES	0.0147038
LEA2	CotAD_46,873	Cotton_A_09615	630	0.00835	0.03452	0.241852	YES	0.0372109
LEA2	CotAD_32,487	Cotton_A_13240	630	0.00425	0.01917	0.221854	YES	0.103356
LEA2	CotAD_17,101	Cotton_A_13469	666	0.00195	0.01318	0.148053	YES	0.121749
LEA2	CotAD_31,535	Cotton_A_13469	666	0.01377	0.04718	0.291898	YES	0.0234164
LEA2	CotAD_31,536	Cotton_A_13470	627	0.00211	0.03373	0.062455	YES	0.00360292
LEA2	CotAD_17,103	Cotton_A_13471	837	2.58712	2.32397	1.11323	NO	0.778217
LEA2	CotAD_17,045	Cotton_A_14354	657	0.00201	0.01262	0.159578	YES	0.13409
LEA2	CotAD_17,062	Cotton_A_14370	732	0.0099	0.02648	0.374024	YES	0.0618224
LEA2	CotAD_21,731	Cotton_A_14370	732	0.00899	0.02354	0.381916	YES	0.138838
LEA2	CotAD_03649	Cotton_A_14478	960	0.04592	0.52972	0.086683	YES	3.29E-35
LEA2	CotAD_37,888	Cotton_A_14478	960	0.01247	0.03528	0.353401	YES	0.0321315
LEA2	CotAD_25,271	Cotton_A_14676	405	0.00647	0.03234	0.200226	YES	0.085476
LEA2	CotAD_31,140	Cotton_A_15998	747	0.00174	0.0058	0.300994	YES	0.356655
LEA2	CotAD_20,308	Cotton_A_17625	573	0.01375	0.02296	0.59881	YES	0.347235
LEA2	CotAD_44,941	Cotton_A_17986	720	0.01233	0.01369	0.900555	YES	0.874489
LEA2	CotAD_13,827	Cotton_A_18645	1104	2.12092	1.89653	1.11832	NO	0.642563
LEA2	CotAD_21,924	Cotton_A_18919	786	0.01028	0.05219	0.196967	YES	0.00026749
LEA2	CotAD_19,078	Cotton_A_23172	648	0	0.00672	0	YES	0
LEA2	CotAD_35,069	Cotton_A_24356	954	0.00551	0.03178	0.173291	YES	0.00508945
LEA2	CotAD_35,091	Cotton_A_24371	699	3.50309	1.61186	2.17333	NO	0.036477
LEA2	CotAD_22,539	Cotton_A_25195	408	1.23265	1.24112	0.993172	YES	1
LEA2	CotAD_23,646	Cotton_A_27282	609	0.02587	0.03738	0.692044	YES	0.542393
LEA2	CotAD_23,646	Cotton_A_27300	609	0.04249	0.13135	0.323481	YES	0.000630664
LEA2	Cotton_A_27282	Cotton_A_27300	609	0.04363	0.11818	0.369227	YES	0.00568388
LEA2	CotAD_08181	Cotton_A_27543	606	0	0.00697	0	YES	0
LEA2	CotAD_40,972	Cotton_A_29659	591	0.96659	2.0709	0.466747	YES	0.00123143
LEA2	CotAD_48,976	Cotton_A_29779	660	0	0.00642	0	YES	0
LEA2	CotAD_19,214	Cotton_A_30889	543	0.00237	0.0083	0.285978	YES	0.347253
LEA2	CotAD_35,514	Cotton_A_30889	543	0.00716	0.01659	0.431351	YES	0.312651
LEA2	CotAD_35,513	Cotton_A_30890	651	0.02193	0.05102	0.429783	YES	0.0738291
LEA2	CotAD_13,115	Cotton_A_31059	576	0.0207	0.0379	0.546252	YES	0.312514
LEA2	CotAD_30,219	Cotton_A_32495	597	0.01105	0.03626	0.304817	YES	0.0618481
LEA2	CotAD_50,359	Cotton_A_33548	633	0.01678	0.03388	0.495283	YES	0.175709
LEA2	CotAD_74,713	Cotton_A_33548	633	0.01678	0.03388	0.495283	YES	0.175709
