Supplementary Table 1Mungbean putative flowering-related homologous genes of Arabidopsis thaliana genes that are involved in the control of flowering time
Pathway / Arabidopsis thaliana identity / Arabidopsis thaliana gene / Vignaradiata homologous gene model IDAu / AT1G03970 / GBF4 / Vradi0048s00750
Au / AT1G62830 / LDL1 (LSD1-LIKE1) / Vradi01g04440
Au / AT2G16780 / MSI2 (MULTICOPY SUPPRESSOR OF IRA1 2) / Vradi02g02900
Au / AT2G18876 / VEL3; At2g18870 / Vradi07g22250
Au / AT2G23380 / CLF (CURLY LEAF) / Vradi11g04630
Au / AT2G43410 / FPA / Vradi0332s00160
Au / AT3G04610 / FLK (flowering locus KH domain) / Vradi0443s00060
Au / AT3G10390 / FLD (FLOWERING LOCUS D) / Vradi08g02950
Au / AT3G13682 / LDL2 (LSD1-LIKE2) / Vradi02g11130
Au / AT4G02560 / LD (luminidependens) / Vradi03g05800
Au / AT5G13480 / FY / Vradi0198s00050
Au, Am / AT2G19520 / FVE / Vradi05g20970
Au, Am / AT4G16280 / FCA / Vradi07g24500
FPI / AT1G18100 / E12A11 / Vradi01g02350
FPI / AT1G26480 / GRF12 (GENERAL REGULATORY FACTOR 12) / Vradi0100s00470
FPI / AT1G34760 / GRF11 (GENERAL REGULATORY FACTOR 11) / Vradi0161s00340
FPI / AT1G35160 / GRF4; GF14 PHI (GF14 PROTEIN PHI CHAIN) / Vradi0187s00040
FPI / AT1G54830 / NF-YC3 (NUCLEAR FACTOR Y, SUBUNIT C3) / Vradi10g04910
FPI / AT1G56170 / HAP5B; NF-YC2 (NUCLEAR FACTOR Y, SUBUNIT C2) / Vradi05g18850
FPI / AT1G78300 / GRF2 (GENERAL REGULATORY FACTOR 2) / Vradi05g07320
FPI / AT2G13570 / NF-YB7 (NUCLEAR FACTOR Y, SUBUNIT B7) / Vradi0361s00030
FPI / AT2G38880 / HAP3A; NF-YB1 (NUCLEAR FACTOR Y, SUBUNIT B1) / Vradi08g15530
FPI / AT3G02520 / GRF7 (GENERAL REGULATORY FACTOR 7) / Vradi04g11330
FPI / AT3G48590 / HAP5A; NF-YC1 (NUCLEAR FACTOR Y, SUBUNIT C1) / Vradi05g05520
FPI / AT5G16260 / ELF9; RNA recognition motif (RRM)-containing protein / Vradi08g13920
FPI, MI / AT5G61850 / LFY (LEAFY) / Vradi0456s00020
G / AT3G04240 / SEC (secret agent) / Vradi08g13750
G / AT3G11540 / SPY (SPINDLY) / Vradi03g04810
L / AT1G01060 / LHY (LATE ELONGATED HYPOCOTYL) / Vradi05g00310
L / AT1G04400 / CRY2 (CRYPTOCHROME 2) / Vradi08g00630
L / AT1G09530 / PIF3 (PHYTOCHROME INTERACTING FACTOR 3) / Vradi08g11790
L / AT1G22770 / GI (GIGANTEA) / Vradi01g11760
L / AT1G25540 / PFT1 (PHYTOCHROME AND FLOWERING TIME 1) / Vradi11g12880
L / AT1G26790 / AT1G26790; Dof-type zinc finger domain-containing protein / Vradi11g10430
L / AT1G53090 / SPA4 (SPA1-RELATED 4) / Vradi0303s00040
