Table S1. Recombination analysis

Genotypes / Recombination signal found in DNAsp / Recombination signal found in RDP3
Overall (At +Dt) / At / Dt
No. of events / positions / No. of events / positions / No. of events / positions / No. of events / Recombined parental member ID [daughter sequence ID] / End and beginning points / Method / average P
Gh_TM1 / 1 / 21,153 / 0 / 0 / 0 / - / 0 / - / - / - / -
Gh_Sisoline / 1 / 21,153 / 1 / 21, 254 / 0 / - / 0 / - / - / - / -
Gh_M315 / 2 / 21, 153; 21, 317 / 2 / 21,151; 153, 306 / 0 / - / 2(9) / 10:12 [3, 4, 5, 6, 7, 8, 9]; 7:13 [14, 15] / unknown / SisScan / 0.0005
Gh_M8 / 1 / 21, 153 / 1 / 21, 151 / 0 / - / 0 / - / unknown
Gh_Clevewilt / 1 / 21, 153 / 0 / 0 / 0 / - / 1(2) / 2:4 [11, 12] / unknown / Siscan / 0.0007
Gh_Golib / 1 / 21, 153 / 1 / 21, 151 / 0 / - / 0 / - / unknown
Gh_M240 / 1 / 21, 153 / 2 / 21,151; 153, 306 / 0 / - / 1 (4) / 8:6 [2, 3, 4, 5] / unknown / SisScan / 0.00004
Gh_REDM / 1 / 21, 153 / 1 / 21,306 / 0 / - / 1(1) / 5:2 [12] / unknown / SisScan / 0.0004
Gh_ST213 / 2 / 21, 153; 21, 317 / 1 / 21, 151 / 0 / - / 0 / - / - / - / -
Gb_Pima-3-79 / 0 / 0 / 0 / 0 / 0 / - / 0 / - / - / - / -
G. mustelinum / 0 / 0 / 0 / 0 / 0 / - / 0 / - / - / - / -
G. tomentosum / 1 / 21, 299 / 0 / 0 / 0 / - / 0 / - / - / - / -
G. herbaceum / 0 / 0 / - / - / - / - / 0 / - / - / - / -
G. raimondii / 0 / 0 / - / - / - / - / 0 / - / - / - / -
G. longicalyx / 1 / 54,171 / - / - / - / - / 0 / - / - / - / -

Gh - G. hirsutum; Gb - G. barbadense; REDM- Red mutant line

Table S2. Between genotype average dN:dS rates of MIC-3 gene family of Gossypium species

# / 1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12 / 13 / 14 / 15
1 / Gh_TM-1 / -
2 / Gh_Sisoline / 0.69 / -
3 / Gh_M315 / 0.69 / 0.67 / -
4 / Gh_M8 / 0.69 / 0.64 / 0.66 / -
5 / Gh_Clevewilt / 0.73 / 0.70 / 0.70 / 0.69 / -
6 / Gh_Golib / 0.64 / 0.62 / 0.62 / 0.61 / 0.65 / -
7 / Gh_M240 / 0.70 / 0.67 / 0.67 / 0.65 / 0.71 / 0.62 / -
8 / Gh_REDM / 0.62 / 0.59 / 0.58 / 0.57 / 0.62 / 0.54 / 0.60 / -
9 / Gh_ST213 / 0.68 / 0.65 / 0.64 / 0.63 / 0.68 / 0.60 / 0.65 / 0.59 / -
10 / Gb_Pima-3-79 / 0.78 / 0.73 / 0.72 / 0.77 / 0.79 / 0.69 / 0.73 / 0.61 / 0.70 / -
11 / G. mustelinum / 0.89 / 0.86 / 0.85 / 0.92 / 0.92 / 0.82 / 0.86 / 0.70 / 0.78 / 1.04 / -
12 / G. tomentosum / 0.84 / 0.81 / 0.81 / 0.86 / 0.86 / 0.76 / 0.80 / 0.65 / 0.74 / 0.99 / 1.20 / -
13 / G. herbaceum / 0.74 / 0.65 / 0.63 / 0.67 / 0.75 / 0.61 / 0.65 / 0.54 / 0.69 / 1.18 / 1.18 / 1.02 / -
14 / G. raimondii / 0.88 / 0.84 / 0.81 / 0.81 / 0.88 / 0.81 / 0.84 / 0.79 / 0.84 / 1.06 / 0.99 / 0.97 / 0.99 / -
15 / G. longicalyx / 0.69 / 0.66 / 0.61 / 0.62 / 0.71 / 0.60 / 0.67 / 0.63 / 0.68 / 0.77 / 0.76 / 0.73 / 0.54 / 0.88 / -

dN:dS >1 values shown in bold-faced letters

Gh - G. hirsutum; Gb - G. barbadense; REDM- Red mutant line

Table S3. Divergence time estimate cotton genomes calculated from mean of pairwise dS estimates of MIC-3 gene family of cotton genotypes

