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
Vvi3g376 . Blo15g00701 . . Bpe07g00426 . . Bma12g00508 . . . Cma20g00846 . Car20g00732 . . . . . . . . . . . . . . . . . . . Cone3ag1166 Cone10ag0967 Lsi10g00372 . Chy11g00376 . . . . . . . . . Sed01g0301 . Cmo20g00856 . . . . Cpe16g00244 . Bhi10g02006 Tan05g1301 Cmetu11g1811 . Hepe08g1013 . . . . . . . . . . Csa02g01260 . Cme11g00115
Vvi3g377 Blo02g00804 Blo15g00700 . Bda08g00933 Bpe07g00427 . Bma05g00457 Bma12g00509 . . . Cma20g00847 Car02g00257 . Sed05g2313 . . Bhi05g01240 Tan02g0787 Cmetu01g0279 . Hepe02g0492 . . . . . . . . . Cone12ag1155 Cone8ag1204 Cone3ag1165 . . . Chy11g00377 . . . . . . . . . . Cmo02g00400 Cmo20g00857 . . . . . Cpe05g01262 Bhi10g02007 Tan05g1302 Cmetu11g0539 . . . . . . . . . . . . Csa02g01259 . Cme11g00114
Vvi3g378 Blo02g00837 . . . . Bpe12g00047 . . Cmo19g00607 Cmo11g01379 . . . . . Cpe04g00293 Cpe15g00477 Bhi05g01086 . . . . . . Cla02g00623 Cam02g0657 Cec02g0660 Cco02g0683 Clacu02g0665 Cmu02g0660 Cre02g0978 . Cone8ag1115 Cone3ag0990 Cone10ag1008 . Csa07g00736 . Cme01g00072 . . . . . . . Bma08g00812 . . . . Cma19g00588 . Car19g00446 . . . . . . . . . . . . . . . . . . Chy01g00078 .
Vvi3g379 . . . . . Bpe12g00048 . . Cmo19g00609 . . . . . . . Cpe15g00478 . . . . . . . Cla02g00622 Cam02g0651 Cec02g0652 Cco02g0680 Clacu02g0659 Cmu02g0654 Cre02g0973 Cone12ag1078 Cone8ag1116 Cone3ag0989 Cone10ag1007 . Csa07g00737 . Cme01g00071 Blo04g00475 . . . . . . Bma08g00811 . . . Cma11g01736 Cma19g00589 . . Cpe14g00287 Cpe01g00429 . . . . . . . . . . . . . . . . Chy01g00077 .
Vvi3g380 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g381 . . . . . Bpe12g00051 . . Cmo19g00611 . . . . . . . . Bhi05g01080 . . . . . . Cla02g00617 . . . . . . . Cone8ag1119 . . Lsi10g00520 Csa07g00741 . Cme01g00064 Blo04g00477 Blo13g00583 Bda15g00041 . Bpe15g00905 . . Bma08g00809 . . . . Cma19g00593 . . . . . . . . . . . . . . . . . . . . Chy01g00069 .
Vvi3g382 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g383 Blo02g00825 . . . . . . . . Cmo11g01377 . . . . . Cpe04g00291 . Bhi05g01078 . . . . . . Cla02g00614 Cam02g0643 Cec02g0642 Cco02g0663 Clacu02g0647 Cmu02g0642 Cre02g0966 . . Cone3ag0986 Cone10ag1004 . Csa07g00746 . Cme01g00062 Blo04g00478 . . Bda14g00508 Bpe15g00904 . Bma03g00510 . . . . Cma11g01738 . . . Cpe14g00288 Cpe01g00430 . . . . . . . . . . . . . . . . Chy01g00065 .
Vvi3g384 . . . . . Bpe12g00052 . . Cmo19g00614 Cmo11g01376 . . . . . Cpe04g00290 Cpe15g00480 Bhi05g01075 . . . . . . Cla02g00613 Cam02g0642 Cec02g0641 Cco02g0662 Clacu02g0646 Cmu02g0641 Cre02g0965 . Cone8ag1121 Cone3ag0985 Cone10ag1003 . Csa07g00747 . Cme01g00061 Blo04g00479 Blo13g00582 Bda15g00040 Bda14g00509 Bpe15g00903 . Bma03g00511 . . . . Cma11g01739 Cma19g00596 . Car19g00450 Cpe14g00289 Cpe01g00431 . . . . . . . . . . . . . . . . Chy01g00064 .