L / AT1G68050 / FKF1 (FLAVIN-BINDING, KELCH REPEAT, F BOX 1) / Vradi07g28150
L / AT1G68840 / TEM2; RAV2 (REGULATOR OF THE ATPASE OF THE VACUOLAR MEMBRANE) / Vradi11g12920
L / AT1G72630 / ELF4-L2 (ELF4-Like 2) / Vradi05g02120
L / AT2G18790 / PHYB (PHYTOCHROME B) / Vradi0083s00610
L / AT2G18915 / LKP2 (LOV KELCH PROTEIN 2) / Vradi0264s00190
L / AT2G22630 / AGL17 (agamous-like 17) / Vradi06g08210
L / AT2G23070 / AT2G23070; casein kinase II alpha chain, putative / Vradi07g11180
L / AT2G23080 / AT2G23080; casein kinase II alpha chain, putative / Vradi11g04230
L / AT2G24790 / COL3 (CONSTANS-LIKE 3) / Vradi05g11170
L / AT2G25920 / AT2G25920 / Vradi08g10610
L / AT2G29950 / ELF4-L1 (ELF4-Like 1) [Arabidopsis thaliana] / Vradi06g08660
L / AT2G32950 / COP1 (CONSTITUTIVE PHOTOMORPHOGENIC 1) / Vradi06g03720
L / AT2G34140 / AT2G34140 / Vradi0161s00220
L / AT2G40080 / ELF4 / Vradi06g04530
L / AT2G46340 / SPA1 (SUPPRESSOR OF PHYA-105 1) / Vradi11g01760
L / AT2G46830 / CCA1 (CIRCADIAN CLOCK ASSOCIATED 1) / Vradi0215s00270
L / AT2G47700 / RFI2 zinc finger (C3HC4-type RING finger) family protein / Vradi10g04650
L / AT3G02380 / COL2 (constans-like 2) / Vradi01g07820
L / AT3G07650 / COL9 (CONSTANS-LIKE 9) / Vradi06g07140
L / AT3G15354 / SPA3 (SPA1-RELATED 3) / Vradi02g10310
L / AT3G15620 / UVR3 (UV REPAIR DEFECTIVE 3) / Vradi09g00930
L / AT3G21320 / AT3G21320 / Vradi09g01790
L / AT3G25730 / AT3G25730 / Vradi08g23210
L / AT3G46640 / LUX; PCL1 (PHYTOCLOCK 1) / Vradi02g04720
L / AT3G47500 / CDF3 (CYCLING DOF FACTOR 3) / Vradi07g17090
L / AT4G08920 / CRY1 (CRYPTOCHROME 1) / Vradi05g07190
L / AT4G34530 / CIB1 (CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1) / Vradi05g14840
L / AT5G23280 / AT5G23280 / Vradi08g22260
L / AT5G24470 / APRR5 (ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 5) / Vradi0106s00110
L / AT5G39660 / CDF2 (CYCLING DOF FACTOR 2) / Vradi04g08830
L / AT5G57660 / ATCOL5; zinc finger (B-box type) family protein / Vradi07g21950
L / AT5G60100 / APRR3 (ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 3) / Vradi02g05440
L / AT5G61380 / TOC1 (TIMING OF CAB EXPRESSION 1) / Vradi07g17180
L / AT5G62430 / CDF1 (CYCLING DOF FACTOR 1) / Vradi03g09010
L / AT5G67380 / CKA1 (CASEIN KINASE ALPHA 1) / Vradi07g11090
L, Am / AT2G25930 / ELF3 (EARLY FLOWERING 3) / Vradi06g14260
L, Am / AT2G46790 / APRR9 (ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 9) / Vradi0179s00390
