Doc-Alignment

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Cucurbitales genomes. We used V.vinifera as a reference, and by comparing homologous gene locus maps and Ks values between V.vinifera and other Cucurbitales, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created a hierarchical lists of homologous genes using V.vinifera as a reference.
  The relevant gene ids can be obtained from the Cucurbitales blast and match under the Tools module. This link is Cucurbitales blast and match.

Orthogroup analysis platform
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Select Vvi1 Blo1 Blo2 Bda1 Bda2 Bpe1 Bpe2 Bma1 Bma2 Cmo1 Cmo2 Cma1 Cma2 Car1 Car2 Sed1 Cpe1 Cpe2 Bhi1 Tan1 Cmetu1 Lac1 Hepe1 Mch1 Lcy1 Cla1 Cam1 Cec1 Cco1 Clacu1 Cmu1 Cre1 Cone1 Cone2 Cone3 Cone4 Lsi1 Csa1 Chy1 Cme1 Blo3 Blo4 Bda3 Bda4 Bpe3 Bpe4 Bma3 Bma4 Sed2 Cmo3 Cmo4 Cma3 Cma4 Car3 Car4 Cpe3 Cpe4 Bhi2 Tan2 Cmetu2 Lac2 Hepe2 Mch2 Lcy2 Cla2 Cam2 Cec2 Cco2 Clacu2 Cmu2 Cre2 Lsi2 Csa2 Chy2 Cme2
Vvi18g660 . . . . . . . . Cmo05g00147 Cmo12g00534 . . . Car12g00538 Sed10g1207 . . Bhi04g00409 Tan02g1743 Cmetu03g0036 . Hepe08g1328 . Lcy13g2129 Cla08g01616 Cam08g2118 Cec08g1703 Cco08g1826 Clacu08g1803 . Cre08g1585 . . . Cone20ag0230 . . . Cme03g02097 Blo17g00861 . . . . Bpe05g00045 . Bma05g00056 . . . Cma12g00594 Cma05g00145 Car05g00126 . . . . . . . . . . . . . . . . . Lsi08g01520 Csa02g01900 Chy03g01586 .
Vvi18g661 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g662 . . Bda01g00585 . . . . Bma01g02251 . . Cma01g01793 Cma09g00281 Car01g01399 . . Cpe06g00193 . . . . . . . . . . . . . . . . . . . Lsi04g01494 Csa04g02468 . . . Blo18g00717 . Bda01g01591 Bpe02g01778 Bpe05g00043 Bma01g00676 . Sed01g2708 Cmo01g01851 Cmo09g00275 . . . Car09g00237 . Cpe02g00212 Bhi09g03239 Tan01g4707 Cmetu07g1035 . Hepe01g1821 Mch11g0355 . Cla05g02100 Cam05g2252 Cec05g2272 Cco05g2313 Clacu05g2248 Cmu05g2111 Cre05g2235 . . Chy07g00181 .
Vvi18g663 . . . . . . . . Cmo05g00149 Cmo12g00532 . Cma09g00280 . Car12g00536 Sed05g2623 Cpe06g00192 Cpe07g00513 Bhi04g00407 Tan02g1017 Cmetu01g0451 . Hepe08g1326 . Lcy13g2128 Cla08g01614 Cam08g2116 Cec08g1701 Cco08g1824 Clacu08g1801 . Cre08g1583 . . Cone17ag0882 Cone20ag0228 Lsi04g01495 Csa04g02466 . Cme03g02095 Blo17g00863 . . . . Bpe05g00386 . Bma05g00054 . . Cmo09g00274 Cma12g00592 Cma05g00148 Car05g00128 Car09g00236 Cpe11g00126 . Bhi09g03240 . . . Hepe01g1820 Mch11g0354 . Cla05g02098 Cam05g2251 Cec05g2270 Cco05g2312 Clacu05g2247 Cmu05g2110 Cre05g2233 Lsi08g01518 Csa02g01902 Chy07g00180 .
