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
Vvi3g606 . . . . . Bpe12g00294 . . . Cmo11g01384 . . . . . Cpe04g00296 Cpe15g00475 . . . . . . . Cla02g00625 . Cec02g0662 . . Cmu02g0661 . . . Cone3ag0992 Cone10ag1013 Lsi03g00522 Csa07g00734 . Cme01g00074 . . Bda15g00847 Bda14g01451 . . Bma03g01356 Bma08g00514 . . . Cma11g01730 Cma19g00587 Car11g01110 . . . . . . . . . . . . . . . . . . . Chy01g00080 .
Vvi3g607 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g608 . . . . . Bpe12g00295 . . Cmo19g00604 Cmo11g01385 . . . . . Cpe04g00297 Cpe15g00474 . . . . . . . Cla02g00626 Cam02g0659 Cec02g0663 Cco02g0686 Clacu02g0667 . Cre02g0980 . . Cone3ag0993 Cone10ag1014 Lsi03g00523 Csa07g00733 . Cme01g00075 . . . . . . . . . . . Cma11g01729 Cma19g00586 Car11g01111 . . . . . . . . . . . . . . . . . . . Chy01g00081 .
Vvi3g609 Blo02g00838 . . Bda08g00772 . . Bma05g00508 . Cmo19g00602 Cmo11g01386 . . . . . Cpe04g00298 Cpe15g00473 . . . . . . . Cla02g00627 Cam02g0660 Cec02g0664 Cco02g0687 Clacu02g0668 Cmu02g0662 Cre02g0981 . Cone8ag1114 . . Lsi03g00524 Csa07g00732 . Cme01g00076 . . Bda15g00846 Bda14g01452 . . Bma03g01357 . . Cmo04g00511 Cmo16g00370 Cma11g01728 Cma19g00585 Car11g01112 . Cpe14g00286 Cpe01g00427 . . . . . . . . . . . . . . . . Chy01g00082 .
Vvi3g610 . . . . . Bpe12g00297 . . . Cmo11g01387 . . . . . Cpe04g00299 . . . . . . . . . . . . . . . . Cone8ag1113 . . . . . . . . Bda15g00845 . . . . . . . . . . Car11g01113 . . . . . . . . . . . . . . . . . . . . .
Vvi3g611 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g612 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag1112 . . . Csa07g00730 . Cme01g00078 . . . Bda14g01455 . . Bma03g01368 . . . . Cma11g01727 . . . . . . . . . . . . . . . . . . . . . Chy01g00084 .
Vvi3g613 . . . . . . . . . Cmo11g01388 . . . . . Cpe04g00300 . . . . . . . . Cla02g00629 Cam02g0663 Cec02g0667 Cco02g0691 Clacu02g0671 Cmu02g0665 Cre02g0984 . . . . Lsi03g00526 Csa07g00729 . Cme01g00079 . . . Bda14g01456 . . Bma03g01359 . . . . . . Car11g01114 . . . . . . . . . . . . . . . . . Lsi03g01043 . Chy01g00085 .
Vvi3g614 . Blo03g00087 . . . Bpe12g00298 . . Cmo19g00600 Cmo11g01389 . . . . . Cpe04g00301 Cpe15g00471 . . . . . . . Cla02g00630 Cam02g0664 Cec02g0668 Cco02g0692 Clacu02g0672 Cmu02g0666 Cre02g0985 . Cone8ag1111 Cone3ag0994 Cone10ag1015 Lsi03g00527 Csa07g00728 . Cme01g00080 . . Bda15g00844 . . . . Bma08g00506 . . . Cma11g01726 . Car11g01115 . . . Bhi11g01177 . . . . . . . . . . . . . . . Chy01g00086 .