Genotypes 1 / Genotype 2 / dS / MYAa / MYAb / MYAc
AD and A
Gh_TM1 / G. herbaceum / 0.018374 / 1.58 / 3.53 / 0.61
Gh_Sus_isoline / G. herbaceum / 0.01891 / 1.63 / 3.64 / 0.63
Gh_M315 / G. herbaceum / 0.020234 / 1.74 / 3.89 / 0.67
Gh_M8 / G. herbaceum / 0.017376 / 1.50 / 3.34 / 0.58
Gh_Clevewilt / G. herbaceum / 0.017299 / 1.49 / 3.33 / 0.58
Gh_Golib / G. herbaceum / 0.019517 / 1.68 / 3.75 / 0.65
Gh_M240 / G. herbaceum / 0.019624 / 1.69 / 3.77 / 0.65
Gh_REDM / G. herbaceum / 0.021012 / 1.81 / 4.04 / 0.70
Gh_ST213 / G. herbaceum / 0.018104 / 1.56 / 3.48 / 0.60
Gb_Pima 3-79 / G. herbaceum / 0.012565 / 1.08 / 2.42 / 0.42
G. mustelinum / G. herbaceum / 0.01254 / 1.08 / 2.41 / 0.42
G. tomentosum / G. herbaceum / 0.013828 / 1.19 / 2.66 / 0.46
Average / 1.50 / 3.36 / 0.58
AD and D
Gh_TM1 / G. raimondii / 0.044863 / 1.44 / 8.63 / 1.50
Gh_Sus_isoline / G. raimondii / 0.046728 / 1.50 / 8.99 / 1.56
Gh_M315 / G. raimondii / 0.047643 / 1.53 / 9.16 / 1.59
Gh_M8 / G. raimondii / 0.047969 / 1.54 / 9.22 / 1.60
Gh_Clevewilt / G. raimondii / 0.045887 / 1.47 / 8.82 / 1.53
Gh_Golib / G. raimondii / 0.047988 / 1.54 / 9.23 / 1.60
Gh_M240 / G. raimondii / 0.046304 / 1.48 / 8.90 / 1.54
Gh_REDM / G. raimondii / 0.048794 / 1.56 / 9.38 / 1.63
Gh_ST213 / G. raimondii / 0.046901 / 1.50 / 9.02 / 1.56
Gb_Pima 3-79 / G. raimondii / 0.037856 / 1.21 / 7.28 / 1.26
G. mustelinum / G. raimondii / 0.041783 / 1.34 / 8.04 / 1.39
G. tomentosum / G. raimondii / 0.041418 / 1.33 / 7.97 / 1.38
Average / 1.45 / 8.72 / 1.51
AD and F
Gh_TM1 / G. longicalyx / 0.028801 / - / 5.54 / 0.96
Gh_Sus_isoline / G. longicalyx / 0.02903 / - / 5.58 / 0.97
Gh_M315 / G. longicalyx / 0.030793 / - / 5.92 / 1.03
Gh_M8 / G. longicalyx / 0.029477 / - / 5.67 / 0.98
Gh_Clevewilt / G. longicalyx / 0.027488 / - / 5.29 / 0.92
Gh_Golib / G. longicalyx / 0.03101 / - / 5.96 / 1.03
Gh_M240 / G. longicalyx / 0.029045 / - / 5.59 / 0.97
Gh_REDM / G. longicalyx / 0.02927 / - / 5.63 / 0.98
Gh_ST213 / G. longicalyx / 0.028067 / - / 5.40 / 0.94
Gb_Pima 3-79 / G. longicalyx / 0.026149 / - / 5.03 / 0.87
G. mustelinum / G. longicalyx / 0.026503 / - / 5.10 / 0.88
G. tomentosum / G. longicalyx / 0.027515 / - / 5.29 / 0.92
Average / - / 5.50 / 0.95
Diploid genomes
G. herbaceum / G. raimondii / 0.036349 / 7.51 / 6.99 / 1.21
G. herbaceum / G. longicalyx / 0.017804 / - / 3.42 / 0.59
G. raimondii / G. longicalyx / 0.047294 / - / 9.10 / 1.58