Vvi18g664 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g665 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g666 . . . . . . . . Cmo05g00150 Cmo12g00530 . . . Car12g00535 Sed10g1209 . Cpe07g00512 Bhi04g00406 Tan02g1751 Cmetu03g1056 . Hepe08g1324 . Lcy13g2127 Cla08g01613 Cam08g2114 Cec08g1700 Cco08g1823 Clacu08g1799 . Cre08g1582 . . . . . . . Cme03g02094 . . . . . Bpe05g00480 . . . . . Cma12g00591 Cma05g00149 Car05g00129 . Cpe11g00127 . . . . . . . . . . . . . . . Lsi08g01517 Csa02g01903 Chy03g01583 .
Vvi18g667 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo17g00865 . . Bda01g01592 . Bpe05g00040 Bma01g00675 Bma05g00052 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g668 . . . . . . . . . Cmo12g00528 . . . Car12g00534 Sed14g1515 . Cpe07g00511 Bhi04g00405 Tan02g1754 Cmetu11g0428 . Hepe08g1323 . Lcy13g2126 Cla08g01612 Cam08g2113 Cec08g1699 Cco08g1822 Clacu08g1798 . Cre08g1581 . . . . . . . Cme03g02093 . . . . . . . . . . . Cma12g00590 . . . . . . . . . . . . . . . . . . . Lsi08g01516 Csa02g01904 Chy03g01582 .
Vvi18g669 . . . . . . . . . . . Cma09g00277 . . . . . . . . . . . . . . . . . . . . . . . . Csa04g02464 . . Blo17g00866 Blo18g00715 . Bda01g01593 Bpe02g01780 Bpe05g00039 Bma01g00674 Bma05g00051 Sed13g1796 . Cmo09g00272 . . . Car09g00233 . . Bhi09g03246 Tan01g4713 Cmetu07g1941 . . Mch11g0349 . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 32868651 32869257 - Bda002605.1 Bda01g00585 585
1 51762676 51763571 + Bda003860.1 Bda01g01591 1591
1 51765306 51770855 + Bda003861.2 Bda01g01592 1592
1 51771852 51773167 - Bda003862.1 Bda01g01593 1593
4 10485725 10490656 - XM_039029167.1 Bhi04g00405 405
4 10491263 10494807 + XM_039029168.1 Bhi04g00406 406
4 10496217 10500178 + XM_039030213.1 Bhi04g00407 407
4 10528522 10531847 + XM_039030569.1 Bhi04g00409 409
9 83251613 83253071 + XM_039043163.1 Bhi09g03239 3239
9 83259709 83265990 - XM_039043085.1 Bhi09g03240 3240
9 83302017 83303186 - XM_039041721.1 Bhi09g03246 3246
17 28084072 28085870 - BLOR08407 Blo17g00861 861
17 28168608 28172808 - BLOR08409 Blo17g00863 863
17 28284555 28290515 + BLOR08411 Blo17g00865 865
17 28291124 28292207 - BLOR08412 Blo17g00866 866
18 17459788 17461268 + BLOR09203 Blo18g00715 715
18 17618546 17619215 - BLOR09205 Blo18g00717 717
1 6158084 6159397 + Bma000885.1 Bma01g00674 674
1 6159690 6165004 - Bma000886.1 Bma01g00675 675
1 6168282 6168950 - Bma000887.2 Bma01g00676 676
1 79682963 79683576 + Bma003104.1 Bma01g02251 2251
5 2350208 2351203 + Bma020740.1 Bma05g00051 51
5 2351764 2358480 - Bma020741.1 Bma05g00052 52
5 2372409 2374764 + Bma020743.1 Bma05g00054 54
5 2385148 2386944 + Bma020745.1 Bma05g00056 56
2 20105653 20106321 + Bpe009610.1 Bpe02g01778 1778
2 20114086 20115464 - Bpe009612.1 Bpe02g01780 1780
