Supplementary Table 4 Ka/Ks ratio for homologous bHLH pairs in R. persica and R. chinensis Gene 1 Gene 2 Ka Ks Ka_Ks Selection Pressure Divergence time(Mya) Note XM_024306107.2 Rbe014420 0.007025813 0.012605339 0.557368005 Purifying 1.033224487 XM_024328554.2 Rbe008930 0.015129106 0.022772148 0.664368867 Purifying 1.866569492 XM_024336836.2 Rbe021771 0.016163451 0.026405367 0.612127481 Purifying 2.164374383 XM_024332706.2 Rbe027154 0.013883929 0.0268185 0.517699694 Purifying 2.198237679 XM_024337436.2 Rbe022458 0.078081397 0.027064792 2.884980454 positive selection 2.218425601 XM_024341578.2 Rbe020352 0.006281115 0.02722622 0.230700955 Purifying 2.231657378 XM_024310785.2 Rbe025541 0.019762362 0.028835844 0.685340165 Purifying 2.363593755 XM_024336328.2 Rbe020713 0.008658105 0.028849711 0.300110629 Purifying 2.364730379 XM_024311246.2 Rbe010620 0.017341813 0.033986397 0.510257471 Purifying 2.785770259 XM_024332787.2 Rbe026742 0.005202709 0.03416961 0.15226129 Purifying 2.800787724 XM_040509096.1 Rbe012920 0.008794746 0.034732196 0.253215944 Purifying 2.846901317 XM_040515252.1 Rbe006856 0.018162693 0.034890012 0.520569982 Purifying 2.859837027 XM_024328549.2 Rbe008998 0.010057815 0.035568543 0.282772752 Purifying 2.915454313 XM_024333665.2 Rbe022818 0.03240737 0.036053802 0.898861372 Purifying 2.955229701 XM_024317156.2 Rbe016021 0.01305516 0.036704572 0.35568212 Purifying 3.008571457 XM_024343223.2 Rbe002857 0.018372015 0.03739092 0.49134963 Purifying 3.064829522 XM_024316767.2 Rbe025614 0.011162997 0.03834701 0.291104751 Purifying 3.143197532 XM_024341742.2 Rbe022459 0.010556121 0.038868801 0.271583392 Purifying 3.185967287 XM_024321093.2 Rbe024626 0.012591416 0.039160607 0.321532696 Purifying 3.209885859 XM_024302272.2 Rbe000884 0.012151286 0.039942883 0.304216543 Purifying 3.274006763 XM_024318022.2 Rbe015680 0.008703859 0.040903737 0.212788847 Purifying 3.3527653 XM_040508285.1 Rbe011770 0.027787947 0.041042895 0.677046473 Purifying 3.364171696 XM_024333979.2 Rbe026922 0.010252189 0.041043675 0.2497873 Purifying 3.364235637 XM_024324483.2 Rbe024953 0.014705066 0.041170298 0.357176583 Purifying 3.374614569 XM_024312639.2 Rbe013927 0.014873832 0.041688529 0.356784757 Purifying 3.417092529 XM_024336703.2 Rbe021366 0.021272634 0.041859162 0.508195402 Purifying 3.431078892 XM_024305079.2 Rbe001952 0.005350477 0.043177389 0.123918505 Purifying 3.539130235 XM_024302789.2 Rbe003122 0.008381146 0.043549647 0.192450377 Purifying 3.569643208 XM_024339411.2 Rbe022586 0.009062932 0.044011648 0.205921218 Purifying 3.607512113 XM_024340555.2 Rbe021951 0.0116797 0.045109422 0.25891929 Purifying 3.697493642 XM_024326963.2 Rbe010374 0.019394308 0.046038486 0.421262938 Purifying 3.773646369 XM_024334069.2 Rbe028654 0.012760232 0.046247525 0.275911675 Purifying 3.790780765 XM_024329479.2 Rbe008431 0.021566766 0.046662276 0.462188464 Purifying 3.824776761 