Vvi3g615 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 10024538 10025922 - Bda029274.1 Bda08g00772 772
14 19537856 19543912 + Bda011196.2 Bda14g01451 1451
14 19597163 19598491 + Bda011197.1 Bda14g01452 1452
14 19735065 19736660 + Bda011201.1 Bda14g01455 1455
14 19744759 19747054 + Bda033247 Bda14g01456 1456
15 12943259 12944670 + Bda012715.1 Bda15g00844 844
15 12966941 12969732 + Bda012718.1 Bda15g00845 845
15 12997850 12999358 - Bda012719.1 Bda15g00846 846
15 13141380 13151660 - Bda012723.1 Bda15g00847 847
11 34330002 34333413 - XM_039049828.1 Bhi11g01177 1177
2 30947685 30948403 + BLOR10568 Blo02g00838 838
3 2932799 2935385 - BLOR11268 Blo03g00087 87
3 29597487 29603603 + Bma017898.1 Bma03g01356 1356
3 29764426 29765751 + Bma017901.1 Bma03g01357 1357
3 30409032 30411277 + Bma031031 Bma03g01359 1359
3 31934253 31936451 - Bma017923.1 Bma03g01368 1368
5 23352071 23354071 - Bma021440.1 Bma05g00508 508
8 26484942 26486132 + Bma027715.1 Bma08g00506 506
8 27821531 27836632 - Bma027727.1 Bma08g00514 514
12 3694760 3703177 + Bpe024885 Bpe12g00294 294
12 3704384 3705033 + Bpe005540.1 Bpe12g00295 295
12 3912265 3915050 - Bpe005542.1 Bpe12g00297 297
12 4029204 4030631 - Bpe005543.1 Bpe12g00298 298
2 7629061 7641107 + CaPI482276_02g006590.1 Cam02g0659 659
2 7659345 7661771 + CaPI482276_02g006600.1 Cam02g0660 660
2 7718216 7723069 - CaPI482276_02g006630.1 Cam02g0663 663
2 7733525 7734703 + CaPI482276_02g006640.1 Cam02g0664 664
11 8814536 8820532 + Carg26849-RA Car11g01110 1110
11 8824023 8826674 + Carg26850-RA Car11g01111 1111
11 8836464 8838349 + Carg26851-RA Car11g01112 1112
11 8852005 8859140 - Carg26852-RA Car11g01113 1113
11 8860149 8863555 - Carg26853-RA Car11g01114 1114
11 8867886 8869049 + Carg26854-RA Car11g01115 1115
2 6863544 6875004 + CcPI632755_02g006860.1 Cco02g0686 686
2 6898797 6901179 + CcPI632755_02g006870.1 Cco02g0687 687
2 6959815 6964594 - CcPI632755_02g006910.1 Cco02g0691 691
2 6975274 6976452 + CcPI632755_02g006920.1 Cco02g0692 692
2 6767504 6773829 + CePI673135_02g006620.1 Cec02g0662 662
2 6780491 6783184 + CePI673135_02g006630.1 Cec02g0663 663
2 6803829 6806231 + CePI673135_02g006640.1 Cec02g0664 664
2 6861920 6866480 - CePI673135_02g006670.1 Cec02g0667 667
2 6876637 6877815 + CePI673135_02g006680.1 Cec02g0668 668
1 535322 540728 + Chy1G000800.1 Chy01g00080 80
1 542704 544875 + Chy1G000810.1 Chy01g00081 81
1 554313 555392 + Chy1G000820.1 Chy01g00082 82
1 574109 576601 - Chy1G000840.1 Chy01g00084 84
1 577794 580788 - Chy1G000850.1 Chy01g00085 85
1 582338 583513 + Chy1G000860.1 Chy01g00086 86
2 6651261 6663389 + ClG42_02g0066700.10 Clacu02g0667 667
2 6681708 6684075 + ClG42_02g0066800.10 Clacu02g0668 668
2 6738615 6743244 - ClG42_02g0067100.10 Clacu02g0671 671
2 6753820 6754998 + ClG42_02g0067200.10 Clacu02g0672 672
2 6960842 6967184 + ClCG02G006200.2 Cla02g00625 625
2 6970216 6973516 + ClCG02G006210.2 Cla02g00626 626
2 6991298 6994274 + ClCG02G006220.2 Cla02g00627 627
2 7046573 7057620 - ClCG02G006240.1 Cla02g00629 629
2 7068500 7069678 + ClCG02G006250.1 Cla02g00630 630
11 11457715 11458875 - CmaCh11G017260.1 Cma11g01726 1726
11 11461640 11473920 + CmaCh11G017270.1 Cma11g01727 1727
11 11487243 11489568 - CmaCh11G017280.1 Cma11g01728 1728
11 11497974 11501598 - CmaCh11G017290.1 Cma11g01729 1729
11 11504002 11508959 - CmaCh11G017300.1 Cma11g01730 1730
19 6507822 6510117 - CmaCh19G005850.1 Cma19g00585 585
19 6511495 6514679 - CmaCh19G005860.1 Cma19g00586 586
19 6516097 6522524 - CmaCh19G005870.1 Cma19g00587 587
1 521937 528246 + MELO3C018474.2.1 Cme01g00074 74
1 530183 533124 + MELO3C018475.2.1 Cme01g00075 75