MI / AT1G26310 / CAL (CAULIFLOWER) / Vradi0189s00040
MI / AT1G30950 / UFO (UNUSUAL FLORAL ORGANS) / Vradi07g09760
MI / AT1G62360 / STM (SHOOT MERISTEMLESS) / Vradi10g07810
MI / AT2G17950 / WUS (WUSCHEL) / Vradi11g06340
MI / AT2G33810 / SPL3 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3) / Vradi02g10650
MI / AT2G42830 / SHP2 (SHATTERPROOF 2) / Vradi10g02120
MI / AT3G54340 / AP3 (APETALA 3) / Vradi05g13630
MI / AT4G09960 / STK (SEEDSTICK) / Vradi0368s00040
MI / AT4G18960 / AG (AGAMOUS) / Vradi10g09690
MI / AT5G17690 / LHP1; TFL2 (TERMINAL FLOWER 2) / Vradi05g15770
MI / AT5G23150 / HUA2 (ENHANCER OF AG-4 2) / Vradi0134s00350
MI / AT5G62040 / BFT (Brother of FT and TFL1 protein / Vradi01g14660
V / AT1G30970 / SUF4 (suppressor of FRIGIDA4) / Vradi01g02160
V / AT1G31814 / FRL2 / Vradi06g01210
V / AT1G77300 / EFS (EARLY FLOWERING IN SHORT DAYS) / Vradi05g06220
V / AT2G33835 / FES1 / Vradi10g10700
V / AT3G12810 / PIE1 (PHOTOPERIOD-INDEPENDENT EARLY FLOWERING 1) / Vradi08g01900
V / AT3G18990 / VRN1 (REDUCED VERNALIZATION RESPONSE 1) / Vradi11g11310
V / AT3G24440 / VRN5 (VERNALIZATION 5) / Vradi01g04290
V / AT3G33520 / ATARP6 / Vradi07g05730
V / AT3G48430 / REF6 (RELATIVE OF EARLY FLOWERING 6) / Vradi07g14630
V / AT4G00650 / FRI (FRIGIDA) / Vradi05g05800
V / AT4G11880 / AGL14 (agamous-like 14) / Vradi07g13200
V / AT4G24540 / AGL24; MADS-box protein AGL24 / Vradi11g09420
V / AT4G26000 / PEP (PEPPER) / Vradi07g22590
V / AT4G30200 / VEL1 (vernalization-like 1) / Vradi07g22290
V / AT5G08230 / AT5G08230 / Vradi02g02330
V / AT5G10140 / FLC (FLOWERING LOCUS C) / Vradi0190s00250
V / AT5G37055 / ATSWC6; SEF (SERRATED LEAVES AND EARLY FLOWERING) / Vradi04g05250
V / AT5G57380 / VIN3; protein VERNALIZATION INSENSITIVE 3 / Vradi0180s00170
V / AT5G61150 / VIP4 (VERNALIZATION INDEPENDENCE 4) / Vradi03g09530
V, Am / AT1G77080 / MAF1 (MADS AFFECTING FLOWERING 1) / Vradi0122s00370, Vradi08g02530
- / AT1G49720 / ABF1 (ABSCISIC ACID RESPONSIVE ELEMENT-BINDING FACTOR 1) / Vradi07g03990
- / AT2G17770 / ATBZIP27 / Vradi11g06620
- / AT2G28550 / TOE1; RAP2.7 (RELATED TO AP2.7) / Vradi03g03260
- / AT2G35670 / FIS2 (FERTILIZATION INDEPENDENT SEED 2) / Vradi11g03240
- / AT2G36270 / ABI5 (ABA INSENSITIVE 5) / Vradi03g04520
- / AT2G41070 / EEL (ENHANCED EM LEVEL) / Vradi01g08230
- / AT2G45650 / AGL6 (AGAMOUS-LIKE 6) / Vradi0194s00260
- / AT3G06910 / ULP1A (UB-LIKE PROTEASE 1A) / Vradi05g01000
