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
Vvi3g596 . . Bda06g00940 . . Bpe12g00262 . . Cmo19g00681 . Cma02g00401 Cma20g00853 Car02g00262 Car20g00736 . Cpe04g00119 Cpe15g00542 Bhi05g01234 . . . . . . Cla02g00520 Cam02g0533 Cec02g0535 Cco02g0543 Clacu02g0533 Cmu02g0528 Cre02g0860 Cone12ag1153 Cone8ag1202 . Cone10ag1173 Lsi10g00365 . Chy11g00382 Cme01g01414 . . Bda15g00008 Bda14g00553 . . . Bma08g00556 . Cmo02g00407 Cmo20g00862 . Cma19g00668 . Car19g00511 . Cpe05g01256 Bhi10g02017 . . . . . . . . . . . . . Lsi11g01105 Csa02g01252 Chy01g00782 .
Vvi3g597 . . . . . Bpe12g00080 . . . . Cma02g00400 Cma20g00852 . . . . . . . . . . . . . . . . . . . . . . . Lsi10g00366 . Chy11g00381 . Blo04g00512 Blo13g00553 Bda15g00006 Bda14g00554 Bpe15g00866 . Bma03g00552 . Sed01g0304 Cmo02g00405 Cmo20g00861 . . . . . Cpe05g01257 Bhi10g02015 Tan05g1313 Cmetu11g0750 . Hepe08g1018 . . . . . . . . . . Csa02g01253 . .
Vvi3g598 . . . Bda08g01283 . Bpe12g00081 . Bma12g00518 Cmo19g00682 . . Cma20g00850 Car02g00260 . . Cpe04g00118 Cpe15g00545 Bhi05g01235 Tan02g0794 . . Hepe02g0503 . . Cla02g00516 Cam02g0528 Cec02g0530 Cco02g0538 Clacu02g0529 Cmu02g0523 . . . Cone3ag1164 Cone10ag0959 Lsi10g00367 . Chy11g00379 Cme01g01409 Blo04g00513 Blo13g00552 Bda15g00005 Bda14g00555 Bpe15g00865 . Bma03g00553 . Sed01g0302 Cmo02g00403 Cmo20g00859 . Cma19g00672 . Car19g00513 . . Bhi10g02012 Tan05g1311 Cmetu11g2150 . Hepe08g1017 . . . . . . . . . Lsi11g01107 Csa02g01255 Chy01g00780 .
Vvi3g599 . . Bda06g00939 Bda08g00932 . . . Bma12g00517 . . Cma02g00396 Cma20g00849 Car02g00259 Car20g00733 . . . . . . . . . . . . . . . . . . . . . Lsi10g00368 . Chy11g00378 . . . . . . . . . Sed05g3621 Cmo02g00402 Cmo20g00858 . . . . . Cpe05g01260 Bhi10g02011 Tan05g1310 Cmetu11g0117 . Hepe08g1016 . . . . . . . . . . Csa02g01256 . .
Vvi3g600 . . Bda06g00937 Bda08g01282 . . . Bma12g00516 . . . . . . . . . . . . . . . . Cla02g00513 Cam02g0524 Cec02g0527 . Clacu02g0525 Cmu02g0522 Cre02g0855 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi11g01110 . . .
Vvi3g601 . . Bda06g00935 . . . . Bma12g00515 . . . . Car02g00258 . . . . . . . . . . . . . . . . . . . . . Cone10ag0964 Lsi10g00369 . . . . . . . . . . . Sed05g3619 Cmo02g00401 . . . . . . Cpe05g01261 Bhi10g02010 Tan05g1308 Cmetu07g0234 . Hepe08g1015 . . . . . . . . . . Csa02g01258 . .
Vvi3g602 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g603 . . Bda06g00933 . . . . Bma12g00512 Cmo19g00684 . . . . . . Cpe04g00117 Cpe15g00548 Bhi05g01236 Tan02g0793 Cmetu01g1593 . Hepe02g0502 . . Cla02g00512 Cam02g0522 Cec02g0526 Cco02g0533 Clacu02g0524 Cmu02g0521 Cre02g0854 . . . . . . . Cme01g01408 . Blo13g00551 . . . . . . . . . . Cma19g00673 . Car19g00514 . . . . . . . . . . . . . . . . Lsi11g01111 . Chy01g00779 .
