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
Vvi3g386 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag1122 . . Lsi10g00525 . . . Blo04g00480 . . Bda14g00510 Bpe15g00902 . Bma03g00512 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g387 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi10g00526 . . . . . . . . . . . . Cmo02g00532 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g388 . . . . . . . . Cmo19g00616 Cmo11g01374 . . . . . Cpe04g00288 Cpe15g00482 Bhi05g01073 . . . . . . Cla02g00610 Cam02g0640 Cec02g0638 Cco02g0660 Clacu02g0644 Cmu02g0639 Cre02g0963 . . Cone3ag1187 Cone10ag1000 . Csa07g00749 . Cme01g00059 Blo04g00483 Blo13g00580 . Bda14g00511 Bpe15g00901 . Bma03g00513 . . . . Cma11g01741 Cma19g00598 . Car19g00451 . . . . . . . . . . . . . . . . . . Chy01g00062 .
Vvi3g389 . Blo15g00754 Bda06g01077 . Bpe07g00370 Bpe12g00053 . Bma12g00434 Cmo19g00617 Cmo11g01373 . . . . . Cpe04g00287 Cpe15g00483 Bhi05g01072 . . . . . . Cla02g00608 Cam02g0639 Cec02g0637 Cco02g0657 Clacu02g0642 Cmu02g0638 Cre02g0962 . . . . . Csa07g00750 . Cme01g00058 Blo04g00484 Blo13g00579 Bda15g00039 . . . Bma03g00514 Bma08g00805 . . . Cma11g01742 Cma19g00599 . Car19g00452 Cpe14g00290 Cpe01g00432 . . . . . . . . . . . . . . . . Chy01g00061 .
Vvi3g390 Blo02g00828 Blo15g00753 . . Bpe07g00372 Bpe12g00054 . Bma12g00435 . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag1124 Cone3ag1185 . . . . . Blo04g00485 Blo13g00578 . Bda14g00513 Bpe15g00900 . Bma03g00515 Bma08g00803 . . . . . Car11g01090 . . . . . . . . . . . . . . . . . . . . .
Vvi3g391 Blo02g00829 Blo15g00751 . . . . . Bma12g00439 . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1184 Cone10ag0997 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g392 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car11g01091 . . . . . . . . . . . . . . . . . . . . .
Vvi3g393 . . . . . . . . . . . Cma20g00922 . Car20g00807 . . . . . . . . . . . . . . . . . . . Cone6ag1272 . . . Chy11g00460 . . . . . . . . . . . Cmo20g00929 . . . . . Cpe01g00435 Bhi10g02092 . . . . . . . . . . . . . . . . .
Vvi3g394 . Blo15g00750 Bda06g01073 . Bpe07g00375 . . Bma12g00441 . . Cma02g00450 . Car02g00306 . . . . . . . . . . . . . . . . . . Cone12ag1084 . Cone3ag1181 Cone10ag0992 Lsi10g00528 . . . . . . . . . . . . Cmo02g00459 . . . . . Cpe14g00291 Cpe01g00437 . . . . . . . . . . . . . . . . . Cme11g00541
Vvi3g395 Blo02g00798 Blo15g00749 . Bda08g00923 Bpe07g00376 . Bma05g00474 Bma12g00444 . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1180 Cone10ag0989 . . . . . . . . . . . . . . . . . . . Cpe14g00292 Cpe01g00438 . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 38076471 38080313 + Bda022837.1 Bda06g01073 1073
6 38310139 38310573 - Bda022846.1 Bda06g01077 1077
8 16984613 16987258 - Bda029555.1 Bda08g00923 923
14 3714630 3717967 + Bda027255.1 Bda14g00510 510
14 3718846 3722380 - Bda027256.5 Bda14g00511 511
14 3727678 3728977 - Bda027258.1 Bda14g00513 513
15 1846428 1846862 - Bda011797.1 Bda15g00039 39
5 38601473 38602255 - XM_039031047.1 Bhi05g01072 1072