- / AT3G20740 / FIE1 (FERTILIZATION-INDEPENDENT ENDOSPERM) / Vradi09g01080
- / AT3G44460 / DPBF2 / Vradi04g03630
- / AT4G29830 / VIP3 (vernalization independence 3) / Vradi07g23130
- / AT4G31380 / FLP1 (FPF1-LIKE PROTEIN 1) / Vradi05g09570
- / AT4G32720 / AtLa1 (Arabidopsis thaliana La protein 1) / Vradi06g12060
- / AT5G04240 / ELF6 (EARLY FLOWERING 6) / Vradi08g16780
- / AT5G11530 / EMF1 (embryonic flower 1) / Vradi05g08940
- / AT5G27220 / AT5G27220 / Vradi07g10960
- / AT5G42910 / AT5G42910; abscisic acid-insensitive 5-like protein 8 / Vradi05g12670
- / AT5G51230 / EMF2 (EMBRYONIC FLOWER 2) / Vradi08g03650
- / AT5G62640 / ELF5; proline-rich family protein / Vradi07g15250
- / AT5G67180 / TOE3 / Vradi11g04600
Supplementary Table 2Mungbeanflowering-related genes exhibiting nonsynonymous substitutions between wild and domesticated mungbean
Pathway / Arabidopsis thaliana identity / Arabidopsis thaliana gene / Vignaradiata homologous gene model IDAu / AT1G03970.1 / GBF4 (G-box binding bZip transcription factor ) / Vradi0048s00750
Au / AT1G62830.1 / LDL1 (LSD1-LIKE1) / Vradi01g04440
Au / AT2G43410.4 / FPA / Vradi0332s00160
Au / AT4G02560.2 / LD (luminidependens) / Vradi03g05800
Au / AT3G04610.1 / FLK (flowering locus KH domain) / Vradi0443s00060
Au / AT3G10390.1 / FLD (FLOWERING LOCUS D) / Vradi08g02950
Au, Am / AT2G19520.1 / FVE / Vradi05g20970
Au, Am / AT4G16280.4 / FCA / Vradi07g24500
FPI / AT1G78300.1 / GRF2 (GENERAL REGULATORY FACTOR 2) / Vradi0187s00040
FPI / AT1G18100.1 / E12A11 / Vradi01g02350
FPI / AT1G65480.1 / FT (FLOWERING LOCUS T) / Vradi01g09590
FPI / AT4G14540.1 / NF-YB3 (NUCLEAR FACTOR Y, SUBUNIT B3) / Vradi0361s00030
FPI / AT3G48590.1 / HAP5A; NF-YC1 (NUCLEAR FACTOR Y, SUBUNIT C1) / Vradi05g05520
FPI / AT5G16260.1 / ELF9; RNA recognition motif (RRM)-containing protein / Vradi08g13920
FPI / AT2G37060.3 / NF-YB8 (NUCLEAR FACTOR Y, SUBUNIT B8) / Vradi08g15530
FPI / AT1G08970.4 / HAP5C; NF-YC9 (NUCLEAR FACTOR Y, SUBUNIT C9) / Vradi10g04910
G / AT3G04240.1 / SEC (secret agent) / Vradi08g13750
L / AT2G18790.1 / PHYB (PHYTOCHROME B) / Vradi0083s00610
L / AT2G46670.1 / AT2G46670 / Vradi0179s00390
L / AT3G02380.1 / COL2 (constans-like 2) / Vradi01g07820
L / AT5G57360.1 / ZTL (ZEITLUPE) / Vradi0264s00190
L / AT3G15354.1 / SPA3 (SPA1-RELATED 3) / Vradi02g10310
L / AT3G15354.1 / SPA3 (SPA1-RELATED 3) / Vradi0303s00040
L / AT3G47500.1 / CDF3 (CYCLING DOF FACTOR 3) / Vradi03g09010