Vvi3g604 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g605 . . . . . Bpe12g00293 . . Cmo19g00605 . . . . . . Cpe04g00295 Cpe15g00476 . . . . . . . Cla02g00624 Cam02g0658 Cec02g0661 Cco02g0685 Clacu02g0666 . Cre02g0979 . . Cone3ag0991 Cone10ag1012 Lsi03g00521 Csa07g00735 . Cme01g00073 . . Bda15g00848 Bda14g01450 . . Bma03g01355 Bma08g00518 . . . Cma11g01732 . Car11g01109 Car19g00445 . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 25196546 25196794 + Bda022556.1 Bda06g00933 933
6 25234680 25244111 - Bda022559.1 Bda06g00935 935
6 25333913 25335283 - Bda022563.1 Bda06g00937 937
6 25526544 25527049 - Bda033707 Bda06g00939 939
6 25593413 25597131 + Bda022569.1 Bda06g00940 940
8 17153174 17153566 - Bda029566.1 Bda08g00932 932
8 52099137 52100669 - Bda030301.1 Bda08g01282 1282
8 52102367 52107815 - Bda030302.3 Bda08g01283 1283
14 4052803 4056549 - Bda027299.1 Bda14g00553 553
14 4061864 4062653 + Bda027300.1 Bda14g00554 554
14 4067071 4067346 + Bda027301.1 Bda14g00555 555
14 19515801 19517707 + Bda011193.1 Bda14g01450 1450
15 1096822 1097097 - Bda011750.1 Bda15g00005 5
15 1101856 1102613 - Bda011751.1 Bda15g00006 6
15 1126668 1130408 + Bda011754.1 Bda15g00008 8
15 13193259 13195432 - Bda012724.1 Bda15g00848 848
5 44152503 44157671 - XM_039032025.1 Bhi05g01234 1234
5 44290794 44292165 - XM_039032710.1 Bhi05g01235 1235
5 44487711 44490036 + XM_039032441.1 Bhi05g01236 1236
10 50301901 50311772 + XM_039046630.1 Bhi10g02010 2010
10 50376489 50378779 + XM_039046160.1 Bhi10g02011 2011
10 50380021 50382881 - XM_039046195.1 Bhi10g02012 2012
10 50428418 50429566 - XM_039045314.1 Bhi10g02015 2015
10 50520809 50526778 + XM_039045832.1 Bhi10g02017 2017
4 4353245 4354022 + BLOR13424 Blo04g00512 512
4 4358437 4367226 + BLOR13425 Blo04g00513 513
13 27471829 27472077 + BLOR05832 Blo13g00551 551
13 27478286 27483391 - BLOR05833 Blo13g00552 552
13 27487818 27488575 - BLOR05834 Blo13g00553 553
3 4542593 4543423 + Bma016838.1 Bma03g00552 552
3 4547910 4548185 + Bma016839.1 Bma03g00553 553
3 29483959 29486095 + Bma017896.1 Bma03g01355 1355
8 27987224 27989397 - Bma027732.1 Bma08g00518 518
8 33652638 33655477 + Bma027824.1 Bma08g00556 556
12 17001741 17001971 - Bma007591.1 Bma12g00512 512
12 17342884 17345294 - Bma007600.1 Bma12g00515 515
12 17436405 17437775 - Bma007603.1 Bma12g00516 516
12 17509542 17510060 + Bma007607.2 Bma12g00517 517
12 17510732 17510983 - Bma007608.1 Bma12g00518 518
12 557093 557922 + Bpe005319.1 Bpe12g00080 80
12 561501 561905 + Bpe005320.1 Bpe12g00081 81
12 2483157 2485980 - Bpe024880 Bpe12g00262 262
12 3686993 3689121 + Bpe024884 Bpe12g00293 293
