T10

1. T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 Figure S2 – Chromosomal rearrangements in the genomes of eggplant, pepper and Nicotiana with respect to the tomato genome. Genetic maps are modified from published work [9-11] with kind permission from Springer Science+Business Media. E1-12 represents the 12 eggplant chromosomes, P1-12 for pepper, and N1-12 for the MRCA of N. tomentosiformis and N. acuminata. Each tomato chromosome is assigned a different color (see color codes below) and the orthologous chromosome segment(s) in eggplant, pepper and Nicotiana are painted with the same color. Putative centromere positions of eggplant and pepper chromosomes are based on their synteny with tomato and indicated by a white dot. It was not possible to determine the centromere positions for the Nicotiana chromosomes due to complex syntenic relationships with tomato. An arrow beside a chromosome indicates an inversion relative to tomato. A black bar indicates the breakpoint region of a translocation, and the chromosome is divided into segments (a-c) accordingly to facilitate comparisons of multiple species. The marker pair used to define the breakpoint region of a translocation (i.e. the two adjacent markers mapped to different tomato chromosomes) or to define the borders of an inversion is highlighted in red. The map of the MRCA of N. tomentosiformis and N. acuminata is deduced based on the comparative maps of N. tomentosiformis,N. acuminata and tomato, and is not presented directly. The actual N. tomentosiformis map is presented, and the 4 inversions relative to its MRCA are indicated by dash arrows and the border markers are underlined.

2. Figure S2 (Wu and Tanksley) E1 E2 E3a, b, c E4a, b R45S TG479 CT197 C2At3g13235 0cM TG31 C2At4g18230 TG276 CAB3 5 CT196 C2At2g46340 10 CT31 TG165 15 TG301 U217183 C2At1g28530 C2At3g51510 T343 C2At3g56210 20 TG230 TG585 C2At5g51970 C2At5g45760 TG313 CT268 TG14 25 TG395 TG451 CT16 30 CD11 C2At1g14810 C2At2g34560 TG303 35 T1391 TG554 40 1+ TG520 CT277 CT209 45 C2At4g04955 TG596 CP116 50 CD15 C2At1g11380 T637 TG619 C2At3g06580 C2At1g11430 55 C2At1g60440 T525 CT244 TG379 CT62 TG386 60 C2At1g67700 C2At3g23590 T877 C2At1g23890 CD55 65 TG198 TG623 TG264 TG469 T564 C2At3g12630 70 TG62 C2At5g62390 C2At5g13700 CT188 CT232 TG564 75 T1241 ovate TG517 TG273 TG140 C2At5g23880 80 CT59 C2At1g72030 CT231 C2At1g09920 85 C2At5g67370 C2At1g51160 TG224 ORFX3 TG555 CT8 TG59 90 TG537 C2At5g17170 C2At4g00740 T708 T1480 C2At3g03100 TG460 TG345 95 CT9 CD51 C2At3g01480 TG129 TG607 100 CD39 C2At3g26900 CT90 TG83 C2At3g27310 C2At5g60160 105 C2At1g19340 CT274 C2At3g48330 CT24 110 TG457 CT173 TG442 CT267 115 C2At5g49970 C2At1g47830 TG528 T757 C2At5g08050 120 T1933 CT85 TG142 125 C2At1g18660 CT163 TG284 C2At5g09580 130 TG157 C2At1g16080 135 TG474 TG152 CT137 CT243 140 C2At3g18860 C2At1g79910 145 TG158 C2At3g13700 150 CT115 CT190 155 C2At3g20240 C2At3g14075

3. Figure S2 continued (Wu and Tanksley) E5a, b E6 E7 E8 C2At2g46580 TG436 CT52 C2At1g29320 0cM CT201 5 C2At2g39690 TG113 10 C2At2g18710 CT119 CT118 T42 15 C2At5g45680 CP52 20 CT172 CD14 C2At4g30580 CT241 25 30 TG351 C2At3g46780 C2At1g18480 CT187 CT216 35 C2At1g30360 C2At3g11210 CT228 40 CT77 TG178 21J7 TG41 45 CT51 TG349 TG513 50 C2At1g79790 C2At1g21640 C2At5g56940 GP130 55 TG185 CD57A CT138 T671 60 TG565 TG143 CT287 T1185 CT43 65 TG283 TG240 CT84 CT88 TG394 70 CT257 TG217 75 C2At5g47010 TG639 TG365 80 T801 C2At2g42750 GP89 85 CT204 C2At5g48300 C2At1g53670 TG510 90 95 TG292 TG216 TG162 CT148 TG438 100 CT146 TG468 CT195 CT265 CT193 105 C2At1g55870 CT156 C2At1g10580 CT109 C2At1g55670 C2At5g41350 CT276 110 C2At5g56130 C2At5g41270 C2At1g48300 CT223 C2At4g23840 115 CT206 CD61 CT252 C2At5g21170 C2At1g56050 120 C2At1g20050 T0463 TG473 TG642 125 CT68 T814 TG482 130 135 140 145 150 155