XM_024311436.2 Rbe014571 0.010002649 0.047302731 0.211460284 Purifying 3.877273014 XM_024337309.2 Rbe019184 0.009607818 0.04777055 0.201124283 Purifying 3.915618814 XM_040518341.1 Rbe020205 0.017771087 0.047856763 0.371339104 Purifying 3.922685468 XM_024327451.2 Rbe007602 0.015417276 0.047934165 0.3216344 Purifying 3.929029928 XM_024309444.2 Rbe010573 0.006417838 0.048421653 0.13254066 Purifying 3.968987955 XM_024333868.2 Rbe027429 0.015420872 0.048702053 0.316636991 Purifying 3.991971565 XM_024343809.2 Rbe000672 0.020435492 0.048731616 0.419347706 Purifying 3.99439479 XM_024330812.2 Rbe029307 0.01644311 0.048753623 0.337269501 Purifying 3.996198585 XM_024325189.2 Rbe006451 0.015852638 0.050555121 0.313571352 Purifying 4.143862397 XM_024319328.2 Rbe018502 0.023327556 0.050732489 0.459814937 Purifying 4.158400759 XM_024322240.2 Rbe006811 0.025457632 0.051145801 0.497746283 Purifying 4.192278759 XM_024332325.2 Rbe027485 0.019053296 0.051464227 0.370224081 Purifying 4.218379292 XM_024320463.2 Rbe024859 0.007086806 0.052959632 0.133815249 Purifying 4.340953474 XM_024308550.2 Rbe012246 0.011474327 0.053288101 0.21532626 Purifying 4.367877093 XM_040516620.1 Rbe027240 0.01900351 0.053499554 0.355208767 Purifying 4.385209304 XM_024335541.2 Rbe027679 0.023455647 0.053763791 0.436272199 Purifying 4.406868127 XM_024306782.2 Rbe012577 0.015506483 0.054127528 0.286480534 Purifying 4.436682597 XM_024330271.2 Rbe008304 0.008854013 0.055070601 0.160775678 Purifying 4.513983723 XM_024319127.2 Rbe015526 0.01584525 0.055145068 0.287337564 Purifying 4.520087545 XM_024308132.1 Rbe011016 0.031213867 0.055839734 0.558990265 Purifying 4.577027348 XM_024344182.2 Rbe001132 0.018003115 0.056603939 0.318054096 Purifying 4.639667134 XM_024309854.2 Rbe026132 0.013232099 0.056707162 0.233340887 Purifying 4.648128018 XM_024327198.2 Rbe005607 0.023262509 0.056966874 0.408351501 Purifying 4.669415917 XM_024309406.2 Rbe012948 0.011200668 0.057604058 0.194442336 Purifying 4.721644133 XM_024344324.1 Rbe001485 0.025439232 0.058579949 0.434265181 Purifying 4.801635163 XM_024326836.2 Rbe005410 0.009345915 0.058757604 0.159058823 Purifying 4.816197044 XM_024318505.2 Rbe016304 0.012832371 0.058901883 0.217860108 Purifying 4.828023234 XM_024313524.2 Rbe017052 0.017903076 0.060078294 0.297995751 Purifying 4.924450345 XM_024322438.2 Rbe007282 0.02065535 0.060152464 0.343383275 Purifying 4.930529862 XM_024335936.2 Rbe021855 0.00980306 0.060573445 0.161837583 Purifying 4.965036507 XM_024338960.2 Rbe019113 0.041428793 0.061189071 0.677061968 Purifying 5.015497605 XM_024315314.2 Rbe018329 0.013893481 0.061235355 0.226886592 Purifying 5.019291386 XM_040518407.1 Rbe021927 0.018602537 0.061345966 0.30323977 Purifying 5.028357904 XM_024323924.2 Rbe006703 0.011722805 0.061460331 0.190737741 Purifying 5.037732013 XM_024310575.2 Rbe012987 0.003009786 0.063607781 0.047317887 Purifying 