5 733877 734829 + Bpe017426.1 Bpe05g00039 39
5 735485 742566 - Bpe017427.3 Bpe05g00040 40
5 766859 767526 - Bpe017430.1 Bpe05g00043 43
5 779054 781094 + Bpe017432.1 Bpe05g00045 45
5 18142131 18161505 + Bpe017803.1 Bpe05g00386 386
5 19068764 19071168 - Bpe017900.1 Bpe05g00480 480
5 30680355 30687297 + CaPI482276_05g022510.1 Cam05g2251 2251
5 30691803 30692520 - CaPI482276_05g022520.1 Cam05g2252 2252
8 26558287 26562610 - CaPI482276_08g021130.1 Cam08g2113 2113
8 26563622 26566582 + CaPI482276_08g021140.1 Cam08g2114 2114
8 26569533 26572525 + CaPI482276_08g021160.1 Cam08g2116 2116
8 26579096 26581921 + CaPI482276_08g021180.1 Cam08g2118 2118
1 12199842 12200812 + Carg10638-RA Car01g01399 1399
5 644507 647358 - Carg11878-RA Car05g00126 126
5 649094 652654 - Carg11876-RA Car05g00128 128
5 653588 655698 - Carg11875-RA Car05g00129 129
9 1292249 1292933 + Carg21788-RA Car09g00233 233
9 1299608 1305042 + Carg21785-RA Car09g00236 236
9 1307442 1308120 - Carg21784-RA Car09g00237 237
12 3553610 3558989 - Carg16400-RA Car12g00534 534
12 3561600 3565787 + Carg16399-RA Car12g00535 535
12 3566548 3569606 + Carg16398-RA Car12g00536 536
12 3573551 3577547 + Carg16396-RA Car12g00538 538
5 31699474 31706396 + CcPI632755_05g023120.1 Cco05g2312 2312
5 31710860 31711564 - CcPI632755_05g023130.1 Cco05g2313 2313
8 29256625 29260936 - CcPI632755_08g018220.1 Cco08g1822 1822
8 29261785 29265216 + CcPI632755_08g018230.1 Cco08g1823 1823
8 29267824 29270758 + CcPI632755_08g018240.1 Cco08g1824 1824
8 29278141 29281121 + CcPI632755_08g018260.1 Cco08g1826 1826
5 34066615 34072548 + CePI673135_05g022700.1 Cec05g2270 2270
5 34078014 34078731 - CePI673135_05g022720.1 Cec05g2272 2272
8 28168685 28172909 - CePI673135_08g016990.1 Cec08g1699 1699
8 28173753 28176868 + CePI673135_08g017000.1 Cec08g1700 1700
8 28179749 28182756 + CePI673135_08g017010.1 Cec08g1701 1701
8 28190031 28192860 + CePI673135_08g017030.1 Cec08g1703 1703
3 17871377 17875846 - Chy3G065620.1 Chy03g01582 1582
3 17876467 17879140 + Chy3G065630.1 Chy03g01583 1583
3 17886508 17890024 + Chy3G065660.1 Chy03g01586 1586
7 1478328 1484671 + Chy7G130100.1 Chy07g00180 180
7 1489053 1489783 - Chy7G130110.1 Chy07g00181 181
5 30883636 30890532 + ClG42_05g0224700.10 Clacu05g2247 2247
5 30895015 30895737 - ClG42_05g0224800.10 Clacu05g2248 2248
8 27315981 27320278 - ClG42_08g0179800.10 Clacu08g1798 1798
8 27321300 27324259 + ClG42_08g0179900.10 Clacu08g1799 1799
8 27327037 27330011 + ClG42_08g0180100.10 Clacu08g1801 1801
8 27336548 27339380 + ClG42_08g0180300.10 Clacu08g1803 1803
5 32574661 32583706 + ClCG05G020500.2 Cla05g02098 2098
5 32588847 32590483 - ClCG05G020520.2 Cla05g02100 2100
8 28736555 28741252 - ClCG08G016370.2 Cla08g01612 1612