4. Figure S2 continued (Wu and Tanksley) E9 E10a1, b, a2, c E11a, b E12a, b T880 CP58 C2At1g30110 TG68 0cM CT283 CT182 TG10 C2At4g22260 5 CT143 C2At3g52640 TG9 10 C2At5g16630 CT167 C2At3g09920 TG523 15 TG18 T0408 20 CT79 TG194 TG254 CD64 25 TG508 C2At3g25690 C2At3g54840 CT211 1+ 30 C2At2g37240 C2At4g28830 C2At5g57970 C2At4g15010 CP44 35 CT19 cLET8K4 C2At2g37500 CD19 TG497 40 CT219 TG629 CT100 45 C2At5g64730 C2At4g03280 C2At5g58410 C2At1g33970 C2At3g62940 C2At4g11120 TG589 50 CT97 C2At3g63190 CT99 T0725 55 CD3 C2At4g18593 C2At1g05055 TG390 C2At1g64770 C2At4g39870 TG47 60 T431 C2At1g24340 CT157 TG35 CT242 65 GP180 TG400 C2At1g26945 C2At1g69420 70 TG348 C2At5g59960 C2At4g24830 TG393 TG248 75 C2At1g26520 TG49 CT177 GP28 CT74 80 CT217 TG280 C2At2g01770 C2At2g28490 85 C2At3g08760 T0529 TG26 C2At3g51010 CT240 TG421 90 TG233 CD49 TG46 TG424 TG63 95 CD32 T0635 100 GP101 TG241 C2At2g45620 105 T1648 TG328 CT124 CT175 CT107 CD72 TG339 110 CT20 C2At5g60600 T1065 115 T0703 TG36 120 C2At3g57270 TG483 125 TG420 130 TG370 TG285 Note: E10a1 and E10a2 correspond to consecutive segments on T5. It’s likely that an inversion(s) occurred in the eggplant genome to reshuffle them with E10b. Therefore E10a1 and E10a2 are combined into E10a.