5.213752562 XM_024319099.2 Rbe015059 0.014367395 0.063664925 0.225672069 Purifying 5.218436479 XM_024307663.2 Rbe013100 0.006276844 0.064288039 0.097636263 Purifying 5.269511363 XM_024312482.2 Rbe011416 0.017281578 0.064781598 0.266766771 Purifying 5.30996708 XM_024318241.2 Rbe015433 0.011937581 0.065065408 0.183470471 Purifying 5.333230163 XM_024305096.2 Rbe000328 0.025191285 0.065072165 0.387128429 Purifying 5.33378401 XM_040518600.1 Rbe022417 0.016883349 0.065276293 0.25864442 Purifying 5.350515841 XM_024343217.2 Rbe002214 0.007512976 0.066158569 0.113560129 Purifying 5.422833512 XM_024314239.2 Rbe015211 0.027216442 0.066594846 0.40868691 Purifying 5.458593941 XM_024331913.2 Rbe029018 0.015412821 0.068035285 0.226541578 Purifying 5.576662727 XM_040507593.1 Rbe010806 0.039240662 0.068834103 0.570075875 Purifying 5.642139598 XM_024327269.2 Rbe006721 0.008728641 0.069426632 0.125724677 Purifying 5.690707541 XM_024339179.2 Rbe019633 0.011267818 0.069574765 0.161952651 Purifying 5.702849554 XM_024342781.2 Rbe002180 0.009634817 0.069960384 0.137718188 Purifying 5.734457743 XM_024341645.2 Rbe019722 0.056309622 0.070335103 0.800590593 Purifying 5.765172401 XM_024317387.2 Rbe015492 0.018391299 0.070867045 0.259518358 Purifying 5.808774155 XM_024341681.2 Rbe021137 0.010173096 0.072272524 0.140760213 Purifying 5.923977405 XM_024317704.2 Rbe015125 0.021184109 0.07300592 0.290169744 Purifying 5.984091792 XM_024306241.2 Rbe013116 0.028442883 0.076922483 0.369760338 Purifying 6.30512158 XM_024302116.2 Rbe000306 0.012448419 0.077296068 0.161048536 Purifying 6.335743268 XM_024313218.2 Rbe025884 0.018258163 0.077681312 0.235039325 Purifying 6.367320628 XM_024305963.2 Rbe014518 0.011309233 0.077964109 0.145056916 Purifying 6.390500726 XM_024312799.2 Rbe018074 0.015805656 0.080344306 0.196724031 Purifying 6.585598843 XM_024313408.2 Rbe017029 0.013003814 0.081280795 0.15998631 Purifying 6.662360257 XM_024330079.2 Rbe005993 0.02079856 0.081647914 0.254734736 Purifying 6.692451973 XM_024302075.2 Rbe004623 0.021904286 0.082358551 0.265962502 Purifying 6.750700899 XM_040518927.1 Rbe020549 0.031210645 0.084041385 0.371372335 Purifying 6.888638129 XM_024331546.2 Rbe024265 0.027174249 0.086252318 0.315055285 Purifying 7.069862099 XM_024309278.2 Rbe014436 0.022835682 0.08680864 0.263057714 Purifying 7.115462275 XM_024304114.2 Rbe000519 0.036606876 0.087217595 0.419718938 Purifying 7.148983198 XM_024330536.2 Rbe006436 0.008665608 0.087416918 0.09912964 Purifying 7.165321172 XM_024313069.2 Rbe015668 0.004900977 0.087883889 0.055766503 Purifying 7.203597482 XM_024317001.2 Rbe018593 0.016843722 0.088543349 0.190231368 Purifying 7.257651558 XM_040512220.1 Rbe016467 0.047871104 0.089388551 0.53553954 Purifying 7.326930415 XM_024317294.2 Rbe015313 0.02553376 0.09043743 0.282336197 Purifying 7.412904102 XM_024314197.2 Rbe018547 0.040542111 0.09148382 0.443161543 Purifying 