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
Vvi3g616 . . . Bda08g00771 . . . . Cmo19g00598 Cmo11g01390 . . . . . Cpe04g00302 Cpe15g00470 . . . . . . . Cla02g00632 . Cec02g0671 Cco02g0695 . . Cre02g0988 . Cone8ag1110 . . Lsi03g00528 Csa07g00726 . Cme01g00082 . . . . . . . . . . . Cma11g01725 Cma19g00582 Car11g01116 Car19g00444 . . . . . . . . . . . . . . . . . . Chy01g00087 .
Vvi3g617 Blo02g00839 . . Bda08g00770 . . Bma05g00524 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag0996 Cone10ag1016 . . . . . . . . . . . . . . Cmo16g00368 . . . . Cpe14g00285 . . . . . . . . . . . . . . . . . . .
Vvi3g618 Blo02g00840 . . Bda08g00769 . . Bma05g00525 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo04g00509 Cmo16g00367 . . . . Cpe14g00284 Cpe01g00426 . . . . . . . . . . . . . . . . . .
Vvi3g619 Blo02g00841 . . Bda08g00768 . . Bma05g00526 . Cmo19g00597 . . . . . . . Cpe15g00469 . . . . . . . Cla02g00633 Cam02g0666 . . Clacu02g0674 Cmu02g0668 . Cone12ag1073 . . . Lsi03g00529 . . . . . . . . . . . . . . . Cma19g00581 . Car19g00443 . . . . . . . . . . . . . . . . . . . .
Vvi3g620 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag1108 . . . . . . . . . . . . . . . Cmo04g00508 Cmo16g00366 . . . . Cpe14g00283 Cpe01g00425 . . . . . . . . . . . . . . . . . .
Vvi3g621 . . . . . Bpe12g00299 . . Cmo19g00596 Cmo11g01391 . . . . . Cpe04g00303 Cpe15g00468 . . . . . . . Cla02g00634 Cam02g0667 Cec02g0673 Cco02g0697 Clacu02g0675 Cmu02g0669 Cre02g0990 Cone12ag1072 Cone8ag1107 . . Lsi03g00530 . . . . . Bda15g00843 . . . Bma03g01367 Bma08g00497 . . . Cma11g01724 . Car11g01117 Car19g00442 . . . . . . . . . . . . . . . . . . . .
Vvi3g622 Blo02g00842 . . Bda08g00767 . . Bma05g00527 . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag1106 Cone3ag0998 Cone10ag1018 . . . . . . . . . . . . . Cmo04g00507 . . . . . . Cpe01g00424 . . . . . . . . . . . . . . . . . .
Vvi3g623 . . . Bda08g00763 . . . . . . . . . . . . . Bhi05g01107 . . . . . . . . . . . . . . . . . . Csa07g00720 . Cme01g00088 . . . . . . . . . . . Cma11g01722 . . . . . . . . . . . . . . . . . . . . . Chy01g00095 .