5. Figure S2 continued (Wu and Tanksley) P4a, b P2 P3a, b, c P1a1, b1, a2, b2 C2At4g18230 R45S-A E492334 C2At1g16590 C2At1g63980 C2At5g44200 0cM Hba181H07SP6 CACCEL1i 5 C2At3g51140 T0156 TG135 C2At5g41350 C2At1g02140 C2At3g24050 10 C2At1g30540 C2At3g24010 C2At1g32900 15 C2At3g19800 T1519 cLPT5E7 TG294 C2At1g04530 C2At4g23840 20 Hpms1-143 C2At3g23400 C2At1g28530 25 C2At1g07310 C2At5g19130 C2At1g63260 30 MboI077E18SP6 35 C2At3g51510 TG132 C2At1g05385 C2At1g78690 C2At2g47580 40 C2At4g12230 CT232 BM059622 GP20031 45 TG510 C2At4g03200 C2At4g20410 C2At5g13200 C2At5g42740 50 C2At1g30360 C2At1g65720 C2At5g47010 TG517 C2At3g18860 55 C2At2g34560 C2At4g18593 Hpms1-165 C2At1g32410 CT128 60 C2At4g18060 C2At3g13180 BM067271 GPMS203 C2At1g64770 U223436 65 NN11 C2At4g19003 C2At4g21710 C2At5g62390 70 C2At1g77250 C2At2g35610 C2At1g10580 TG130 C2At3g45900 C2At3g63530 C2At4g04955 75 C2At2g45620 C2At5g23880 C2At1g11430 NN7 C2At1g51160 80 BD076366 C2At3g61140 85 C2At5g37260 ComT C2At4g00740 pun1 90 C2At5g51970 C2At1g71810 C2At5g17170 C2At4g35560 Hpms1-281 C2At3g03100 TG62 95 CP10081 C2At2g34860 C2At5g41040 C2At5g66090 C2At3g12685 CAN130829 100 C2At3g51130 Hpms1-41 C2At1g78230 105 Ovate C2At3g06790 BM061461 C2At4g37280 C2At1g14310 C2At5g52820 C2At4g09010 110 C2At4g10030 C2At5g67370 C2At5g49970 C2At1g09920 C2At5g13450 115 C2At1g27530 C2At5g23060 C2At4g37130 C2At1g05055 C2At1g18660 Bcat 120 CA526211 C2At3g02220 C2At3g16150 C2At1g80170 C2At4g01880 125 C2At2g04690 C2At1g46480 C2At3g47640 C2At3g23590 C2At2g04700 C2At1g16180 C2At5g18590 130 C2At5g25900 C2At1g18270 C2At3g01480 Skdh-1 135 CA847580 C2At5g40530 C2At3g13700 Pgm-2 GP1049 C2At1g75350 C2At3g27200 BM062655 140 C2At1g14810 C2At1g63610 C2At3g14075 C2At1g67730 C2At3g11210 C2At1g20575 145 Idh-1 C2At1g42990 C2At3g20240 C2At5g45680 150 CA523715 CP10020 155 GP20095 C2At1g76080 C2At5g11490 160 GP20062 165 C2At5g11480 C2At5g25630 170 C2At4g00560 CT77 175 Note: P1a1 and P1a2 correspond to consecutive segments on T1. So do P1b1 and P1b2. It’s likely that an inversion(s) occurred in the pepper genome to reshuffle them. Therefore, P1a1 and P1a2 are combined into P1a , and P1b1 and P1b2 are combined into P1b. C2At2g45910 180 185 190 C2At3g06730 Hpms1-139 195 TG83 200 TG19 CP10060 205 C2At1g02560 210 CP10061 215 NN1 220 AF039662 225 C2At5g64350 C2At3g19630 230 235 C2At4g34350 240 245 C2At4g34700 250 C2At2g16920

6. Figure S2 continued (Wu and Tanksley) P8 R45S-C P5a, b P6 P7 C2At4g25650 C2At4g01900 C2At2g18710 0cM C2At4g31130 C2At2g24390 C2At1g72030 C2At1g31410 5 C2At5g22010 C2At3g52155 C2At3g52860 C2At2g39690 10 T0635 C2At2g39580 C2At4g30580 15 C2At1g08630 NN8 NN9 20 C2At1g60560 C2At2g24270 GP1102 25 C2At4g17380 NN4 asu5 30 NN2 CT135 T0707 35 C2At5g34850 C2At3g25120 C2At3g17040 C2At2g16060 40 C2At3g51010 C2At2g30100 C2At4g33250 C2At1g33970 C2At3g46780 45 C2At5g20520 C2At2g29630 C2At2g32970 C2At2g01770 50 C2At3g56130 C2At4g26680 C2At1g27385 C2At3g56040 55 C2At5g14520 Hpms2-45 C2At1g06110 C2At2g04842 C2At2g46580 60 C2At1g44760 NN6 65 C2At4g03210 C2At3g10920 70 CA516334 U221402 75 C2At2g20860 C2At3g55800 C2At3g06440 80 C2At1g03150 C2At4g12590 85 C2At2g42750 6B11 90 C2At1g79810 C2At3g58790 C2At1g73885 C2At2g38020 95 C2At1g78620 C2At5g07960 C2At3g55360 100 C2At3g15290 C2At1g24360 C2At3g14910 105 C2At1g53670 CD74 C2At1g55880 110 C2At2g43360 C2At3g54860 C2At3g15430 C2At5g04270 115 C2At4g26750 CA523558 T0633 C2At1g55670 120 GPMS178A T0463 125 C2At1g18640 TG199 CA516044 C2At5g48300 130 C2At1g07080 135 C2At1g16870 C2At4g28530 140 C2At4g32280 145 C2At1g20050 150 155