L / AT1G01060.5 / LHY (LATE ELONGATED HYPOCOTYL) / Vradi05g00310
L / AT4G08920.1 / CRY1 (CRYPTOCHROME 1) / Vradi05g07190
L / AT5G24930.1 / ATCOL4; zinc finger (B-box type) family protein / Vradi05g11170
L / AT4G34530.1 / CIB1 (CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1) / Vradi05g14840
L / AT2G32950.1 / COP1 (CONSTITUTIVE PHOTOMORPHOGENIC 1) / Vradi06g03720
L / AT2G40080.1 / ELF4 / Vradi06g04530
L / AT2G22630.1 / AGL17 (agamous-like 17) / Vradi06g08210
L / AT2G29950.1 / ELF4-L1 (ELF4-Like 1) / Vradi06g08660
L / AT5G67380.1 / CKA1 (CASEIN KINASE ALPHA 1) / Vradi07g11090
L / AT5G61380.1 / TOC1 (TIMING OF CAB EXPRESSION 1) / Vradi07g17180
L / AT1G68050.1 / FKF1 (FLAVIN-BINDING, KELCH REPEAT, F BOX 1) / Vradi07g28150
L / AT1G04400.2 / CRY2 (CRYPTOCHROME 2) / Vradi08g00630
L / AT2G25920.1 / AT2G25920 / Vradi08g10610
L / AT1G09530.2 / PIF3 (PHYTOCHROME INTERACTING FACTOR 3) / Vradi08g11790
L / AT1G09570.1 / PHYA (PHYTOCHROME A) / Vradi08g11890
L / AT3G15620.1 / UVR3 (UV REPAIR DEFECTIVE 3) / Vradi09g00930
L / AT3G21320.1 / AT3G21320 / Vradi09g01790
L / AT4G11110.1 / SPA2 (SPA1-RELATED 2) / Vradi11g01760
L / AT1G25540.1 / PFT1 (PHYTOCHROME AND FLOWERING TIME 1) / Vradi11g12880
L / AT1G25560.1 / TEM1 (TEMPRANILLO 1) / Vradi11g12920
MI / AT5G23150.1 / PI (PISTILLATA) / Vradi0134s00350
MI / AT5G15800.1 / SEP1 (SEPALLATA1) / Vradi0189s00030
MI / AT5G17690.1 / LHP1; TFL2 (TERMINAL FLOWER 2) / Vradi05g15770
MI / AT3G57390.1 / AGL18 / Vradi08g02530
MI / AT3G58780.1 / SHP1 (SHATTERPROOF 1) / Vradi10g02120
MI / AT4G36920.2 / AP2 (APETALA 2) / Vradi11g04600
MI / AT4G35900.1 / FD / Vradi11g06620
V / AT4G30200.3 / VEL1 (vernalization5/VIN3-like protein) / Vradi0180s00170
V / AT5G61150.2 / VIP4 (VERNALIZATION INDEPENDENCE 4) / Vradi03g09530
V / AT5G37055.1 / ATSWC6; SEF (SERRATED LEAVES AND EARLY FLOWERING) / Vradi04g05250
V / AT4G00650.1 / FRI (FRIGIDA) / Vradi05g05800
V / AT1G31814.1 / FRL2 / Vradi06g01210
V / AT3G33520.1 / ATARP6 / Vradi07g05730
V / AT4G22950.1 / AGL19 (AGAMOUS-LIKE 19) / Vradi07g13200
V / AT3G48430.1 / REF6 (RELATIVE OF EARLY FLOWERING 6) / Vradi07g14630
V / AT4G30200.3 / VEL1 (vernalization-like 1) / Vradi07g22290
V / AT4G26000.1 / PEP (PEPPER) / Vradi07g22590
V / AT3G12810.1 / PIE1 (PHOTOPERIOD-INDEPENDENT EARLY FLOWERING 1) / Vradi08g01900
V / AT3G18990.1 / VRN1 (REDUCED VERNALIZATION RESPONSE 1) / Vradi11g11310
- / AT3G56850.1 / AREB3 (ABA-RESPONSIVE ELEMENT BINDING PROTEIN 3) / Vradi01g08230