Vvi3g385 . Blo15g00755 Bda06g01078 . Bpe07g00369 . . Bma12g00433 Cmo19g00615 Cmo11g01375 . . . . . Cpe04g00289 Cpe15g00481 Bhi05g01074 . . . . . . Cla02g00612 Cam02g0641 Cec02g0640 Cco02g0661 Clacu02g0645 Cmu02g0640 Cre02g0964 . . Cone3ag0981 Cone10ag1001 . Csa07g00748 . Cme01g00060 . . . . . . . . . . . Cma11g01740 Cma19g00597 . . . . . . . . . . . . . . . . . . . . Chy01g00063 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 38311620 38318892 + Bda022847.1 Bda06g01078 1078
8 17209090 17210843 + Bda034030 Bda08g00933 933
14 3703102 3705637 - Bda027253.1 Bda14g00508 508
14 3707904 3712195 + Bda027254.1 Bda14g00509 509
15 1849466 1853931 - Bda011798.2 Bda15g00040 40
15 1856579 1861854 + Bda011799.1 Bda15g00041 41
5 38767221 38772592 + XM_039031701.1 Bhi05g01074 1074
5 38774445 38778150 - XM_039031752.1 Bhi05g01075 1075
5 38928806 38933577 + XM_039032477.1 Bhi05g01078 1078
5 38987530 38989563 + XM_039031364.1 Bhi05g01080 1080
5 39247574 39250464 - XM_039031207.1 Bhi05g01086 1086
5 44812916 44816630 + XM_039032899.1 Bhi05g01240 1240
10 50122002 50124290 + XM_039045688.1 Bhi10g02006 2006
10 50176855 50181534 - XM_039046034.1 Bhi10g02007 2007
2 27792248 27794261 + BLOR10534 Blo02g00804 804
2 29594451 29598800 - BLOR10555 Blo02g00825 825
2 30721586 30723019 - BLOR10567 Blo02g00837 837
4 3926819 3928351 + BLOR13387 Blo04g00475 475
4 3958078 3959517 - BLOR13389 Blo04g00477 477
4 3960653 3964335 - BLOR13390 Blo04g00478 478
4 3968617 3974127 + BLOR13391 Blo04g00479 479
13 27941169 27944216 - BLOR19634 Blo13g00582 582
13 27952721 27954190 + BLOR19635 Blo13g00583 583
15 22161819 22163180 + BLOR07094 Blo15g00700 700
15 22223526 22231068 - BLOR07095 Blo15g00701 701
15 25672625 25680006 + BLOR07149 Blo15g00755 755
3 3964733 3967691 - Bma016791.1 Bma03g00510 510
3 3976725 3980793 + Bma016792.1 Bma03g00511 511
5 15581208 15582972 - Bma021320.1 Bma05g00457 457
8 45719275 45720696 + Bma028199.2 Bma08g00809 809
8 45741424 45742671 - Bma028201.1 Bma08g00811 811
8 45744474 45745145 - Bma028202.1 Bma08g00812 812
12 10885920 10893071 - Bma007432.1 Bma12g00433 433
12 16291013 16293267 + Bma007573.1 Bma12g00508 508
12 16505688 16506706 - Bma007583.1 Bma12g00509 509
7 3105187 3112405 - Bpe021182.1 Bpe07g00369 369
7 4793868 4796019 + Bpe021250.1 Bpe07g00426 426
7 4811294 4812829 - Bpe021251.1 Bpe07g00427 427
12 383664 384335 + Bpe005286.1 Bpe12g00047 47
12 386704 387963 + Bpe005287.1 Bpe12g00048 48
12 403455 404921 - Bpe005290.1 Bpe12g00051 51
12 406231 410662 + Bpe005291.1 Bpe12g00052 52
15 18896488 18900693 - Bpe001825.1 Bpe15g00903 903
15 18902969 18905544 + Bpe001826.1 Bpe15g00904 904
