Computational identification of receptor-like kinases “RLK” and receptor-like proteins “RLP” in legumes

BMC Genomics

Table 2 Summary of total number of RLK and RLP identified across legumes/non-legumes

		Signal peptide			Transmembrane helices		RLK/RLP proteins identified per species
Species	Total proteins reported	Pre/Abs	Number of proteins	%	Number of proteins	%	RLK^a	% RLK	RLP^a	% RLP
C. cajan	48,331	P	2679	5.5	1031	2.1	197		62
		A	45,652	94.4	5760	11.9	253		80
						total	450	0.9	142	0.3
G. max	88,647	P	8125	9.1	3934	4.4	1182		282
		A	80,522	90.8	15,459	17.4	682		186
						total	1864	2.1	468	0.5
M. truncatula	62,319	P	6251	10.0	2961	4.7	647		196
		A	56,068	89.9	10,383	16.6	413		167
						total	1060	1.7	363	0.6
P. vulgaris	36,995	P	4120	11.1	1895	5.1	571		138
		A	32,875	88.8	6349	17.1	271		79
						total	842	2.3	217	0.6
V. angularis	37,769	P	3570	9.4	1681	4.4	557		124
		A	34,199	90.5	6364	16.8	278		91
						total	835	2.2	215	0.6
V. radiata	35,143	P	3450	9.8	1584	4.5	505		142
		A	31,693	90.1	5934	16.8	265		99
						total	770	2.2	241	0.7
V. unguiculata	42,287	P	4698	11.1	2105	4.9	660		190
		A	37,589	88.9	7962	18.8	332		104
						total	992	2.3	294	0.7
V. vinifera	26,346	P	2043	7.7	842	3.2	269		99
		A	24,303	92.2	4980	18.9	174		73
						total	443	1.7	172	0.6
A. thaliana	35,386	P	4088	11.5	1935	5.4	408		121
		A	31,298	88.4	5784	16.3	147		51
						total	555	1.6	172	0.5
S. lycopersicum	34,725	P	3258	9.3	1480	4.2	316		107
		A	1467	90.6	5727	16.4	160		54
						total	476	1.4	161	0.5

For each species, the results were distinguished by the present “P” and absent “A” of signal peptide and follow the logic flow presented in Fig. 1. ^aNon-redundant data reported. For the RLK-nonRD, the results per species are: A. thaliana: 48 proteins (8.6%), C. cajan: 61 proteins (13.6%), G. max: 223 proteins (11.9%), M. truncatula: 194 proteins (18.3%), P. vulgaris: 124 proteins (14.7%), S. lycopersicum: 83 proteins (17.4%), V. angularis: 122 proteins (14.6%), V. radiata: 113 proteins (14.7%), V. unguiculata: 158 proteins (15.9%), and V. vinifera: 59 proteins (13.3%). RLK-nonRD IDs are reported in the Additional file 3: Table S3. The kinome (total set of proteins with a kinase in a genome) per species was calculated and the results for the species are CC: 1268 p. (35.5% - RLK), GM: 4497 p. (41.4% - RLK), MT: 2281 p. (46.6% - RLK), PV: 1888 p. (44.7% - RLK), VA: 1898 p. (44% - RLK), VR: 1772 p. (43.5% - RLK), VU: 2090 p. (47.5% - RLK), VV: 1064 p. (41.7% - RLK), AT: 1431 p. (38.9% - RLK), and SL: 1194 p. (39.9% - RLK)

ISSN: 1471-2164