8 28741888 28745627 + ClCG08G016380.2 Cla08g01613 1613
8 28747818 28751041 + ClCG08G016390.1 Cla08g01614 1614
8 28758874 28762124 + ClCG08G016410.2 Cla08g01616 1616
1 11993723 11995070 + CmaCh01G017930.1 Cma01g01793 1793
5 647024 649476 - CmaCh05G001450.1 Cma05g00145 145
5 651683 655675 - CmaCh05G001480.1 Cma05g00148 148
5 656029 658258 - CmaCh05G001490.1 Cma05g00149 149
9 1140286 1141050 + CmaCh09G002770.1 Cma09g00277 277
9 1147853 1152839 + CmaCh09G002800.1 Cma09g00280 280
9 1154490 1155679 - CmaCh09G002810.1 Cma09g00281 281
12 3077997 3083286 - CmaCh12G005900.1 Cma12g00590 590
12 3085730 3089969 + CmaCh12G005910.1 Cma12g00591 591
12 3090529 3094389 + CmaCh12G005920.1 Cma12g00592 592
12 3097246 3102644 + CmaCh12G005940.1 Cma12g00594 594
3 28262020 28266635 - MELO3C010816.2.1 Cme03g02093 2093
3 28267368 28270704 + MELO3C010815.2.1 Cme03g02094 2094
3 28271650 28274512 + MELO3C010814.2.1 Cme03g02095 2095
3 28277635 28280973 + MELO3C010812.2.1 Cme03g02097 2097
1 927820 938895 + PI0002311.2 Cmetu01g0451 451
3 1042423 1045884 - PI0026209.1 Cmetu03g0036 36
3 1054569 1058129 - PI0004764.1 Cmetu03g1056 1056
7 22858318 22859573 - PI0005563.1 Cmetu07g1035 1035
7 22828177 22828845 + PI0016556.1 Cmetu07g1941 1941
11 2982027 2986127 + PI0028894.1 Cmetu11g0428 428
1 13487541 13488687 + CmoCh01G018510.1 Cmo01g01851 1851
5 648481 651758 - CmoCh05G001470.1 Cmo05g00147 147
5 653145 656770 - CmoCh05G001490.1 Cmo05g00149 149
5 657611 659672 - CmoCh05G001500.1 Cmo05g00150 150
9 1195274 1196251 + CmoCh09G002720.1 Cmo09g00272 272
9 1203160 1208331 + CmoCh09G002740.1 Cmo09g00274 274
9 1210913 1212057 - CmoCh09G002750.1 Cmo09g00275 275
12 3236322 3241778 - CmoCh12G005280.1 Cmo12g00528 528
12 3244237 3246922 + CmoCh12G005300.1 Cmo12g00530 530
12 3249089 3252419 + CmoCh12G005320.1 Cmo12g00532 532
12 3256535 3260254 + CmoCh12G005340.1 Cmo12g00534 534
5 30621021 30627915 + CmPI595203_05g021100.1 Cmu05g2110 2110
5 30632392 30633127 - CmPI595203_05g021110.1 Cmu05g2111 2111
17 6977182 6981740 + Conep17aG0090300.1 Cone17ag0882 882
20 980446 984990 + Conep20aG0023800.1 Cone20ag0228 228
20 993978 996883 + Conep20aG0024000.1 Cone20ag0230 230
2 1091004 1092373 - Cp4.1LG02g06550.1 Cpe02g00212 212
6 1028122 1034383 + Cp4.1LG06g01880.1 Cpe06g00192 192
6 1035430 1036744 - Cp4.1LG06g01970.1 Cpe06g00193 193
7 3357969 3363162 - Cp4.1LG07g04940.1 Cpe07g00511 511
7 3365939 3370498 + Cp4.1LG07g05010.1 Cpe07g00512 512
7 3371284 3385561 + Cp4.1LG07g05030.1 Cpe07g00513 513
11 691333 695134 - Cp4.1LG11g01390.1 Cpe11g00126 126
11 695684 697962 - Cp4.1LG11g01420.1 Cpe11g00127 127
5 33947908 33953844 + CrPI670011_05g022330.1 Cre05g2233 2233
5 33959300 33960009 - CrPI670011_05g022350.1 Cre05g2235 2235
8 28362151 28366470 - CrPI670011_08g015810.1 Cre08g1581 1581