15 18906279 18907703 + Bpe001827.1 Bpe15g00905 905
2 7408837 7418848 + CaPI482276_02g006410.1 Cam02g0641 641
2 7421315 7424709 - CaPI482276_02g006420.1 Cam02g0642 642
2 7440540 7444279 + CaPI482276_02g006430.1 Cam02g0643 643
2 7553479 7555791 - CaPI482276_02g006510.1 Cam02g0651 651
2 7605963 7610151 - CaPI482276_02g006570.1 Cam02g0657 657
2 1749504 1751108 - Carg22942-RA Car02g00257 257
19 6192217 6194193 + Carg22078-RA Car19g00446 446
19 6228990 6232906 + Carg22074-RA Car19g00450 450
20 4273289 4275666 + Carg26479-RA Car20g00732 732
2 6632842 6643099 + CcPI632755_02g006610.1 Cco02g0661 661
2 6645631 6648989 - CcPI632755_02g006620.1 Cco02g0662 662
2 6664178 6668321 + CcPI632755_02g006630.1 Cco02g0663 663
2 6791200 6793619 - CcPI632755_02g006800.1 Cco02g0680 680
2 6837501 6841748 - CcPI632755_02g006830.1 Cco02g0683 683
2 6488591 6496112 + CePI673135_02g006400.1 Cec02g0640 640
2 6498534 6501937 - CePI673135_02g006410.1 Cec02g0641 641
2 6519777 6523740 + CePI673135_02g006420.1 Cec02g0642 642
2 6643482 6645872 - CePI673135_02g006520.1 Cec02g0652 652
2 6738408 6742700 - CePI673135_02g006600.1 Cec02g0660 660
1 467864 472945 + Chy1G000630.1 Chy01g00063 63
1 474595 477987 - Chy1G000640.1 Chy01g00064 64
1 482118 483628 + Chy1G000650.1 Chy01g00065 65
1 491322 492755 + Chy1G000690.1 Chy01g00069 69
1 517189 522986 - Chy1G000770.1 Chy01g00077 77
1 523037 524389 - Chy1G000780.1 Chy01g00078 78
11 3488075 3489947 + Chy11G189560.1 Chy11g00376 376
11 3494250 3497069 - Chy11G189570.1 Chy11g00377 377
2 6419834 6429755 + ClG42_02g0064500.10 Clacu02g0645 645
2 6432224 6435616 - ClG42_02g0064600.10 Clacu02g0646 646
2 6456168 6460025 + ClG42_02g0064700.10 Clacu02g0647 647
2 6568031 6570479 - ClG42_02g0065900.10 Clacu02g0659 659
2 6627565 6631773 - ClG42_02g0066500.10 Clacu02g0665 665
2 6722504 6729120 + ClCG02G006070.1 Cla02g00612 612
2 6731074 6735001 - ClCG02G006080.2 Cla02g00613 613
2 6757090 6761474 + ClCG02G006090.1 Cla02g00614 614
2 6792567 6803502 + ClCG02G006120.1 Cla02g00617 617
2 6874031 6876389 - ClCG02G006170.1 Cla02g00622 622
2 6936998 6941349 - ClCG02G006180.1 Cla02g00623 623
11 11524791 11526649 - CmaCh11G017360.1 Cma11g01736 1736
11 11537557 11539942 - CmaCh11G017380.1 Cma11g01738 1738
11 11541978 11546095 + CmaCh11G017390.1 Cma11g01739 1739
11 11546724 11552235 - CmaCh11G017400.1 Cma11g01740 1740
19 6526942 6529105 + CmaCh19G005880.1 Cma19g00588 588
19 6530100 6532343 + CmaCh19G005890.1 Cma19g00589 589
19 6550199 6551641 - CmaCh19G005930.1 Cma19g00593 593
19 6565911 6569545 + CmaCh19G005960.1 Cma19g00596 596
19 6569919 6575430 - CmaCh19G005970.1 Cma19g00597 597
20 4053476 4055838 + CmaCh20G008460.1 Cma20g00846 846