- / AT2G36290.1 / AT2G36290.1 / Vradi03g04520
- / AT5G22460.2 / AT5G22460.2 / Vradi04g03630
- / AT4G15880.1 / ESD4 (EARLY IN SHORT DAYS 4) / Vradi05g01000
- / AT2G06210.1 / AT2G06210.1 / Vradi05g02090
- / AT4G32720.2 / ATLA1 (Arabidopsis thaliana La protein 1) / Vradi06g12060
- / AT5G62640.1 / ELF5; proline-rich family protein / Vradi07g15250
- / AT5G57410.1 / AT5G57410.1 / Vradi07g22250
- / AT5G51230.1 / EMF2 (EMBRYONIC FLOWER 2) / Vradi08g03650
- / AT5G04240.1 / ELF6 (EARLY FLOWERING 6) / Vradi08g16780
- / AT1G50680.1 / AT1G50680 / Vradi08g23210
- / AT1G52360.1 / AT1G52360.1 / Vradi09g01080
- / AT1G79730.1 / AT1G79730.1 / Vradi09g01560
- / AT3G05545.1 / AT3G05545.1 / Vradi10g04650
- / AT5G51230.1 / EMF2 (EMBRYONIC FLOWER 2) / Vradi11g03240
Supplementary Table 3Mungbean flowering-related paralogs and their orthologs of the Arabidopsis thalianagenes involved in flowering time
Synteny no. / Paralog 1 / Paralog 2 / Arabidopsis flowering-related gene / Ks value3 / Vradi01g07820.1 / Vradi04g09860.1 / Paralog 1: CO, COL1, COL2; Paralog 2: CCA1 / 0.6638517
165 / Vradi05g00310.1 / Vradi0215s00270.1 / Paralog 1: LHY / 0.64938
30 / Vradi01g09590.1 / Vradi0007s01810.1 / Paralog 1: FT, TSF, GmFT2a; Paralog 2: GmFT5a / 0.6882007
121 / Vradi04g09520.1 / Vradi0190s00250.1 / Paralog 2: FLC, SEP1,2,3,4 / 0.6734987
175 / Vradi06g01210.1 / Vradi10g02550.1 / Paralog 1: FRL2 / 0.6059818
203 / Vradi07g29690.1 / Vradi11g01760.1 / Paralog 2: SPA1, SPA2 / 0.684525
152 / Vradi05g20170.1 / Vradi09g01080.1 / Paralog 2: FIE / 0.6150035
63 / Vradi02g04000.1 / Vradi0332s00160.1 / Paralog 2: FPA / 0.6122039
202 / Vradi07g06270.1 / Vradi11g10430.1 / Paralog 2: Dof-type zinc figer dc / 0.6829713
88 / Vradi03g07220.1 / Vradi08g11790.1 / Paralog 2: PIF3 / 0.607824
139 / Vradi05g01000.1 / Vradi07g25190.1 / Paralog 1: ULP1A, ULP1B, ESD4 / 0.642472
193 / Vradi07g26830.1 / Vradi10g07810.1 / Paralog 2: STM / 0.6308083
127 / Vradi05g09040.1 / Vradi06g12060.1 / Paralog 2: AtLa1 / 0.6511153
144 / Vradi05g02680.1 / Vradi07g22590.1 / Paralog 2: PEP / 0.6495068
42 / Vradi02g03290.1 / Vradi05g14840.1 / Paralog 2: CIB1 / 0.6888623
88 / Vradi03g07170.1 / Vradi08g11890.1 / Paralog 2: GmPhA2, GmPhA3, PHYA / 0.607824
206 / Vradi07g11090.1 / Vradi11g04230.1 / Paralog 1: CKA1; Paralog 2: CKA2 / 0.6964741
206 / Vradi07g10680.1 / Vradi11g04600.1 / Paralog 2: TOE3, AP2 / 0.6964741