7. Figure S2 continued (Wu and Tanksley) P9a, b P10 P11a, b P12a, b , c C2At4g22260 C2At1g79260 C2At3g13235 C2At5g06130 0cM C2At2g01110 C2At3g52640 TG395 C2At5g16630 5 C2At1g13380 TG619 C2At3g09920 C2At5g16710 NN3 10 C2At5g60990 T0408 C2At1g26520 C2At3g09925 GP20056 C2At1g69420 15 C2At3g60830 20 GPMS171 C2At3g54840 GP20064 C2At2g37240 GP1127 25 NN10 C2At1g14790 Hpms1-117 30 NN5 C2At2g28600 CA519548 Hpms1-3 C2At4g15010 GP20087 35 Hpms2-41 C2At5g64730 C2At1g70160 C2At5g09880 C2At2g29210 CT101 40 C2At5g58410 C2At3g24490 C2At1g67325 C2At4g03400 45 GPMS163 C2At4g39660 C2At1g23890 C2At1g11380 C2At4g39870 C2At1g60440 50 GP20068 TG180 C2At1g65230 C2At1g27980 C2At5g01990 C2At4g03280 55 C2At1g79790 GP20117 T0801 GP20036 60 C2At2g46340 CP10131a C2At4g28830 C2At5g04590 C2At3g08760 CP10023 65 C2At5g59960 U217183 C2At1g17410 C2At1g51350 GPMS159 70 GP1017 C2At2g28800 C2At3g51840 C2At3g25910 C2At2g28490 75 C2At5g01350 C2At4g33360 80 CD32 C2At4g16580 85 90 C2At2g27450 C2At1g76150 C2At5g19690 GP1078 95 C2At1g21690 CA516439 C2At5g38530 C2At3g44600 100 CT57 C2At4g31150 C2At3g44890 C2At5g60540 105 C2At2g06530 C2At5g11550 C2At4g30220 110 C2At2g28250 C2At1g48300 Hpms2-21 115 TG36 C2At3g57270 T0800 120 C2At5g57970 TG350 125 C2At4g16710 130 C2At1g67740 135 140 C2At4g11120

8. Figure S2 continued (Wu and Tanksley) N1a,b, c N2 N3a, b N4a, b, c 2g34560 PT52769c PT61304 PT51247 4g20070 PT60981 5g13450 0cM PT60915 2g35130 PT60930 1g30000 PT61203 3g52120 5 4g21120 PT60152 PT61314 4g18060 PT52597 PT54596 5g08430 10 1g33970 PT52794 1g64770 5g37290 PT61564 2g14260 PT50336 1g02150 3g02220 15 PT55130 2g39580 5g45950 2g26210 1g60560 3g28670 PT53100 PT53353 20 PT60901 PT55100 1g07310 1g25260 PT61293 3g19895 PT54944 1g33270 PT60648 25 PT60269 PT53143 4g21710 3g51010 3g56040 PT51554 1g10240 1g68100 5g51110 4g04955 PT55106 30 PT60172 1g10580 5g02270 PT52937 PT52347 3g28720 1g56500 35 1g65900 PT50861 PT60297 PT60913 1g61620 5g03905 PT54295 PT53932 1g09070 PT60140 40 PT60037 1g11430 PT50819 PT50655 cLPT2E21 PT61390 4g00740 1g44790 PT50762 4g34090 4g01210 45 3g17590 1g51160 5g67370 3g19230 1g05385 1g80460 PT54911 5g15410 1g21690 50 PT51912 3g01480 4g32280 PT61315 5g17170 3g01180 PT54978 1g77250 PT51682 2g45600 3g26900 PT60276 55 1g79600 2g04700 PT60155 1g71810 1g74470 3g27200 PT50500 1g78230 PT61454 PT60613 3g28050 60 PT51166 PT50120 1g54520 3g55250 PT60934 3g02910 PT53545 PT52749 65 PT52722 3g04780 4g37130 5g10920 3g03100 2g45910 4g33985 PT55077 PT60200 2g38730 PT51562 PT60053 70 1g67740 PT50645 PT50692 1g46480 PT61594 3g18860 PT60665 3g48610 5g25900 4g00090 PT50693 75 PT51314 PT50738 PT50028 1g30580 PT53970 1g19340 2g16920 PT54378 4g39630 80 PT53481 3g08030 5g37260 PT60273 5g60620 1g30540 5g42950 5g13050 3g46780 4g30890 85 5g63380 1g74730 PT61218 PT60771 1g80170 1g18640 1g20575 U214603 90 PT61436 PT50334 PT54245 4g03200 PT61171 1g79720 PT51919 1g42990 3g17970 95 1g03360 3g18270 PT55086 1g80360 PT54888 100 1g52080 PT61348 PT52939 PT54845 3g13700 105 PT52848 PT50794 PT61286 PT54598 5g25760 110 3g14075 5g11810 3g14200 1g65700 3g21215 3g63200

