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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) Ka Ks Ka/Ks Negative/purifying selection P-Value (Fisher)
A B
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
  1. 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