15 18621101 18621376 - Bpe001788.1 Bpe15g00865 865
15 18625804 18626582 - Bpe001789.1 Bpe15g00866 866
2 5997043 5998901 + CaPI482276_02g005220.1 Cam02g0522 522
2 6008453 6009304 - CaPI482276_02g005240.1 Cam02g0524 524
2 6039629 6043900 - CaPI482276_02g005280.1 Cam02g0528 528
2 6128740 6132910 + CaPI482276_02g005330.1 Cam02g0533 533
2 7623423 7625865 + CaPI482276_02g006580.1 Cam02g0658 658
2 1753542 1754368 + Carg22943-RA Car02g00258 258
2 1757399 1758267 + Carg22944-RA Car02g00259 259
2 1758392 1759520 - Carg22945-RA Car02g00260 260
2 1772335 1785904 + Carg22947-RA Car02g00262 262
11 8810869 8813831 + Carg26848-RA Car11g01109 1109
19 6186291 6187958 - Carg22079-RA Car19g00445 445
19 6752073 6757163 - Carg19409-RA Car19g00511 511
19 6771403 6777889 + Carg19407-RA Car19g00513 513
19 6781430 6781666 + Carg19406-RA Car19g00514 514
20 4287782 4288600 + Carg26480-RA Car20g00733 733
20 4312988 4315774 + Carg27532-RA Car20g00736 736
2 5043752 5045589 + CcPI632755_02g005330.1 Cco02g0533 533
2 5093358 5093579 - CcPI632755_02g005380.1 Cco02g0538 538
2 5172245 5176410 + CcPI632755_02g005430.1 Cco02g0543 543
2 6856973 6859403 + CcPI632755_02g006850.1 Cco02g0685 685
2 5019640 5021476 + CePI673135_02g005260.1 Cec02g0526 526
2 5028564 5029016 - CePI673135_02g005270.1 Cec02g0527 527
2 5074515 5074763 - CePI673135_02g005300.1 Cec02g0530 530
2 5150477 5154646 + CePI673135_02g005350.1 Cec02g0535 535
2 6760832 6763274 + CePI673135_02g006610.1 Cec02g0661 661
1 6072614 6072853 + Chy1G007790.1 Chy01g00779 779
1 6108545 6111387 - Chy1G007800.1 Chy01g00780 780
1 6193280 6197168 + Chy1G007820.1 Chy01g00782 782
11 3507372 3521495 + Chy11G189580.1 Chy11g00378 378
11 3522481 3524746 - Chy11G189590.1 Chy11g00379 379
11 3539940 3540725 - Chy11G189610.1 Chy11g00381 381
11 3559845 3564081 + Chy11G189620.1 Chy11g00382 382
2 4968064 4969879 + ClG42_02g0052400.10 Clacu02g0524 524
2 4976849 4978515 - ClG42_02g0052500.10 Clacu02g0525 525
2 5009828 5014983 - ClG42_02g0052900.10 Clacu02g0529 529
2 5095040 5099211 + ClG42_02g0053300.10 Clacu02g0533 533
2 6645622 6648029 + ClG42_02g0066600.10 Clacu02g0666 666
2 5187321 5189178 + ClCG02G004900.1 Cla02g00512 512
2 5196132 5197936 - ClCG02G004910.1 Cla02g00513 513
2 5249604 5249843 - ClCG02G004940.1 Cla02g00516 516
2 5333749 5338279 + ClCG02G004980.2 Cla02g00520 520
2 6955198 6957605 + ClCG02G006190.2 Cla02g00624 624
2 2006494 2011256 + CmaCh02G003960.1 Cma02g00396 396
2 2018144 2019211 - CmaCh02G004000.1 Cma02g00400 400
2 2021915 2032103 + CmaCh02G004010.1 Cma02g00401 401
11 11510182 11513104 - CmaCh11G017320.1 Cma11g01732 1732
19 6995635 6999989 - CmaCh19G006680.1 Cma19g00668 668