Vvi3g624 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag0999 Cone10ag1019 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g625 Blo02g00844 . . Bda08g00755 . . Bma05g00530 . Cmo19g00595 Cmo11g01392 . . . . . Cpe04g00304 Cpe15g00467 . . . . . . . . . . . . . . . . Cone3ag1001 Cone10ag1020 Lsi03g00531 . . . . . . . . . . . . . . . Cma19g00580 Car11g01118 Car19g00441 . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 9562560 9563264 + Bda029245.1 Bda08g00755 755
8 9858705 9860267 + Bda029263.1 Bda08g00763 763
8 9960832 9962237 + Bda029268.1 Bda08g00767 767
8 10007601 10008842 + Bda029270.1 Bda08g00768 768
8 10010480 10013310 + Bda029271.1 Bda08g00769 769
8 10013898 10017409 - Bda029272.2 Bda08g00770 770
8 10019926 10020405 + Bda029273.1 Bda08g00771 771
15 12912603 12915270 - Bda012714.1 Bda15g00843 843
5 40023926 40025573 + XM_039031073.1 Bhi05g01107 1107
2 31010493 31014074 + BLOR10569 Blo02g00839 839
2 31014514 31022337 - BLOR10570 Blo02g00840 840
2 31050823 31052666 - BLOR10571 Blo02g00841 841
2 31080351 31082357 - BLOR10572 Blo02g00842 842
2 31569345 31569935 - BLOR10574 Blo02g00844 844
3 31656950 31659496 - Bma017921.1 Bma03g01367 1367
5 26485074 26488557 + Bma031190 Bma05g00524 524
5 26489121 26491958 - Bma031191 Bma05g00525 525
5 26492908 26494465 - Bma021475.1 Bma05g00526 526
5 26595135 26605047 - Bma021476.1 Bma05g00527 527
5 27290406 27291023 - Bma021490.1 Bma05g00530 530
8 25251818 25254521 + Bma027700.1 Bma08g00497 497
12 4148388 4151054 + Bpe005545.1 Bpe12g00299 299
2 7769652 7778490 - CaPI482276_02g006660.1 Cam02g0666 666
2 7787859 7794903 + CaPI482276_02g006670.1 Cam02g0667 667
11 8878837 8881402 - Carg26855-RA Car11g01116 1116
11 8885157 8889484 + Carg26856-RA Car11g01117 1117
11 8890736 8896720 + Carg26857-RA Car11g01118 1118
19 6147443 6153553 - Carg16363-RA Car19g00441 441
19 6154639 6160212 - Carg16364-RA Car19g00442 442
19 6161027 6163732 + Carg16365-RA Car19g00443 443
19 6164689 6166879 + Carg16366-RA Car19g00444 444
2 7010699 7018933 - CcPI632755_02g006950.1 Cco02g0695 695
2 7049866 7055776 + CcPI632755_02g006970.1 Cco02g0697 697
2 6905340 6913747 - CePI673135_02g006710.1 Cec02g0671 671
2 6938935 6944994 + CePI673135_02g006730.1 Cec02g0673 673
1 584897 594233 - Chy1G000870.1 Chy01g00087 87
1 616486 618836 - Chy1G000950.1 Chy01g00095 95
2 6782917 6791821 - ClG42_02g0067400.10 Clacu02g0674 674
2 6801218 6808179 + ClG42_02g0067500.10 Clacu02g0675 675
2 7098289 7099924 - ClCG02G006290.2 Cla02g00632 632
2 7104209 7107221 - ClCG02G006300.1 Cla02g00633 633
2 7116431 7132117 + ClCG02G006310.2 Cla02g00634 634
11 11415101 11417438 + CmaCh11G017220.1 Cma11g01722 1722
11 11433737 11446037 - CmaCh11G017240.1 Cma11g01724 1724
11 11449349 11451895 + CmaCh11G017250.1 Cma11g01725 1725
19 6473219 6484982 - CmaCh19G005800.1 Cma19g00580 580
19 6485869 6487986 + CmaCh19G005810.1 Cma19g00581 581
19 6488919 6490749 + CmaCh19G005820.1 Cma19g00582 582
1 578750 581977 - MELO3C018482.2.1 Cme01g00082 82
1 594978 597257 - MELO3C018488.2.1 Cme01g00088 88
4 2517550 2522523 + CmoCh04G005070.1 Cmo04g00507 507
4 2523908 2526956 + CmoCh04G005080.1 Cmo04g00508 508