7.498673784 XM_040515665.1 Rbe005790 0.027587732 0.095868301 0.287766984 Purifying 7.858057429 XM_040507371.1 Rbe023794 0.012271216 0.096379387 0.127321999 Purifying 7.89994974 XM_024329807.2 Rbe009686 0.021540632 0.098162246 0.219439076 Purifying 8.046085728 XM_040508637.1 Rbe014435 0.038914311 0.100746132 0.386261087 Purifying 8.257879706 XM_024339088.2 Rbe020251 0.027362816 0.103450091 0.26450258 Purifying 8.479515616 XM_024320582.2 Rbe024914 0.014448487 0.103528817 0.139560047 Purifying 8.485968578 XM_024333230.2 Rbe028663 0.041581655 0.106592226 0.390100258 Purifying 8.737067705 XM_024311287.2 Rbe010899 0.031364821 0.108541192 0.288966987 Purifying 8.896819029 XM_024316015.2 Rbe017177 0.060465559 0.110397061 0.547709865 Purifying 9.048939396 XM_024308246.2 Rbe012735 0.052491902 0.112380723 0.467089914 Purifying 9.211534703 XM_024328156.2 Rbe005022 0.014890146 0.114640486 0.12988558 Purifying 9.396761173 XM_024323241.1 Rbe009442 0.043456685 0.118636653 0.366300662 Purifying 9.724315847 XM_024300671.2 Rbe003379 0.049655483 0.126957926 0.391117631 Purifying 10.40638734 XM_024344358.1 Rbe001526 0.068127627 0.130209922 0.523213791 Purifying 10.6729444 XM_024321132.2 Rbe025271 0.006133436 0.13409468 0.04573959 Purifying 10.99136718 XM_024341761.2 Rbe022526 0.062989563 0.138928478 0.45339562 Purifying 11.38758017 XM_024341021.2 Rbe019948 0.059499654 0.146413981 0.406379593 Purifying 12.00114602 XM_024324389.2 Rbe008584 0.077186573 0.188161707 0.410214033 Purifying 15.42309075 XM_024325286.2 Rbe023094 0.080634034 0.203997589 0.395269545 Purifying 16.72111384 XM_024339076.2 Rbe019992 0.116314797 0.228233928 0.509629739 Purifying 18.70769902 XM_024343217.2 Rbe000306 0.248835603 1.026731184 0.24235711 Purifying 84.15829377 XM_024302116.2 Rbe002214 0.221980875 1.102963126 0.201258655 Purifying 90.40681359 XM_024318022.2 Rbe021366 0.369085153 1.27881262 0.288615507 Purifying 104.8207066 XM_024319099.2 Rbe022526 0.24470105 1.334394298 0.183379868 Purifying 109.3765818 XM_024318505.2 Rbe024626 0.358274645 1.349359225 0.265514652 Purifying 110.6032152 XM_024335450.2 Rbe025271 0.137661978 1.352106979 0.101812934 Purifying 110.8284409 XM_024316767.2 Rbe027429 0.233960885 1.394174079 0.167813251 Purifying 114.2765639 XM_024309278.2 Rbe006451 0.489307317 1.407351406 0.34767956 Purifying 115.3566726 XM_024336836.2 Rbe015433 0.409607621 1.430948176 0.286249096 Purifying 117.2908341 XM_024317294.2 Rbe009686 0.429744967 1.469251694 0.292492409 Purifying 120.4304667 XM_024327269.2 Rbe018329 0.296051955 1.479316519 0.200127526 Purifying 121.2554524 XM_024318241.2 Rbe021771 0.433628185 1.527086623 0.283957818 Purifying 125.1710346 XM_024319328.2 Rbe006811 0.658385684 1.582994597 0.415911517 Purifying 129.7536555 XM_040515252.1 Rbe018593 0.368619064 1.592512259 0.231470158 Purifying 130.5337917 XM_024341681.2 Rbe027154 0.415789213 1.635313094 0.25425664 