aan average divergence time in MYA was calculated based on mean dS distance of MIC-3 gene family of each genotype and synonymous substitutions per site per year estimate calculated in Table S3, considering divergence of AD-genome from their diploid ancestors is 1.5 MYA (Wendel et al. 2003)

ban average divergence time in MYA was calculated based on mean dS distance of MIC-3 gene family of each genotype and synonymous substitutions per site per year rate of 2.6 x 10-9 (slower rate)

can average divergence time in MYA was calculated based on mean dS distance of MIC-3 gene family of each genotype and synonymous substitutions per site per year rate of 1.5 x 10-8 (faster rate); Gh- G. hirsutum; Gb- G. barbadense; Sisoline- Susceptible isoline; REDM- Red mutant line

Table S4. Divergence time estimate for cotton genomes calculated from mean of pairwise dS estimates of At - and Dt-genome MIC-3 gene members.

Genotypes 1 / Genotype 2 / Mean dS / MYA calculated using 2.6 x 10-9 rate / MYA calculated using 1.5 x 10-9 rate
At and A
Gh_TM-1_At / G. herbaceum / 0.01642 / 3.16 / 0.55
Gh_Sisoline _At / G. herbaceum / 0.01767 / 3.40 / 0.59
Gh_M315_At / G. herbaceum / 0.01878 / 3.61 / 0.63
Gh_M8_At / G. herbaceum / 0.01723 / 3.31 / 0.57
Gh_Clevewilt_At / G. herbaceum / 0.01709 / 3.29 / 0.57
Gh_Golib_At / G. herbaceum / 0.01845 / 3.55 / 0.61
Gh_M240_At / G. herbaceum / 0.01841 / 3.54 / 0.61
Gh_REDM_At / G. herbaceum / 0.02045 / 3.93 / 0.68
Gh_ST213_At / G. herbaceum / 0.01778 / 3.42 / 0.59
Gb_Pima 3-79_At / G. herbaceum / 0.00724 / 1.39 / 0.24
G. mustelinum_At / G. herbaceum / 0.01098 / 2.11 / 0.37
G. tomentosum_At / G. herbaceum / 0.01244 / 2.39 / 0.41
Average / 0.01608 / 3.09 / 0.54
At and D
Gh_TM-1_At / G. raimondii / 0.04836 / 9.30 / 1.61
Gh_Sisoline _At / G. raimondii / 0.04976 / 9.57 / 1.66
Gh_M315_At / G. raimondii / 0.05036 / 9.68 / 1.68
Gh_M8_At / G. raimondii / 0.0498 / 9.58 / 1.66
Gh_Clevewilt_At / G. raimondii / 0.04874 / 9.37 / 1.62
Gh_Golib_At / G. raimondii / 0.05138 / 9.88 / 1.71
Gh_M240_At / G. raimondii / 0.0497 / 9.56 / 1.66
Gh_REDM_At / G. raimondii / 0.05196 / 9.99 / 1.73
Gh_ST213_At / G. raimondii / 0.04994 / 9.60 / 1.66
Gb_Pima 3-79_At / G. raimondii / 0.03963 / 7.62 / 1.32
G. mustelinum_At / G. raimondii / 0.04365 / 8.39 / 1.45
G. tomentosum_At / G. raimondii / 0.04504 / 8.66 / 1.50
Average / 0.04819 / 9.27 / 1.61
Dt and A
Gh_TM-1_Dt / G. herbaceum / 0.02327 / 4.47 / 0.78
Gh_Sisoline _Dt / G. herbaceum / 0.02327 / 4.47 / 0.78
Gh_M315_Dt / G. herbaceum / 0.02351 / 4.52 / 0.78
Gh_M8_Dt / G. herbaceum / 0.01788 / 3.44 / 0.60
Gh_Clevewilt_Dt / G. herbaceum / 0.01793 / 3.45 / 0.60
