The evolutionary history of LysM-RLKs (LYKs/LYRs) in wild tomatoes

Richards, Sarah; Rose, Laura E.

doi:10.1186/s12862-019-1467-3

BMC Ecology and Evolution

Table 2 Summary of allelic diversity applied separately to extracellular and intracellular domains of LysM-RLKs from wild tomatoes

From: The evolutionary history of LysM-RLKs (LYKs/LYRs) in wild tomatoes

	Gene region	No. Seqs	No. Sites	Haplotypes	π all sites (non,syn,silent)	π_a/π_s	S
LYK1
chil v ochr	Extracellular	17 v 1	699	8	0.0026 (0.0025, 0.0032, 0.0032)	0.79	8
chil v ochr	Intracellular		1101	9	0.0028 (0.0011, 0.0079, 0.0078)	0.14	10
chil v lyco	Extracellular	17 v 1	699	8	0.0026 (0.0025, 0.0032, 0.0032)	0.80	8
chil v lyco	Intracellular		1101	9	0.0028 (0.0011, 0.0079, 0.0078)	0.14	10
peru v ochr	Extracellular	17 v 1	699	12	0.0063 (0.0042, 0.0129, 0.0129)	0.33	21
peru v ochr	Intracellular		1101	15	0.0043 (0.0018, 0.0117, 0.0116)	0.16	21
peru v lyco	Extracellular	17 v 1	699	12	0.0063 (0.0043, 0.0130, 0.0130)	0.33	21
peru v lyco	Intracellular		1101	15	0.0043 (0.0018, 0.0117, 0.0116)	0.16	21
LYK3
chil v ochr	Extracellular	17 v 1	705	12	0.0046 (0.0005, 0.0176, 0.0176)	0.03	13
chil v ochr	Intracellular		1203	16	0.0044 (0.0009, 0.0158, 0.0156)	0.06	21
chil v lyco	Extracellular	17 v 1	705	12	0.0046 (0.0005, 0.0155, 0.0155)	0.03	13
chil v lyco	Intracellular		1203	16	0.0044 (0.0009, 0.0158, 0.0156)	0.06	21
peru v ochr	Extracellular	16 v 1	705	13	0.0086 (0.0008, 0.0328, 0.0328)	0.03	24
peru v ochr	Intracellular		1203	14	0.0042 (0.0008, 0.0155, 0.0153)	0.05	25
peru v lyco	Extracellular	16 v 1	705	13	0.0088 (0.0009, 0.0349, 0.0349)	0.02	24
peru v lyco	Intracellular		1203	14	0.0042 (0.0008, 0.0155, 0.0153)	0.05	25
LYK4
chil v ochr	Extracellular	15 v 1	801	15	0.0089 (0.0074, 0.0136, 0.0136)	0.54	18
chil v ochr	Intracellular		1053	14	0.0074 (0.0053, 0.0139, 0.0137)	0.38	31
chil v lyco	Extracellular	15 v 1	801	15	0.0089 (0.0074, 0.0136, 0.0136)	0.54	18
chil v lyco	Intracellular		1053	14	0.0074 (0.0053, 0.0139, 0.0137)	0.38	31
peru v ochr	Extracellular	16 v 1	801	16	0.0106 (0.0087, 0.0161, 0.0089)	0.54	41
peru v ochr	Intracellular		1053	11	0.0075 (0.0029, 0.0236, 0.0233)	0.12	33
peru v lyco	Extracellular	16 v 1	801	16	0.0106 (0.0087, 0.0161, 0.0161)	0.54	41
peru v lyco	Intracellular		1053	11	0.0075 (0.0029, 0.0236, 0.0233)	0.12	33
LYK6
chil v ochr	Extracellular	15 v 1	780	12	0.0146 (0.0132, 0.0198, 0.0198)	0.66	29
chil v ochr	Intracellular		741	13	0.0150 (0.0105, 0.0265, 0.0265)	0.39	31
chil v lyco	Extracellular	15 v 1	780	12	0.0146 (0.0132, 0.0198, 0.0198)	0.66	29
chil v lyco	Intracellular		741	13	0.0150 (0.0105, 0.0265, 0.0265)	0.39	31
peru v ochr	Extracellular	8 v 1	780	8	0.0152 (0.0149, 0.0166, 0.0166)	0.90	33
peru v ochr	Intracellular		741	8	0.0188 (0.0127, 0.0397, 0.0397)	0.31	30
peru v lyco	Extracellular	8 v 1	780	8	0.0152 (0.0149, 0.0165, 0.0165)	0.90	33
peru v lyco	Intracellular		741	8	0.0188 (0.0127, 0.0397, 0.0397)	0.31	30
LYK8
chil v ochr	Extracellular	13 v 1	771	9	0.0042 (0.0053, 0.0006, 0.0006)	9.1	9
chil v ochr	Intracellular*		300	3	0.0022 (0.0000, 0.0116, 0.0116)	0.00	3
peru v ochr	Extracellular	17 v 1	771	13	0.0038 (0.0032, 0.0058, 0.0058)	0.55	16
peru v ochr	Intracellular*		300	9	0.0047 (0.0035, 0.0101, 0.0101)	0.34	11
LYK9
chil v ochr	Extracellular	17 v 1	774	14	0.0086 (0.0068, 0.0145, 0.0145)	0.47	22
chil v ochr	Intracellular		1038	14	0.0060 (0.0020, 0.0199, 0.0202)	0.10	22
chil v lyco	Extracellular	17 v 1	774	14	0.0086 (0.0068, 0.0145, 0.0145)	0.47	22
chil v lyco	Intracellular		1038	14	0.0060 (0.0020, 0.0199, 0.0202)	0.10	22
peru v ochr	Extracellular	17 v 1	774	14	0.0053 (0.0040, 0.0092, 0.0092)	0.44	25
peru v ochr	Intracellular		1038	17	0.0082 (0.0051, 0.0168, 0.0188)	0.30	32
peru v lyco	Extracellular	17 v 1	774	14	0.0053 (0.0040, 0.0092, 0.0092)	0.44	25
peru v lyco	Intracellular		1038	17	0.0082 (0.0052, 0.0169, 0.0189)	0.30	32

Population samples were available for Solanum chilense (chil) and Solanum peruvianum (peru). Single allelic sequences from Solanum ochranthum (ochr) and Solanum lycopersicoides (lyco) were used for outgroup comparisons. Haplotypes, the number of unique alleles in each population sample, apply to the first species listed in column 1, as do values for S, the number of segregating sites. The ratio of non-synonymous to synonymous average pairwise differences (π_a/π_s) was calculated for S. chilense and S. peruvianum. *The kinase domain of LYK8 is truncated

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