Purifying 134.0420569 XM_040507593.1 Rbe014518 0.49395285 1.657192121 0.298066134 Purifying 135.8354198 XM_024333868.2 Rbe025614 0.236715944 1.667803608 0.141932745 Purifying 136.7052138 XM_024322240.2 Rbe018502 0.596398551 1.694354925 0.351991511 Purifying 138.8815513 XM_024342781.2 Rbe000328 0.404677341 1.7208731 0.235158154 Purifying 141.0551721 XM_024341761.2 Rbe015059 0.315166038 1.721013363 0.183128176 Purifying 141.0666691 XM_024315314.2 Rbe006721 0.280963507 1.748880338 0.160653362 Purifying 143.3508474 XM_024305096.2 Rbe002180 0.388697573 1.786215618 0.217609548 Purifying 146.4111162 XM_024340555.2 Rbe015313 0.436611658 1.789972492 0.243920876 Purifying 146.7190567 XM_024340555.2 Rbe009686 0.402247853 1.867471065 0.215397101 Purifying 153.0713988 XM_024317294.2 Rbe021951 0.385611454 1.89651542 0.203326295 Purifying 155.4520836 XM_024306107.2 Rbe006436 0.336223928 1.954218616 0.172050315 Purifying 160.1818538 XM_024325189.2 Rbe014436 0.512751327 2.002583875 0.25604487 Purifying 164.1462193 XM_040508637.1 Rbe011016 0.45458159 2.072479985 0.219341848 Purifying 169.8754086 XM_024304496.2 Rbe025614 0.299064673 2.07340772 0.144238236 Purifying 169.9514525 XM_024313069.2 Rbe010374 0.3548479 2.138659961 0.165920673 Purifying 175.2999968 XM_024305963.2 Rbe010806 0.563370388 2.193361394 0.256852514 Purifying 179.7837208 XM_024326963.2 Rbe015668 0.358576298 2.339179618 0.153291477 Purifying 191.7360343 XM_024317001.2 Rbe006856 0.38267478 2.346146185 0.163107816 Purifying 192.3070644 XM_024332787.2 Rbe012987 0.220031594 2.34876196 0.093679819 Purifying 192.5214721 XM_024310575.2 Rbe026742 0.224102009 2.376199368 0.094311114 Purifying 194.77044 XM_024321943.1 Rbe008584 0.524272346 2.431227307 0.215641024 Purifying 199.2809268 XM_024334069.2 Rbe022818 0.433112092 2.553313497 0.169627464 Purifying 209.2879916 XM_024336328.2 Rbe026922 0.538264346 2.574808585 0.209050237 Purifying 211.049884 XM_024302186.2 Rbe025271 0.071825179 2.675033865 0.026850194 Purifying 219.2650709 XM_024313218.2 Rbe016467 0.48738366 2.728609435 0.178619796 Purifying 223.6565111 XM_024333665.2 Rbe028654 0.463441448 2.792050376 0.165986062 Purifying 228.8565882 XM_024304114.2 Rbe007602 0.496025025 2.884412402 0.171967443 Purifying 236.4272461 XM_024330536.2 Rbe014420 0.33184172 2.912361438 0.113942492 Purifying 238.7181507 XM_024333979.2 Rbe020713 0.606540203 3.352247112 0.180935409 Purifying 274.7743535 XM_024327451.2 Rbe000519 0.474843155 NaN NaN NaN NaN High Sequence Divergence Value (pS>=0.75) XM_024320582.2 Rbe015526 0.434607442 NaN NaN NaN NaN High Sequence Divergence Value (pS>=0.75) XM_024319127.2 Rbe024914 0.44186011 NaN NaN NaN NaN High Sequence Divergence Value (pS>=0.75) XM_040512220.1 Rbe025884 0.502616432 NaN NaN NaN NaN High Sequence Divergence Value (pS>=0.75) XM_024336703.2 Rbe015680 0.456393755 NaN NaN NaN NaN High Sequence Divergence Value (pS>=0.75)