9. Figure S2 continued (Wu and Tanksley) N5a, b, c N6a, b N7a, b N8a, b PT61385 4g03400 PT52768 PT51085 3g15410 PT54079 PT51896 PT51873 2g46580 PT60682 5g19690 0cM PT60677 PT60122 PT60212 4g33250 PT50225 5 PT60165 PT50856 PT60606 TG230 PT50311 2g32950 4g26750 2g06010 10 5g49510 1g24340 PT60849 4g26680 3g13235 PT54819 PT51241 3g55800 PT61214 PT51638 15 2g42750 5g05270 4g11120 2g20860 PT55194 2g46370 PT55012 3g58790 5g09380 20 PT52509 PT61281 PT54184 PT51123 4g19003 2g38020 PT61319 3g14910 PT50346 25 PT51152 1g78600 PT51180 2g43770 1g78620 PT52156 30 PT51054 1g53670 PT60739 3g13180 1g16900 PT60649 3g55360 4g32770 4g27700 PT53203 PT61226 35 5g62530 3g15290 5g11480 PT61396 PT53595 PT53574 3g15380 3g54860 PT53563 5g11450 5g54310 40 PT52736 PT53054 1g04970 PT60728 2g01720 45 PT53857 PT61143 3g53920 1g55840 5g22620 PT61217 4g34215 PT61426 50 5g56130 5g56940 PT60089 PT61488 PT50838 PT54210 4g12740 PT51259 PT53175 55 PT51706 PT52353 2g28880 5g58410 PT52565 5g44200 PT60870a 1g20830 60 3g54770 5g47010 1g44760 2g37500 5g37360 1g32410 PT50539 65 PT53026 5g46630 3g53580 1g62780 PT53472 5g09880 PT51779 PT53802 PT51132 PT52378 70 5g64730 PT61419 4g10030 3g52220 PT53673 PT54322 PT60561 75 1g16870 2g37025 PT53499 3g54840 1g14850 PT51575 PT52760 PT60291 80 5g41350 PT51913 PT50790 PT53216 4g23840 PT54484 5g50720 1g12060 3g09920 PT61467 85 5g16710 1g20050 3g52610 PT55072 PT60603 90 3g52640 4g28530 PT60129 5g14520 95 100 105 110

10. Figure S2 continued (Wu and Tanksley) N9a, b, c N10a, b N11a, b,c N12a, b 3g23400 5g06360 1g16590 4g31410 2g18710 PT52935 0cM 5 PT53522 2g24090 10 5g04200 PT60939 PT51076 PT61522 3g24160 15 5g58200 PT60146 4g14570 PT51666 PT54242 2g24580 20 PT54896 1g14790 3g16840 1g30360 25 PT61362 PT51212 1g04530 PT51161 PT52988 3g24050 1g22860 PT60870b 30 1g67325 3g51840 1g24360 U221455 1g67700 35 5g06430 PT51339 3g06790 1g67730 2g06925 PT61494 PT60228 PT54965 3g08760 40 5g18580 PT60572 PT61141 5g36210 PT60937 5g38530 PT51534 PT61457 PT53607 4g29735 4g24750 1g56050 45 4g15520 PT60205 PT60675 3g23590 4g16580 PT60877 PT61530 50 PT50226 1g70160 PT60863 1g76150 PT54871 1g26940 PT60938 PT50989 1g60440 55 PT52449 1g07040 1g17410 1g04190 1g14270 4g35930 60 2g03510 3g16290 PT50510 PT51070 1g26520 PT52906 PT60115 1g61150 5g60990 PT54772 PT50344 65 PT52640 PT53434 3g17000 1g28530 PT61583 3g44600 PT53009 1g26670 PT52058 1g30825 70 PT55265 5g21170 3g53400 PT61224 1g48300 cLPT5E7 75 2g28490 E492334 1g25580 2g28800 5g59960 5g53000 80 PT51717 5g12200 PT61367 85 PT52176 PT54576 2g01110 3g22660 90 PT54525 5g13030 3g12685 95 PT51967