19 7022037 7022276 + CmaCh19G006720.1 Cma19g00672 672
19 7026526 7026762 + CmaCh19G006730.1 Cma19g00673 673
20 4066871 4067524 + CmaCh20G008490.1 Cma20g00849 849
20 4067706 4069472 - CmaCh20G008500.1 Cma20g00850 850
20 4075158 4076881 - CmaCh20G008520.1 Cma20g00852 852
20 4081771 4091257 + CmaCh20G008530.1 Cma20g00853 853
1 516480 519680 + MELO3C018473.2.1 Cme01g00073 73
1 17685167 17686506 - MELO3C012507.2.1 Cme01g01408 1408
1 17701570 17701815 - MELO3C012508.2.1 Cme01g01409 1409
1 17905365 17910588 + MELO3C012515.2.1 Cme01g01414 1414
1 6162219 6163174 - PI0027508.1 Cmetu01g1593 1593
7 4566075 4568561 + PI0017885.1 Cmetu07g0234 234
11 27418489 27427095 - PI0024539.1 Cmetu11g0117 117
11 27405583 27407299 + PI0006797.1 Cmetu11g0750 750
11 27415396 27417630 + PI0002725.1 Cmetu11g2150 2150
2 2074033 2075827 + CmoCh02G004010.1 Cmo02g00401 401
2 2076529 2078589 + CmoCh02G004020.1 Cmo02g00402 402
2 2079125 2080515 - CmoCh02G004030.1 Cmo02g00403 403
2 2084484 2087078 - CmoCh02G004050.1 Cmo02g00405 405
2 2095531 2100494 + CmoCh02G004070.1 Cmo02g00407 407
19 6699930 6709590 - CmoCh19G006050.1 Cmo19g00605 605
19 7223032 7233497 - CmoCh19G006810.1 Cmo19g00681 681
19 7242683 7243374 - CmoCh19G006820.1 Cmo19g00682 682
19 7253445 7254840 + CmoCh19G006840.1 Cmo19g00684 684
20 4321729 4326955 + CmoCh20G008580.1 Cmo20g00858 858
20 4328662 4328973 - CmoCh20G008590.1 Cmo20g00859 859
20 4334695 4336494 - CmoCh20G008610.1 Cmo20g00861 861
20 4345946 4352579 + CmoCh20G008620.1 Cmo20g00862 862
2 4892896 4894722 + CmPI595203_02g005210.1 Cmu02g0521 521
2 4901666 4903509 - CmPI595203_02g005220.1 Cmu02g0522 522
2 4907948 4909751 - CmPI595203_02g005230.1 Cmu02g0523 523
2 5012318 5017203 + CmPI595203_02g005280.1 Cmu02g0528 528
3 28721852 28725112 + Conep03aG0149000.1 Cone3ag0991 991
3 30301211 30301441 + Conep03aG0166900.1 Cone3ag1164 1164
8 10219306 10223045 - Conep08aG0123800.1 Cone8ag1202 1202
10 6429348 6430848 + Conep10aG0098500.1 Cone10ag0959 959
10 6479678 6479968 + Conep10aG0099000.1 Cone10ag0964 964
10 7009428 7012678 + Conep10aG0103900.1 Cone10ag1012 1012
10 8529363 8531547 - Conep10aG0120800.1 Cone10ag1173 1173
12 9188170 9192191 - Conep12aG0119100.1 Cone12ag1153 1153
4 1067393 1067698 + Cp4.1LG04g00950.1 Cpe04g00117 117
4 1074963 1076402 - Cp4.1LG04g00900.1 Cpe04g00118 118
4 1093670 1098508 + Cp4.1LG04g00960.1 Cpe04g00119 119
4 3733287 3736173 + Cp4.1LG04g07890.1 Cpe04g00295 295
5 8793508 8795586 - Cp4.1LG05g12680.1 Cpe05g01256 1256
5 8798566 8802856 + Cp4.1LG05g12570.1 Cpe05g01257 1257
5 8811282 8811662 - Cp4.1LG05g12670.1 Cpe05g01260 1260
5 8813871 8815678 - Cp4.1LG05g12630.1 Cpe05g01261 1261