20 4056892 4059201 - CmaCh20G008470.1 Cma20g00847 847
1 459065 464673 + MELO3C018461.2.1 Cme01g00060 60
1 465786 470108 - MELO3C018462.2.1 Cme01g00061 61
1 473991 475769 + MELO3C018463.2.1 Cme01g00062 62
1 479238 481041 + MELO3C018465.2.1 Cme01g00064 64
1 506671 508750 - MELO3C018471.2.1 Cme01g00071 71
1 510118 512166 - MELO3C018472.2.1 Cme01g00072 72
11 1054206 1057302 + MELO3C023299.2.1 Cme11g00114 114
11 1062359 1064730 - MELO3C023300.2.1 Cme11g00115 115
1 6047255 6050672 - PI0005605.1 Cmetu01g0279 279
11 27451275 27455182 - PI0007882.1 Cmetu11g0539 539
11 27444605 27446960 + PI0010099.1 Cmetu11g1811 1811
2 2069636 2071039 - CmoCh02G004000.1 Cmo02g00400 400
11 9605842 9611273 + CmoCh11G013750.1 Cmo11g01375 1375
11 9611881 9615897 - CmoCh11G013760.1 Cmo11g01376 1376
11 9618141 9620619 + CmoCh11G013770.1 Cmo11g01377 1377
11 9632804 9635027 + CmoCh11G013790.1 Cmo11g01379 1379
19 6722807 6724956 + CmoCh19G006070.1 Cmo19g00607 607
19 6726297 6728556 + CmoCh19G006090.1 Cmo19g00609 609
19 6742624 6744066 - CmoCh19G006110.1 Cmo19g00611 611
19 6757298 6760972 + CmoCh19G006140.1 Cmo19g00614 614
19 6761852 6767300 - CmoCh19G006150.1 Cmo19g00615 615
20 4310781 4313995 + CmoCh20G008560.1 Cmo20g00856 856
20 4313087 4316705 - CmoCh20G008570.1 Cmo20g00857 857
2 6326263 6336177 + CmPI595203_02g006400.1 Cmu02g0640 640
2 6338645 6342037 - CmPI595203_02g006410.1 Cmu02g0641 641
2 6362593 6366451 + CmPI595203_02g006420.1 Cmu02g0642 642
2 6474501 6476946 - CmPI595203_02g006540.1 Cmu02g0654 654
2 6534041 6538279 - CmPI595203_02g006600.1 Cmu02g0660 660
3 28620068 28625671 + Conep03aG0147800.1 Cone3ag0981 981
3 28639047 28643821 - Conep03aG0148200.1 Cone3ag0985 985
3 28662533 28666864 + Conep03aG0148400.1 Cone3ag0986 986
3 28688154 28689636 - Conep03aG0148700.1 Cone3ag0989 989
3 28702515 28704603 - Conep03aG0148900.1 Cone3ag0990 990
3 30320347 30322625 + Conep03aG0167000.1 Cone3ag1165 1165
3 30331468 30333195 - Conep03aG0167100.1 Cone3ag1166 1166
8 9899313 9901197 + Conep08aG0114600.1 Cone8ag1115 1115
8 9902230 9903510 + Conep08aG0114700.1 Cone8ag1116 1116
8 9913310 9914821 - Conep08aG0115000.1 Cone8ag1119 1119
8 9919319 9922786 + Conep08aG0115200.1 Cone8ag1121 1121
8 10239336 10242256 + Conep08aG0124000.1 Cone8ag1204 1204
10 6506844 6508262 - Conep10aG0099300.1 Cone10ag0967 967
10 6846126 6851719 + Conep10aG0102800.1 Cone10ag1001 1001
10 6865475 6869685 - Conep10aG0103000.1 Cone10ag1003 1003
10 6897063 6903077 + Conep10aG0103100.1 Cone10ag1004 1004
10 6961823 6963800 + Conep10aG0103400.1 Cone10ag1007 1007
10 6964648 6966416 + Conep10aG0103500.1 Cone10ag1008 1008
