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
Vvi3g536 Blo02g00788 . . Bda08g00906 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1132 Cone10ag1142 Lsi10g00648 . . . . . . . . . . . . . . . . . . . . Bhi10g02041 . . . . . . . . . . . . . . . . Cme11g00226
Vvi3g537 Blo02g00791 Blo15g00713 Bda06g01014 Bda08g00905 Bpe07g00412 . . Bma12g00494 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi10g02040 . . . . . . . . . . . . . . . . .
Vvi3g538 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g539 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g540 . . . Bda08g00904 . . Bma05g00503 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g541 Blo02g00792 . . Bda08g00916 . . Bma05g00500 . . . . . . Car20g00749 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g542 Blo02g00793 Blo15g00712 . Bda08g00903 Bpe07g00413 . . Bma12g00495 Cmo19g00655 Cmo11g01327 . Cma20g00866 . . Sed01g0313 Cpe04g00254 Cpe15g00518 Bhi05g01178 Tan02g0851 Cmetu11g2117 . Hepe02g0547 . . Cla02g00556 Cam02g0582 Cec02g0584 Cco02g0594 Clacu02g0581 Cmu02g0578 Cre02g0908 . . . Cone10ag1147 . . . Cme01g00007 . . . . . . . . Sed05g3633 . Cmo20g00876 Cma11g01782 Cma19g00642 Car11g01069 . . . Bhi10g02039 Tan05g1340 Cmetu11g1828 . . . . . . . . . . . Lsi11g01054 . Chy01g00008 .
Vvi3g543 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1128 Cone8ag1175 . . . Csa07g00820 . . Blo04g00500 . . Bda14g00534 . . Bma03g01401 . . . . . . . Car19g00488 . . . . . . . . . . . . . . . . . . . .
Vvi3g544 . . . . Bpe07g00414 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1137 Cone10ag1148 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g545 . . . . . Bpe12g00072 . . Cmo19g00656 . . . . . Sed10g2078 . Cpe15g00519 Bhi05g01180 Tan02g0850 Cmetu01g2149 . Hepe02g0546 . . Cla02g00555 Cam02g0580 Cec02g0582 Cco02g0592 Clacu02g0580 Cmu02g0576 Cre02g0906 Cone12ag1129 . . . . Csa07g00828 . Cme01g00005 . Blo13g00558 Bda15g00020 . . . . . . . . . Cma19g00645 . . . . . . . . . . . . . . . . . . Lsi11g01056 . Chy01g00006 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 35437731 35438447 - Bda022748.1 Bda06g01014 1014
8 16486865 16489342 + Bda029522.1 Bda08g00903 903
8 16489820 16490508 + Bda029523.1 Bda08g00904 904
8 16490893 16491609 - Bda029524.1 Bda08g00905 905
8 16506914 16508347 + Bda029526.1 Bda08g00906 906
8 16816802 16817421 - Bda029541.1 Bda08g00916 916
14 3859164 3861070 - Bda027280.1 Bda14g00534 534
15 1426875 1431849 + Bda011771.1 Bda15g00020 20
5 42123742 42127162 + XM_039033094.1 Bhi05g01178 1178
5 42138802 42141874 + XM_039031761.1 Bhi05g01180 1180
10 50991414 51000389 + XM_039046553.1 Bhi10g02039 2039
10 51051890 51053944 - XM_039045905.1 Bhi10g02040 2040
10 51060553 51064893 - XM_039045693.1 Bhi10g02041 2041
2 26726658 26728151 - BLOR10518 Blo02g00788 788
2 26819201 26819902 + BLOR10521 Blo02g00791 791
2 26820218 26820917 - BLOR10522 Blo02g00792 792
2 26821353 26823507 - BLOR10523 Blo02g00793 793
4 4151146 4162068 - BLOR13412 Blo04g00500 500
13 27576515 27588065 + BLOR19610 Blo13g00558 558
15 23101189 23112084 + BLOR07106 Blo15g00712 712
15 23142313 23156389 - BLOR07107 Blo15g00713 713
3 35611548 35623677 - Bma018000.1 Bma03g01401 1401
5 22797650 22798175 - Bma021430.1 Bma05g00500 500
5 23045625 23046101 - Bma021435.1 Bma05g00503 503
12 14874790 14875509 + Bma007541.1 Bma12g00494 494
12 14876416 14886262 - Bma007542.1 Bma12g00495 495
7 4169339 4170055 + Bpe021235.1 Bpe07g00412 412
7 4171009 4173066 - Bpe026057 Bpe07g00413 413
7 4176421 4181934 - Bpe021236.1 Bpe07g00414 414
12 506282 508517 - Bpe005310.1 Bpe12g00072 72