8 28367314 28370459 + CrPI670011_08g015820.1 Cre08g1582 1582
8 28373371 28376352 + CrPI670011_08g015830.1 Cre08g1583 1583
8 28385631 28388471 + CrPI670011_08g015850.1 Cre08g1585 1585
2 17979681 17983315 - CsaV3_2G026200.1 Csa02g01900 1900
2 17987377 17990319 - CsaV3_2G026220.1 Csa02g01902 1902
2 17991594 17994260 - CsaV3_2G026230.1 Csa02g01903 1903
2 17994558 17999562 + CsaV3_2G026240.1 Csa02g01904 1904
4 24649361 24650015 + CsaV3_4G034900.1 Csa04g02464 2464
4 24665018 24672848 + CsaV3_4G034920.1 Csa04g02466 2466
4 24675485 24677384 - CsaV3_4G034940.1 Csa04g02468 2468
1 83148578 83155451 + Hsped.01g18200.1 Hepe01g1820 1820
1 83160114 83161426 - Hsped.01g18210.1 Hepe01g1821 1821
8 15073255 15078158 - Hsped.08g13230.1 Hepe08g1323 1323
8 15083779 15087165 + Hsped.08g13240.1 Hepe08g1324 1324
8 15098157 15100280 + Hsped.08g13260.1 Hepe08g1326 1326
8 15114245 15116916 + Hsped.08g13280.1 Hepe08g1328 1328
13 40162144 40169876 - Maker00025201 Lcy13g2126 2126
13 40169808 40173193 + Maker00025181 Lcy13g2127 2127
13 40174238 40179981 + Maker00025133 Lcy13g2128 2128
13 40188667 40191423 + Maker00025442 Lcy13g2129 2129
4 22637568 22638890 + Lsi04G014940.1 Lsi04g01494 1494
4 22642560 22650498 - Lsi04G014950.1 Lsi04g01495 1495
8 23237930 23243251 - Lsi08G015160.1 Lsi08g01516 1516
8 23244871 23248239 + Lsi08G015170.1 Lsi08g01517 1517
8 23251279 23254884 + Lsi08G015180.1 Lsi08g01518 1518
8 23263235 23266647 + Lsi08G015210.1 Lsi08g01520 1520
11 2155330 2156010 + MC11g0272 Mch11g0349 349
11 2175632 2182553 + MC11g0277 Mch11g0354 354
11 2185633 2187149 - MC11g0278 Mch11g0355 355
1 21710980 21711980 - Sed0018191.1 Sed01g2708 2708
5 37840561 37849865 + Sed0000800.1 Sed05g2623 2623
10 24446972 24451238 - Sed0024439.2 Sed10g1207 1207
10 24548905 24558928 - Sed0001701.1 Sed10g1209 1209
13 22990765 22992088 + Sed0013002.1 Sed13g1796 1796
14 23465468 23469813 + Sed0020791.1 Sed14g1515 1515
1 112959317 112960629 + Tan0008333.1 Tan01g4707 4707
1 113021279 113022993 - Tan0002494.1 Tan01g4713 4713
2 14451366 14466093 + Tan0019038.2 Tan02g1017 1017
2 81257693 81260498 - Tan0018086.2 Tan02g1743 1743
2 81462541 81466454 - Tan0010932.3 Tan02g1751 1751
2 81487043 81491625 + Tan0009224.1 Tan02g1754 1754
18 7722608 7729941 - Vvi18g660 Vvi18g660 660
18 7732524 7734308 - Vvi18g661 Vvi18g661 661
18 7746213 7747271 + Vvi18g662 Vvi18g662 662
18 7749436 7763469 - Vvi18g663 Vvi18g663 663
18 7770219 7773282 - Vvi18g664 Vvi18g664 664
18 7787288 7788777 - Vvi18g665 Vvi18g665 665
18 7788779 7796734 - Vvi18g666 Vvi18g666 666
18 7798156 7812824 + Vvi18g667 Vvi18g667 667
18 7813570 7833032 + Vvi18g668 Vvi18g668 668
18 7834357 7836853 + Vvi18g669 Vvi18g669 669
       

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