LEA2	CotAD_23,118	Cotton_A_38117	1215	0.01611	0.06077	0.265138	YES	0.000321992
LEA2	CotAD_56,699	Cotton_A_38534	639	0.02021	0.04493	0.449883	YES	0.106618
LEA2	CotAD_56,696	Cotton_A_38535	630	0.01838	0.02269	0.809786	YES	0.670475
LEA2	CotAD_59,405	Cotton_A_40363	627	0.00636	0.04016	0.158424	YES	0.00848415
LEA2	CotAD_46,888	Gorai.001G122700.1	573	0.0046	0.0148	0.310385	YES	0.238274
LEA2	CotAD_46,873	Gorai.001G124400.1	630	0.00208	0.00674	0.30909	YES	0.361889
LEA2	CotAD_28,872	Gorai.005G203000.1	720	0.01233	0.02762	0.446407	YES	0.170613
LEA2	CotAD_44,941	Gorai.005G203000.1	720	0.00175	0.01368	0.127787	YES	0.0998325
LEA2	Cotton_A_17986	Gorai.005G203000.1	720	0.01055	0.02762	0.382183	YES	0.12817
LEA2	CotAD_30,219	Gorai.006G104100.1	597	0.00884	0.00707	1.25015	NO	0.743557
LEA2	Cotton_A_32495	Gorai.006G104100.1	597	0.01106	0.04362	0.25359	YES	0.0255988
LEA2	CotAD_17,101	Gorai.006G150200.1	666	0.01977	0.04018	0.491966	YES	0.209339
LEA2	CotAD_31,535	Gorai.006G150200.1	666	0.00391	0.01981	0.197433	YES	0.082505
LEA2	Cotton_A_13469	Gorai.006G150200.1	666	0.01777	0.04018	0.442182	YES	0.10598
LEA2	CotAD_23,646	Gorai.006G199800.1	609	0.04249	0.11411	0.372373	YES	0.00460089
LEA2	Cotton_A_27282	Gorai.006G199800.1	609	0.04364	0.10127	0.4309	YES	0.0292702
LEA2	Cotton_A_27300	Gorai.006G199800.1	609	0.00852	0.01474	0.578415	YES	0.130872
LEA2	Cotton_A_02294	Gorai.007G048400.1	576	2.54671	1.77281	1.43654	NO	0.3084
LEA2	Gorai.002G235700.1	Gorai.007G048400.1	576	2.49387	1.6786	1.48568	NO	0.261229
LEA2	Cotton_A_29142	Gorai.007G365600.1	630	0.02641	0.05237	0.504231	YES	0.0996897
LEA2	CotAD_08181	Gorai.009G305100.1	606	0.00435	0.02103	0.206723	YES	0.090366
LEA2	CotAD_19,214	Gorai.010G176400.1	543	0.00955	0.01664	0.574182	YES	0.403293
LEA2	CotAD_35,514	Gorai.010G176400.1	543	0	0.00822	0	YES	0
LEA2	Cotton_A_30889	Gorai.010G176400.1	543	0.00716	0.00825	0.8675	YES	0.63691
LEA3	CotAD_31,344	CotAD_37,888	960	0.0445	0.58201	0.076463	YES	1.76E-39
LEA3	CotAD_31,344	CotAD_73,966	960	0.04525	0.56675	0.079847	YES	1.38E-37
LEA3	CotAD_31,344	Cotton_A_08663	960	0.01103	0.02662	0.414477	YES	0.0917464
LEA3	CotAD_31,344	Cotton_A_14478	960	0.0452	0.56976	0.079332	YES	9.48E-38
LEA3	CotAD_68,063	Cotton_A_35039	654	0.0041	0.00611	0.670634	YES	0.565408
LEA3	CotAD_76,129	Cotton_A_40363	627	0.00636	0.03331	0.190971	YES	0.0241426
LEA4	CotAD_73,966	Cotton_A_08663	960	0.04453	0.54363	0.081917	YES	8.99E-37
LEA4	CotAD_73,966	Cotton_A_14478	960	0.00552	0.00865	0.63778	YES	0.447461
LEA4	Cotton_A_08663	Cotton_A_14478	960	0.04448	0.54647	0.081397	YES	6.22E-37
LEA4	CotAD_48,769	Cotton_A_14676	405	0	0.02141	0	YES	0