5 38662342 38667242 + XM_039032630.1 Bhi05g01073 1073
10 52488776 52500236 + XM_039045083.1 Bhi10g02092 2092
2 27198106 27200077 + BLOR10528 Blo02g00798 798
2 29714595 29715756 - BLOR10558 Blo02g00828 828
2 29905024 29914171 + BLOR10559 Blo02g00829 829
4 3983129 3986452 + BLOR13392 Blo04g00480 480
4 4015745 4017796 - BLOR13395 Blo04g00483 483
4 4019041 4019475 + BLOR13396 Blo04g00484 484
4 4025084 4031097 - BLOR13397 Blo04g00485 485
13 27919463 27920006 + BLOR19630 Blo13g00578 578
13 27924540 27926127 - BLOR19631 Blo13g00579 579
13 27926351 27928291 + BLOR19632 Blo13g00580 580
15 25402779 25406460 - BLOR07143 Blo15g00749 749
15 25434709 25438905 + BLOR07144 Blo15g00750 750
15 25503272 25505733 - BLOR07145 Blo15g00751 751
15 25660661 25662076 + BLOR07147 Blo15g00753 753
15 25667037 25667468 - BLOR07148 Blo15g00754 754
3 3983352 3986069 + Bma016793.1 Bma03g00512 512
3 3986955 3988768 - Bma016794.1 Bma03g00513 513
3 3990286 3990720 + Bma016795.1 Bma03g00514 514
3 3991540 3993501 - Bma016796.1 Bma03g00515 515
5 17633591 17635678 - Bma021367.1 Bma05g00474 474
8 45633751 45634843 + Bma028191.1 Bma08g00803 803
8 45649075 45656663 - Bma028194.1 Bma08g00805 805
12 10893670 10894104 + Bma007433.1 Bma12g00434 434
12 10926811 10928133 - Bma007436.1 Bma12g00435 435
12 11073626 11080894 + Bma007443.1 Bma12g00439 439
12 11109356 11112584 - Bma007445.1 Bma12g00441 441
12 11231440 11234928 + Bma007449.1 Bma12g00444 444
7 3113306 3113740 + Bpe021183.1 Bpe07g00370 370
7 3129263 3130424 - Bpe021185.1 Bpe07g00372 372
7 3219047 3222777 - Bpe021190.1 Bpe07g00375 375
7 3240847 3245352 + Bpe021191.1 Bpe07g00376 376
12 413236 413670 + Bpe005292.1 Bpe12g00053 53
12 415057 418962 - Bpe005293.1 Bpe12g00054 54
15 18884480 18885711 + Bpe001822.1 Bpe15g00900 900
15 18888438 18890248 + Bpe001823.1 Bpe15g00901 901
15 18891190 18893762 - Bpe001824.1 Bpe15g00902 902
2 7372155 7372592 - CaPI482276_02g006390.1 Cam02g0639 639
2 7391555 7397485 + CaPI482276_02g006400.1 Cam02g0640 640
2 2079154 2081130 + Carg24051-RA Car02g00306 306
11 8560992 8561443 - Carg26412-RA Car11g01090 1090
11 8599152 8601218 + Carg26411-RA Car11g01091 1091
19 6233252 6242873 - Carg22073-RA Car19g00451 451
19 6244860 6245294 + Carg22072-RA Car19g00452 452
20 4934481 4938264 - Carg26841-RA Car20g00807 807
2 6571020 6571457 - CcPI632755_02g006570.1 Cco02g0657 657
2 6614614 6620674 + CcPI632755_02g006600.1 Cco02g0660 660
2 6457270 6457707 - CePI673135_02g006370.1 Cec02g0637 637
2 6468237 6474112 + CePI673135_02g006380.1 Cec02g0638 638
1 447463 457450 - Chy1G000610.1 Chy01g00061 61
1 462433 464859 + Chy1G000620.1 Chy01g00062 62
11 4806322 4809465 + Chy11G190400.1 Chy11g00460 460
2 6382786 6383223 - ClG42_02g0064200.10 Clacu02g0642 642
2 6401908 6407725 + ClG42_02g0064400.10 Clacu02g0644 644
2 6679642 6680079 - ClCG02G006030.1 Cla02g00608 608
2 6698768 6704582 + ClCG02G006050.2 Cla02g00610 610
2 2333105 2335081 + CmaCh02G004500.1 Cma02g00450 450
11 11557246 11560231 - CmaCh11G017410.1 Cma11g01741 1741
11 11562857 11563291 + CmaCh11G017420.1 Cma11g01742 1742