2 6602397 6609740 - CaPI482276_02g005800.1 Cam02g0580 580
2 6618261 6621342 - CaPI482276_02g005820.1 Cam02g0582 582
11 8266416 8269589 - Carg26483-RA Car11g01069 1069
19 6492102 6495360 + Carg22035-RA Car19g00488 488
20 4389893 4394573 - Carg23634-RA Car20g00749 749
2 5751516 5762378 - CcPI632755_02g005920.1 Cco02g0592 592
2 5771175 5774257 - CcPI632755_02g005940.1 Cco02g0594 594
2 5634945 5642256 - CePI673135_02g005820.1 Cec02g0582 582
2 5651126 5654206 - CePI673135_02g005840.1 Cec02g0584 584
1 48427 51033 - Chy1G000060.1 Chy01g00006 6
1 65536 68377 - Chy1G000080.1 Chy01g00008 8
2 5572846 5587087 - ClG42_02g0058000.10 Clacu02g0580 580
2 5588752 5591833 - ClG42_02g0058100.10 Clacu02g0581 581
2 5837356 5848382 - ClCG02G005360.1 Cla02g00555 555
2 5852445 5860478 - ClCG02G005370.2 Cla02g00556 556
11 11921966 11924592 + CmaCh11G017820.1 Cma11g01782 1782
19 6828123 6835704 + CmaCh19G006420.1 Cma19g00642 642
19 6839543 6850584 - CmaCh19G006450.1 Cma19g00645 645
20 4155344 4161641 - CmaCh20G008660.1 Cma20g00866 866
1 43014 46131 - MELO3C018408.2.1 Cme01g00005 5
1 59833 63211 - MELO3C018410.2.1 Cme01g00007 7
11 2622146 2629508 + MELO3C020947.2.1 Cme11g00226 226
1 62769 65369 - PI0008632.1 Cmetu01g2149 2149
11 27114342 27115611 + PI0010715.1 Cmetu11g1828 1828
11 27110462 27112732 + PI0027906.1 Cmetu11g2117 2117
11 9163720 9167106 - CmoCh11G013270.1 Cmo11g01327 1327
19 7045313 7054052 + CmoCh19G006550.1 Cmo19g00655 655
19 7068906 7072954 - CmoCh19G006560.1 Cmo19g00656 656
20 4423800 4427376 - CmoCh20G008760.1 Cmo20g00876 876
2 5490998 5498309 - CmPI595203_02g005760.1 Cmu02g0576 576
2 5506902 5509983 - CmPI595203_02g005780.1 Cmu02g0578 578
3 29909707 29911294 + Conep03aG0163600.1 Cone3ag1132 1132
3 29958169 29963156 - Conep03aG0164100.1 Cone3ag1137 1137
8 10122511 10125090 - Conep08aG0120800.1 Cone8ag1175 1175
10 8260022 8262281 + Conep10aG0117400.1 Cone10ag1142 1142
10 8298832 8300641 - Conep10aG0117900.1 Cone10ag1147 1147
10 8302117 8306806 - Conep10aG0118000.1 Cone10ag1148 1148
12 9079072 9081870 - Conep12aG0116400.1 Cone12ag1128 1128
12 9084969 9088781 - Conep12aG0116500.1 Cone12ag1129 1129
4 3139652 3143492 + Cp4.1LG04g08340.1 Cpe04g00254 254
15 6105929 6109040 + Cp4.1LG15g05210.1 Cpe15g00518 518
15 6111926 6115902 - Cp4.1LG15g05230.1 Cpe15g00519 519
2 6093830 6104764 - CrPI670011_02g009060.1 Cre02g0906 906
2 6113587 6116651 - CrPI670011_02g009080.1 Cre02g0908 908
7 5765785 5770205 + CsaV3_7G010180.1 Csa07g00820 820
7 5832137 5834973 - CsaV3_7G010260.1 Csa07g00828 828
2 5515535 5518412 + Hsped.02g05460.1 Hepe02g0546 546
2 5520387 5523834 - Hsped.02g05470.1 Hepe02g0547 547
10 9047967 9051845 - Lsi10G006480.1 Lsi10g00648 648
11 18286398 18308260 + Lsi11G010540.1 Lsi11g01054 1054
11 18319346 18322636 + Lsi11G010560.1 Lsi11g01056 1056
1 2398635 2401262 - Sed0023769.1 Sed01g0313 313
5 44619000 44620300 - Sed0006680.1 Sed05g3633 3633
10 37252001 37255485 - Sed0002261.3 Sed10g2078 2078
2 9179003 9184775 + Tan0006391.1 Tan02g0850 850
2 9189467 9192762 - Tan0016241.1 Tan02g0851 851
5 17713733 17715223 - Tan0017963.1 Tan05g1340 1340
3 5234027 5235506 - Vvi3g536 Vvi3g536 536
3 5237934 5238870 + Vvi3g537 Vvi3g537 537
3 5239375 5239970 + Vvi3g538 Vvi3g538 538
3 5243538 5244774 + Vvi3g539 Vvi3g539 539
3 5258909 5261637 - Vvi3g540 Vvi3g540 540
3 5261664 5263653 - Vvi3g541 Vvi3g541 541
3 5264338 5268000 - Vvi3g542 Vvi3g542 542
3 5269487 5273645 - Vvi3g543 Vvi3g543 543
3 5278121 5285565 - Vvi3g544 Vvi3g544 544
3 5287560 5290476 - Vvi3g545 Vvi3g545 545
       

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