Gh_Golib_Dt / G. herbaceum / 0.02327 / 4.47 / 0.78
Gh_M240_Dt / G. herbaceum / 0.02327 / 4.47 / 0.78
Gh_REDM_Dt / G. herbaceum / 0.02327 / 4.47 / 0.78
Gh_ST213_Dt / G. herbaceum / 0.01956 / 3.76 / 0.65
Gb_Pima 3-79_Dt / G. herbaceum / 0.01656 / 3.18 / 0.55
G. mustelinum_Dt / G. herbaceum / 0.01472 / 2.83 / 0.49
G. tomentosum_Dt / G. herbaceum / 0.01615 / 3.11 / 0.54
Average / 0.02022 / 3.89 / 0.67
Dt and D
Gh_TM-1_Dt / G. raimondii / 0.03612 / 6.95 / 1.20
Gh_Sisoline _Dt / G. raimondii / 0.03612 / 6.95 / 1.20
Gh_M315_Dt / G. raimondii / 0.04154 / 7.99 / 1.38
Gh_M8_Dt / G. raimondii / 0.04155 / 7.99 / 1.39
Gh_Clevewilt_Dt / G. raimondii / 0.03732 / 7.18 / 1.24
Gh_Golib_Dt / G. raimondii / 0.03612 / 6.95 / 1.20
Gh_M240_Dt / G. raimondii / 0.03612 / 6.95 / 1.20
Gh_REDM_Dt / G. raimondii / 0.03612 / 6.95 / 1.20
Gh_ST213_Dt / G. raimondii / 0.03321 / 6.39 / 1.11
Gb_Pima 3-79_Dt / G. raimondii / 0.03653 / 7.02 / 1.22
G. mustelinum_Dt / G. raimondii / 0.03917 / 7.53 / 1.31
G. tomentosum_Dt / G. raimondii / 0.03538 / 6.80 / 1.18
Average / 0.03711 / 7.14 / 1.24
At and F
Gh_TM-1_At / G. longicalyx / 0.02637 / 5.07 / 0.88
Gh_Sisoline _At / G. longicalyx / 0.02736 / 5.26 / 0.91
Gh_M315_At / G. longicalyx / 0.02944 / 5.66 / 0.98
Gh_M8_At / G. longicalyx / 0.02859 / 5.50 / 0.95
Gh_Clevewilt_At / G. longicalyx / 0.0265 / 5.10 / 0.88
Gh_Golib_At / G. longicalyx / 0.02991 / 5.75 / 1.00
Gh_M240_At / G. longicalyx / 0.0271 / 5.21 / 0.90
Gh_REDM_At / G. longicalyx / 0.02787 / 5.36 / 0.93
Gh_ST213_At / G. longicalyx / 0.02734 / 5.26 / 0.91
Gb_Pima 3-79_At / G. longicalyx / 0.02158 / 4.15 / 0.72
G. mustelinum_At / G. longicalyx / 0.02546 / 4.90 / 0.85
G. tomentosum_At / G. longicalyx / 0.02685 / 5.16 / 0.89
Avearge / 0.02703 / 5.20 / 0.90
Dt and F
Gh_TM-1_Dt / G. longicalyx / 0.03488 / 6.71 / 1.16
Gh_Sisoline _Dt / G. longicalyx / 0.03488 / 6.71 / 1.16
Gh_M315_Dt / G. longicalyx / 0.03384 / 6.51 / 1.13
Gh_M8_Dt / G. longicalyx / 0.03258 / 6.27 / 1.09
Gh_Clevewilt_Dt / G. longicalyx / 0.03046 / 5.86 / 1.02
Gh_Golib_Dt / G. longicalyx / 0.03488 / 6.71 / 1.16
Gh_M240_Dt / G. longicalyx / 0.03488 / 6.71 / 1.16
Gh_REDM_Dt / G. longicalyx / 0.03488 / 6.71 / 1.16
Gh_ST213_Dt / G. longicalyx / 0.03135 / 6.03 / 1.05
Gb_Pima 3-79_Dt / G. longicalyx / 0.02957 / 5.69 / 0.99
G. mustelinum_Dt / G. longicalyx / 0.02894 / 5.56 / 0.96
G. tomentosum_Dt / G. longicalyx / 0.02862 / 5.50 / 0.95
Avearge / 0.03248 / 6.25 / 1.08

Gh - G.hirsutum; Gb - G. barbadense; Sisoline- Susceptible isoline; REDM- Red mutant line

Table S5. Details for 56 unique coding sequences generated for the phylogenetic analysis in Figure 2