4 2528288 2531952 + CmoCh04G005090.1 Cmo04g00509 509
11 9737520 9743442 - CmoCh11G013900.1 Cmo11g01390 1390
11 9746643 9749835 + CmoCh11G013910.1 Cmo11g01391 1391
11 9749864 9756624 + CmoCh11G013920.1 Cmo11g01392 1392
16 1674648 1682608 + CmoCh16G003660.1 Cmo16g00366 366
16 1684042 1687295 + CmoCh16G003670.1 Cmo16g00367 367
16 1687401 1693061 - CmoCh16G003680.1 Cmo16g00368 368
19 6653037 6658631 - CmoCh19G005950.1 Cmo19g00595 595
19 6659482 6664864 - CmoCh19G005960.1 Cmo19g00596 596
19 6666050 6669463 + CmoCh19G005970.1 Cmo19g00597 597
19 6669841 6672379 + CmoCh19G005980.1 Cmo19g00598 598
2 6689220 6698143 - CmPI595203_02g006680.1 Cmu02g0668 668
2 6707535 6714498 + CmPI595203_02g006690.1 Cmu02g0669 669
3 28773752 28776382 + Conep03aG0149500.1 Cone3ag0996 996
3 28780830 28785279 - Conep03aG0149700.1 Cone3ag0998 998
3 28796362 28797300 + Conep03aG0149800.1 Cone3ag0999 999
3 28817504 28822159 + Conep03aG0150000.1 Cone3ag1001 1001
8 9861949 9863282 + Conep08aG0113700.1 Cone8ag1106 1106
8 9864025 9866001 - Conep08aG0113800.1 Cone8ag1107 1107
8 9866904 9869963 + Conep08aG0113900.1 Cone8ag1108 1108
8 9873951 9875552 + Conep08aG0114100.1 Cone8ag1110 1110
10 7046770 7051759 + Conep10aG0104300.1 Cone10ag1016 1016
10 7056107 7059486 - Conep10aG0104500.1 Cone10ag1018 1018
10 7068109 7069047 + Conep10aG0104600.1 Cone10ag1019 1019
10 7082484 7086416 + Conep10aG0104700.1 Cone10ag1020 1020
12 8824232 8826354 - Conep12aG0110600.1 Cone12ag1072 1072
12 8828538 8829638 + Conep12aG0110700.1 Cone12ag1073 1073
1 2450337 2455651 + Cp4.1LG01g02500.1 Cpe01g00424 424
1 2456344 2459944 + Cp4.1LG01g02440.1 Cpe01g00425 425
1 2460939 2464818 + Cp4.1LG01g02430.1 Cpe01g00426 426
4 3796186 3801192 - Cp4.1LG04g07800.1 Cpe04g00302 302
4 3804482 3809567 + Cp4.1LG04g07830.1 Cpe04g00303 303
4 3810459 3816515 + Cp4.1LG04g07850.1 Cpe04g00304 304
14 1648635 1656801 + Cp4.1LG14g04440.1 Cpe14g00283 283
14 1657934 1662149 + Cp4.1LG14g04450.1 Cpe14g00284 284
14 1660505 1667042 - Cp4.1LG14g04350.1 Cpe14g00285 285
15 5697640 5703337 - Cp4.1LG15g04720.1 Cpe15g00467 467
15 5704138 5709741 - Cp4.1LG15g04700.1 Cpe15g00468 468
15 5711700 5714624 + Cp4.1LG15g04630.1 Cpe15g00469 469
15 5715363 5720353 + Cp4.1LG15g04620.1 Cpe15g00470 470
2 7315354 7330829 - CrPI670011_02g009880.1 Cre02g0988 988
2 7355636 7361543 + CrPI670011_02g009900.1 Cre02g0990 990
7 5131184 5132713 + CsaV3_7G008190.1 Csa07g00720 720
7 5155816 5157445 + CsaV3_7G008250.1 Csa07g00726 726
3 6216173 6223574 - Lsi03G005280.1 Lsi03g00528 528
3 6229586 6232847 + Lsi03G005290.1 Lsi03g00529 529
3 6246369 6254860 + Lsi03G005300.1 Lsi03g00530 530
3 6255917 6263192 + Lsi03G005310.1 Lsi03g00531 531
3 6033618 6037846 - Vvi3g616 Vvi3g616 616
3 6038009 6059773 + Vvi3g617 Vvi3g617 617
3 6060014 6064496 - Vvi3g618 Vvi3g618 618
3 6071390 6072507 - Vvi3g619 Vvi3g619 619
3 6078669 6081676 - Vvi3g620 Vvi3g620 620
3 6090643 6100274 + Vvi3g621 Vvi3g621 621
3 6101673 6106138 - Vvi3g622 Vvi3g622 622
3 6124464 6126180 - Vvi3g623 Vvi3g623 623
3 6146662 6148747 + Vvi3g624 Vvi3g624 624
3 6154935 6178237 + Vvi3g625 Vvi3g625 625
       

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