LEA4	CotAD_64,120	Cotton_A_22932	654	0.00607	0.01278	0.475195	YES	0.348209
LEA4	Gorai.004G155000.1	Cotton_A_22932	630	2.64206	3.59311	0.735312	YES	0.675748
LEA4	CotAD_46,550	Cotton_A_27543	606	0.00654	0.04242	0.154221	YES	0.00764013
LEA4	CotAD_64,120	Gorai.004G155000.1	630	2.60195	2.91277	0.893293	YES	0.834736
LEA4	Cotton_A_22932	Gorai.004G155000.1	630	2.64206	3.59311	0.735312	YES	0.675748
LEA4	CotAD_70,003	Gorai.006G083600.1	573	0.01378	0.02282	0.603673	YES	0.351221
LEA4	Cotton_A_17625	Gorai.006G083600.1	573	0.01841	0.02287	0.804972	YES	0.670413
LEA4	CotAD_46,550	Gorai.009G305100.1	606	0.00655	0.02791	0.234738	YES	0.0613694
LEA4	Cotton_A_27543	Gorai.009G305100.1	606	0.00435	0.01395	0.311662	YES	0.239375
LEA5	CotAD_39,719	Cotton_A_14009	822	0.00325	0.00976	0.333365	YES	0.258994
LEA5	CotAD_53,263	Cotton_A_22889	492	0.01631	0.04279	0.38131	YES	0.103316
LEA5	CotAD_74,061	Cotton_A_38117	1215	0.00426	0.01476	0.28873	YES	0.0817353
LEA6	CotAD_42,408	Cotton_A_13854	642	3.29524	1.27099	2.59265	NO	0.00291028
LEA6	CotAD_60,617	Gorai.001G124400.1	630	0.01046	0.04152	0.251878	YES	0.00495557
LEA6	Cotton_A_09615	Gorai.001G124400.1	630	0.01046	0.04152	0.251878	YES	0.00495557
SMP	Cotton_A_31083	CotAD_62,996	939	2.26658	1.80077	1.25867	NO	0.353457
SMP	CotAD_47,454	Cotton_A_07451	810	0.01141	0.05967	0.191218	YES	0.000658403
SMP	CotAD_61,391	Cotton_A_09596	573	0.0046	0.00736	0.624435	YES	0.545436
SMP	CotAD_64,657	Cotton_A_18919	786	0.00683	0.00508	1.345	NO	0.764969
SMP	CotAD_62,996	Cotton_A_24356	954	0	0.01351	0	YES	0
SMP	Cotton_A_31083	Cotton_A_24356	939	2.26658	1.8524	1.22359	NO	0.3981
SMP	CotAD_61,391	Gorai.001G122700.1	573	0.01855	0.05313	0.349233	YES	0.0424313
SMP	Cotton_A_09596	Gorai.001G122700.1	573	0.01387	0.0453	0.306205	YES	0.042074
SMP	Cotton_A_02294	Gorai.002G235700.1	627	0.00614	0.0377	0.162756	YES	0.0142575
SMP	CotAD_61,173	Gorai.004G137100.1	645	0.01861	0.04646	0.400532	YES	0.0204369
SMP	Cotton_A_31127	Gorai.004G137100.1	645	0.01965	0.0431	0.45597	YES	0.124339
SMP	CotAD_47,454	Gorai.009G452500.1	810	1.79916	1.14125	1.57648	NO	0.0145321
SMP	Cotton_A_07451	Gorai.009G452500.1	810	1.85045	1.14684	1.61353	NO	0.0110846

A B: paralogous gene pair; aa amino acids, K_a non-synonymous substitutions per non-synonymous site, K_s synonymous substitutions per synonymous site); K_a/K_s the ratio, SMP seed maturation protein, LEA Late embryogenesis abundance, Yes presence of purifying selection while NO absence of purifying selection

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