Coding sequence number and their genomic origin / MIC-3 gene members originally cloned from each genotype
2 At / Gh_TM1 (4), Gh_TM1 (5), Gh_Sisoline (4), Gh_Sisoline (5), Gh_Gh_ST213 (3), Gh_M8 (4), Gh_M8 (5), Gh_REDM (4), Gh_REDM (3), Gh_Golib (7), Gh_Golib (8), Gh_Golib (9), Gh_Clevewilt (4), Gh_Clevewilt (5), Gh_M240 (3), Gh_M240 (4), Gh_M315 (7), Gh_M315 (8)
11 At / Gh_REDM (5)
12 At / Gh_REDM (7)
8 At / Gh_ST213 (5)
13 At / Gh_REDM (6)
7 At / Gh_Sisoline (6), Gh_ST213 (4), Gh_Clevewilt (6)
1 At / Gh_TM1 (6), Gh_TM1 (7), Gh_Sisoline (7), Gh_ST213 (6), Gh_M8 (6), Gh_M8 (7), Gh_REDM (10), Gh_REDM (9), Gh_Golib (10), Gh_Clevewilt (7), Gh_M240 (6), Gh_M315 (10)
16 At / Gh_Clevewilt (8)
14 At / Gh_Golib (1), Gh_Golib (3)
6 At / Gh_Sisoline (9), Gh_ST213 (8), Gh_Clevewilt (10)
5 At / Gh_TM1 (8), Gh_Sisoline (8), Gh_ST213 (7), Gh_M8 (8), Gh_REDM (11), Gh_Golib (11), Gh_Golib (12), Gh_Clevewilt (9), Gh_M240 (7), Gh_M315 (11)
10 At / Gh_M8 (9)
36 Dt / Gb_3-79 (9)
3 At / Gh_TM1 (1), Gh_Sisoline (1), Gh_Sisoline (2), Gh_ST213 (1), Gh_M8 (1), Gh_REDM (1), Gh_Golib (2), Gh_Clevewilt (1), Gh_M240 (1), Gh_M315 (1), Gb_3-79 (2), Gb_3-79 (3), Gb_3-79 (4), Gb_3-79 (1), G. tomentosum (1), G. tomentosum (3), G. mustelinum (1), G. mustelinum (3)
22 At / G. tomentosum (4), G. mustelinum (4)
19 At / Gh_M315 (2)
21 At / G. tomentosum (2), G. mustelinum (2)
23 At / G. tomentosum (5), G. mustelinum (6), G. mustelinum (7)
24 At / G. tomentosum (6), G. mustelinum (5)
26 At / G. mustelinum (15)
27 At / G. mustelinum (14)
25 At / Gb_3-79 (6)
41 A / G. herbaceum (8), G. herbaceum (9), G. herbaceum (7), G. herbaceum (6)
9 At / Gh_M8 (3), Gh_M315 (5)
15 At / Gh_Golib (6)
20 At / Gh_M315 (4)
8 At / Gh_M240 (5), Gh_M315 (9)
4 At / Gh_TM1 (2), Gh_TM1 (3), Gh_Sisoline (3), Gh_ST213 (2), Gh_M8 (2), Gh_REDM (2), Gh_REDM (8), Gh_Golib (4), Gh_Golib (5), Gh_Clevewilt (2), Gh_M240 (2), Gh_M315 (3), Gh_M315 (6), Gb_3-79 (5)
17 At / Gh_Clevewilt (3)
32 Dt / Gh_Clevewilt (12), Gb_3-79 (7), G. tomentosum (7), G. mustelinum (8)
35 Dt / Gb_3-79 (8)
29 Dt / Gh_TM1 (9), Gh_Sisoline (10), Gh_ST213 (9), Gh_M8 (10), Gh_M8 (11), Gh_REDM (12), Gh_Golib (13), Gh_Golib (14), Gh_Clevewilt (11), Gh_M240 (8), Gh_M315 (12)
30 Dt / Gh_ST213 (10)
39 Dt / G. mustelinum (11)
34 Dt / Gh_M315 (13)
37 Dt / G. tomentosum (8), G. mustelinum (10)
38 Dt / G. mustelinum (9)
42 A / G. herbaceum (1)
43 A / G. herbaceum (2)
44 A / G. herbaceum (3), G. herbaceum (5)
45 A / G. herbaceum (4)
52 F / G. longicalyx (5)
51 F / G. longicalyx (1), G. longicalyx (4), G. longicalyx (2)
53 F / G. longicalyx (3)
54 F / G. longicalyx (8)
50 F / G. longicalyx (10), G. longicalyx (11), G. longicalyx (6)
55F / G. longicalyx (9)