12 8852791 8855165 - Conep12aG0111200.1 Cone12ag1078 1078
12 9213888 9216787 + Conep12aG0119300.1 Cone12ag1155 1155
1 2476975 2479388 + Cp4.1LG01g02450.1 Cpe01g00429 429
1 2482589 2487750 - Cp4.1LG01g02330.1 Cpe01g00430 430
1 2489190 2494261 + Cp4.1LG01g02470.1 Cpe01g00431 431
4 3616201 3621726 + Cp4.1LG04g07940.1 Cpe04g00289 289
4 3623251 3627301 - Cp4.1LG04g07920.1 Cpe04g00290 290
4 3630541 3631911 + Cp4.1LG04g07970.1 Cpe04g00291 291
4 3655511 3657849 + Cp4.1LG04g07950.1 Cpe04g00293 293
5 8818978 8820879 + Cp4.1LG05g12530.1 Cpe05g01262 1262
14 1681202 1687366 + Cp4.1LG14g04300.1 Cpe14g00287 287
14 1685830 1692114 - Cp4.1LG14g04200.1 Cpe14g00288 288
14 1694337 1699206 + Cp4.1LG14g04280.1 Cpe14g00289 289
15 5767108 5769103 + Cp4.1LG15g04840.1 Cpe15g00477 477
15 5769119 5772721 + Cp4.1LG15g04850.1 Cpe15g00478 478
15 5807407 5811574 + Cp4.1LG15g04820.1 Cpe15g00480 480
15 5811927 5818170 - Cp4.1LG15g04880.1 Cpe15g00481 481
16 4496131 4499086 - Cp4.1LG16g02400.1 Cpe16g00244 244
2 6948025 6958290 + CrPI670011_02g009640.1 Cre02g0964 964
2 6960819 6964219 - CrPI670011_02g009650.1 Cre02g0965 965
2 6985778 6989759 + CrPI670011_02g009660.1 Cre02g0966 966
2 7100009 7102410 - CrPI670011_02g009730.1 Cre02g0973 973
2 7161015 7165002 - CrPI670011_02g009780.1 Cre02g0978 978
2 12321166 12324655 + CsaV3_2G014750.1 Csa02g01259 1259
2 12328771 12330864 - CsaV3_2G014760.1 Csa02g01260 1260
7 5224312 5226559 + CsaV3_7G008350.1 Csa07g00736 736
7 5228844 5231105 + CsaV3_7G008360.1 Csa07g00737 737
7 5245465 5253498 - CsaV3_7G008400.1 Csa07g00741 741
7 5256795 5258814 - CsaV3_7G008450.1 Csa07g00746 746
7 5262014 5266176 + CsaV3_7G008460.1 Csa07g00747 747
7 5267076 5272868 - CsaV3_7G008470.1 Csa07g00748 748
2 4842224 4845300 - Hsped.02g04920.1 Hepe02g0492 492
8 9653357 9655446 + Hsped.08g10130.1 Hepe08g1013 1013
10 5733628 5736477 - Lsi10G003720.1 Lsi10g00372 372
10 7405315 7407823 - Lsi10G005200.1 Lsi10g00520 520
1 2297315 2300600 + Sed0010470.1 Sed01g0301 301
5 35584524 35588321 - Sed0008512.2 Sed05g2313 2313
2 7608675 7611859 - Tan0005387.2 Tan02g0787 787
5 15472584 15474906 + Tan0012481.2 Tan05g1301 1301
5 15486171 15489336 - Tan0019417.1 Tan05g1302 1302
3 3482511 3484808 + Vvi3g376 Vvi3g376 376
3 3488693 3491726 - Vvi3g377 Vvi3g377 377
3 3554243 3555820 + Vvi3g378 Vvi3g378 378
3 3567876 3569214 + Vvi3g379 Vvi3g379 379
3 3587103 3588547 - Vvi3g380 Vvi3g380 380
3 3591022 3593043 - Vvi3g381 Vvi3g381 381
3 3594090 3594261 + Vvi3g382 Vvi3g382 382
3 3594412 3603340 - Vvi3g383 Vvi3g383 383
3 3610207 3626250 + Vvi3g384 Vvi3g384 384
3 3628435 3643357 - Vvi3g385 Vvi3g385 385
       

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