1 541452 543924 + MELO3C018476.2.1 Cme01g00076 76
1 560716 563539 - MELO3C018478.2.1 Cme01g00078 78
1 563982 567421 - MELO3C018479.2.1 Cme01g00079 79
1 569752 571174 + MELO3C018480.2.1 Cme01g00080 80
4 2537126 2538960 - CmoCh04G005110.1 Cmo04g00511 511
11 9670549 9679642 + CmoCh11G013840.1 Cmo11g01384 1384
11 9683459 9686641 + CmoCh11G013850.1 Cmo11g01385 1385
11 9696714 9699068 + CmoCh11G013860.1 Cmo11g01386 1386
11 9710942 9720385 - CmoCh11G013870.1 Cmo11g01387 1387
11 9721806 9725244 - CmoCh11G013880.1 Cmo11g01388 1388
11 9730110 9731273 + CmoCh11G013890.1 Cmo11g01389 1389
16 1697863 1699603 - CmoCh16G003700.1 Cmo16g00370 370
19 6680362 6681537 - CmoCh19G006000.1 Cmo19g00600 600
19 6691342 6693804 - CmoCh19G006020.1 Cmo19g00602 602
19 6695864 6698078 - CmoCh19G006040.1 Cmo19g00604 604
2 6551902 6569666 + CmPI595203_02g006610.1 Cmu02g0661 661
2 6588004 6590378 + CmPI595203_02g006620.1 Cmu02g0662 662
2 6645086 6649617 - CmPI595203_02g006650.1 Cmu02g0665 665
2 6660171 6661349 + CmPI595203_02g006660.1 Cmu02g0666 666
3 28728692 28734006 + Conep03aG0149100.1 Cone3ag0992 992
3 28746892 28749013 + Conep03aG0149200.1 Cone3ag0993 993
3 28750106 28751660 + Conep03aG0149300.1 Cone3ag0994 994
8 9876610 9877997 - Conep08aG0114200.1 Cone8ag1111 1111
8 9878702 9881188 - Conep08aG0114300.1 Cone8ag1112 1112
8 9884538 9887367 + Conep08aG0114400.1 Cone8ag1113 1113
8 9891151 9893094 - Conep08aG0114500.1 Cone8ag1114 1114
10 7023423 7028799 + Conep10aG0104000.1 Cone10ag1013 1013
10 7036219 7038481 + Conep10aG0104100.1 Cone10ag1014 1014
10 7039543 7040851 + Conep10aG0104200.1 Cone10ag1015 1015
1 2468894 2471504 - Cp4.1LG01g02390.1 Cpe01g00427 427
4 3737062 3742686 + Cp4.1LG04g07880.1 Cpe04g00296 296
4 3746274 3749405 + Cp4.1LG04g07900.1 Cpe04g00297 297
4 3757790 3760173 + Cp4.1LG04g07870.1 Cpe04g00298 298
4 3771645 3780826 - Cp4.1LG04g07860.1 Cpe04g00299 299
4 3782081 3785238 - Cp4.1LG04g07780.1 Cpe04g00300 300
4 3788710 3789876 + Cp4.1LG04g07820.1 Cpe04g00301 301
14 1670885 1675313 - Cp4.1LG14g04220.1 Cpe14g00286 286
15 5726752 5727927 - Cp4.1LG15g04690.1 Cpe15g00471 471
15 5737985 5740755 - Cp4.1LG15g04710.1 Cpe15g00473 473
15 5742362 5745378 - Cp4.1LG15g04730.1 Cpe15g00474 474
15 5747188 5753065 - Cp4.1LG15g04760.1 Cpe15g00475 475
2 7185701 7197818 + CrPI670011_02g009800.1 Cre02g0980 980
2 7216459 7218837 + CrPI670011_02g009810.1 Cre02g0981 981
2 7269457 7274173 - CrPI670011_02g009840.1 Cre02g0984 984
2 7284130 7285308 + CrPI670011_02g009850.1 Cre02g0985 985
7 5166923 5168512 - CsaV3_7G008270.1 Csa07g00728 728
7 5169803 5173804 + CsaV3_7G008280.1 Csa07g00729 729
7 5173992 5177055 + CsaV3_7G008290.1 Csa07g00730 730
7 5194238 5197055 - CsaV3_7G008310.1 Csa07g00732 732
7 5204455 5208181 - CsaV3_7G008320.1 Csa07g00733 733
7 5208981 5215476 - CsaV3_7G008330.1 Csa07g00734 734
3 6061136 6067072 + Lsi03G005220.1 Lsi03g00522 522
3 6071229 6074694 + Lsi03G005230.1 Lsi03g00523 523
3 6105614 6108737 + Lsi03G005240.1 Lsi03g00524 524
3 6171094 6183236 - Lsi03G005260.1 Lsi03g00526 526
3 6187341 6188519 + Lsi03G005270.1 Lsi03g00527 527
3 20033749 20041525 - Lsi03G010430.1 Lsi03g01043 1043
3 5941803 5961856 + Vvi3g606 Vvi3g606 606
3 5961867 5961984 - Vvi3g607 Vvi3g607 607
3 5962591 5966795 + Vvi3g608 Vvi3g608 608
3 5973764 5975813 + Vvi3g609 Vvi3g609 609
3 5981435 5989264 - Vvi3g610 Vvi3g610 610
3 5989503 5993941 + Vvi3g611 Vvi3g611 611
3 5995077 6001048 - Vvi3g612 Vvi3g612 612
3 6009081 6020768 - Vvi3g613 Vvi3g613 613
3 6023243 6024532 + Vvi3g614 Vvi3g614 614
3 6030244 6032840 + Vvi3g615 Vvi3g615 615
       

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