19 6575759 6579776 - CmaCh19G005980.1 Cma19g00598 598
19 6581743 6582177 + CmaCh19G005990.1 Cma19g00599 599
20 4516169 4521749 - CmaCh20G009220.1 Cma20g00922 922
1 449138 450012 - MELO3C018459.2.1 Cme01g00058 58
1 454795 457979 + MELO3C018460.2.1 Cme01g00059 59
11 5715881 5728425 + MELO3C021891.2.1 Cme11g00541 541
2 2434221 2436197 + CmoCh02G004590.1 Cmo02g00459 459
2 3016760 3020534 + CmoCh02G005320.1 Cmo02g00532 532
11 9582373 9582807 - CmoCh11G013730.1 Cmo11g01373 1373
11 9591076 9594824 + CmoCh11G013740.1 Cmo11g01374 1374
19 6767617 6772233 - CmoCh19G006160.1 Cmo19g00616 616
19 6774093 6774527 + CmoCh19G006170.1 Cmo19g00617 617
20 4811069 4816761 - CmoCh20G009290.1 Cmo20g00929 929
2 6289253 6289690 - CmPI595203_02g006380.1 Cmu02g0638 638
2 6308388 6314191 + CmPI595203_02g006390.1 Cmu02g0639 639
3 30464253 30469036 - Conep03aG0168700.1 Cone3ag1180 1180
3 30475236 30479204 + Conep03aG0168800.1 Cone3ag1181 1181
3 30512251 30520477 - Conep03aG0169100.1 Cone3ag1184 1184
3 30530874 30532360 + Conep03aG0169200.1 Cone3ag1185 1185
3 30545155 30548611 + Conep03aG0169400.1 Cone3ag1187 1187
6 10165236 10166474 + Conep06aG0132000.1 Cone6ag1272 1272
8 9923097 9926357 + Conep08aG0115300.1 Cone8ag1122 1122
8 9929186 9930686 - Conep08aG0115500.1 Cone8ag1124 1124
10 6688146 6689096 - Conep10aG0101500.1 Cone10ag0989 989
10 6720565 6723275 + Conep10aG0101900.1 Cone10ag0992 992
10 6797150 6806543 - Conep10aG0102400.1 Cone10ag0997 997
10 6839676 6842216 - Conep10aG0102700.1 Cone10ag1000 1000
12 8878209 8879898 - Conep12aG0111800.1 Cone12ag1084 1084
1 2494980 2495414 + Cp4.1LG01g02420.1 Cpe01g00432 432
1 2508832 2510097 - Cp4.1LG01g02230.1 Cpe01g00435 435
1 2517150 2519801 - Cp4.1LG01g02200.1 Cpe01g00437 437
1 2522297 2527875 + Cp4.1LG01g02310.1 Cpe01g00438 438
4 3575780 3576214 - Cp4.1LG04g07910.1 Cpe04g00287 287
4 3581759 3585220 + Cp4.1LG04g07960.1 Cpe04g00288 288
14 1700281 1700715 + Cp4.1LG14g04260.1 Cpe14g00290 290
14 1701702 1710250 - Cp4.1LG14g04190.1 Cpe14g00291 291
14 1714613 1720884 + Cp4.1LG14g04310.1 Cpe14g00292 292
15 5818206 5822876 - Cp4.1LG15g04890.1 Cpe15g00482 482
15 5824907 5825341 + Cp4.1LG15g04770.1 Cpe15g00483 483
2 6909771 6910208 - CrPI670011_02g009620.1 Cre02g0962 962
2 6928675 6934657 + CrPI670011_02g009630.1 Cre02g0963 963
7 5274832 5278203 - CsaV3_7G008480.1 Csa07g00749 749
7 5281660 5282965 + CsaV3_7G008490.1 Csa07g00750 750
10 7503788 7508410 + Lsi10G005250.1 Lsi10g00525 525
10 7509978 7514571 - Lsi10G005260.1 Lsi10g00526 526
10 7549052 7553953 + Lsi10G005280.1 Lsi10g00528 528
3 3656156 3664784 + Vvi3g386 Vvi3g386 386
3 3664806 3668161 - Vvi3g387 Vvi3g387 387
3 3675407 3678032 - Vvi3g388 Vvi3g388 388
3 3717641 3718712 - Vvi3g389 Vvi3g389 389
3 3733845 3735258 - Vvi3g390 Vvi3g390 390
3 3769535 3782588 + Vvi3g391 Vvi3g391 391
3 3785856 3788100 + Vvi3g392 Vvi3g392 392
3 3794272 3796050 - Vvi3g393 Vvi3g393 393
3 3812817 3816504 - Vvi3g394 Vvi3g394 394
3 3823722 3830160 + Vvi3g395 Vvi3g395 395
       

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