15 5754029 5763131 - Cp4.1LG15g04750.1 Cpe15g00476 476
15 6275604 6281037 - Cp4.1LG15g05480.1 Cpe15g00542 542
15 6300543 6306179 + Cp4.1LG15g05450.1 Cpe15g00545 545
15 6321161 6321583 - Cp4.1LG15g05510.1 Cpe15g00548 548
2 5426969 5428766 + CrPI670011_02g008540.1 Cre02g0854 854
2 5434357 5434860 - CrPI670011_02g008550.1 Cre02g0855 855
2 5565753 5569921 + CrPI670011_02g008600.1 Cre02g0860 860
2 7179803 7182245 + CrPI670011_02g009790.1 Cre02g0979 979
2 12258510 12264087 - CsaV3_2G014680.1 Csa02g01252 1252
2 12279985 12281888 + CsaV3_2G014690.1 Csa02g01253 1253
2 12292648 12294898 + CsaV3_2G014710.1 Csa02g01255 1255
2 12294559 12302282 - CsaV3_2G014720.1 Csa02g01256 1256
2 12311152 12313801 - CsaV3_2G014740.1 Csa02g01258 1258
7 5217495 5220714 - CsaV3_7G008340.1 Csa07g00735 735
2 5013191 5013454 + Hsped.02g05020.1 Hepe02g0502 502
2 5017537 5017782 + Hsped.02g05030.1 Hepe02g0503 503
8 9696336 9699017 + Hsped.08g10150.1 Hepe08g1015 1015
8 9726795 9727395 + Hsped.08g10160.1 Hepe08g1016 1016
8 9731224 9731508 - Hsped.08g10170.1 Hepe08g1017 1017
8 9744275 9745100 - Hsped.08g10180.1 Hepe08g1018 1018
3 6054071 6057089 + Lsi03G005210.1 Lsi03g00521 521
10 5626808 5628960 - Lsi10G003650.1 Lsi10g00365 365
10 5657381 5660065 + Lsi10G003660.1 Lsi10g00366 366
10 5673126 5680589 + Lsi10G003670.1 Lsi10g00367 367
10 5674961 5679172 - Lsi10G003680.1 Lsi10g00368 368
10 5684474 5693629 - Lsi10G003690.1 Lsi10g00369 369
11 19223249 19228088 - Lsi11G011050.1 Lsi11g01105 1105
11 19275905 19276144 + Lsi11G011070.1 Lsi11g01107 1107
11 19352537 19354613 + Lsi11G011100.1 Lsi11g01110 1110
11 19366872 19367159 - Lsi11G011110.1 Lsi11g01111 1111
1 2302818 2303433 - Sed0025286.1 Sed01g0302 302
1 2316684 2318264 - Sed0018809.2 Sed01g0304 304
5 44523120 44527504 + Sed0027094.1 Sed05g3619 3619
5 44537637 44545439 + Sed0008972.2 Sed05g3621 3621
2 7900021 7901667 - Tan0013040.1 Tan02g0793 793
2 7933674 7933889 + Tan0002074.1 Tan02g0794 794
5 15832692 15833358 + Tan0021888.1 Tan05g1308 1308
5 15998841 16007476 + Tan0016045.1 Tan05g1310 1310
5 16011561 16012520 - Tan0010211.1 Tan05g1311 1311
5 16044031 16046106 - Tan0019603.1 Tan05g1313 1313
3 5808409 5815024 - Vvi3g596 Vvi3g596 596
3 5832903 5834101 + Vvi3g597 Vvi3g597 597
3 5845677 5849261 + Vvi3g598 Vvi3g598 598
3 5851027 5859014 - Vvi3g599 Vvi3g599 599
3 5870396 5873133 + Vvi3g600 Vvi3g600 600
3 5885526 5887512 + Vvi3g601 Vvi3g601 601
3 5887914 5897060 + Vvi3g602 Vvi3g602 602
3 5902158 5903523 - Vvi3g603 Vvi3g603 603
3 5919584 5923304 - Vvi3g604 Vvi3g604 604
3 5934426 5937550 + Vvi3g605 Vvi3g605 605
       

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