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
Vvi1g861 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g862 . . . . . . Bma14g01634 . Cmo04g01714 Cmo18g01195 . Cma18g01170 . Car18g01079 Sed08g0035 Cpe09g00157 Cpe01g01449 Bhi07g01598 Tan04g1112 Cmetu10g1744 Lac13g0290 . . . Cla05g02467 Cam05g2652 Cec05g2687 Cco05g2721 Clacu05g2656 Cmu05g2508 Cre05g2624 . Cone19ag0967 . . Lsi04g00452 Csa05g02423 Chy10g00979 Cme10g00442 . . Bda07g01459 . Bpe11g01631 . . . . . . Cma04g01636 . Car04g01677 . . . . . . . . . . . . . . . . . . . . .
Vvi1g863 . . . . . Bpe10g00857 . Bma15g00168 Cmo04g01715 . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0966 . . . . . . . . . . . . . . . . . Cma04g01637 . Car04g01678 . . . . . . . . . . . . . . . . . . . . .
Vvi1g864 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g865 Blo01g00420 Blo16g01129 Bda01g02169 Bda11g01230 Bpe13g01427 . . . Cmo04g01716 Cmo18g01194 . Cma18g01169 . Car18g01078 . Cpe09g00159 Cpe01g01450 Bhi07g01596 Tan04g1110 . Lac13g0292 . . . Cla05g02464 Cam05g2651 Cec05g2686 Cco05g2720 Clacu05g2655 Cmu05g2507 Cre05g2623 Cone13ag0975 Cone19ag0965 Cone6ag0608 Cone9ag0612 Lsi04g00451 Csa05g02426 Chy10g00980 Cme10g00439 . . . Bda11g01230 . Bpe02g02356 Bma01g00086 Bma06g00663 . . . Cma04g01638 . Car04g01679 . . . . . . . . . . . . . . . . . . . . .
Vvi1g866 . . . . . Bpe10g00858 . Bma15g00250 . Cmo18g01192 . Cma18g01168 . Car18g01077 . Cpe09g00160 . Bhi07g01594 . . Lac13g0294 . . . Cla05g02463 Cam05g2650 Cec05g2685 Cco05g2719 Clacu05g2654 Cmu05g2506 Cre05g2622 Cone13ag0974 Cone19ag0964 . . Lsi04g00446 Csa05g02427 Chy10g00981 Cme10g00438 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g867 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g868 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g869 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g870 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57611237 57612790 - Bda004508.1 Bda01g02169 2169
7 27096219 27097988 + Bda028289.1 Bda07g01459 1459
11 12828591 12830029 - Bda033143 Bda11g01230 1230
7 45484880 45488309 + XM_039036173.1 Bhi07g01594 1594
7 45494057 45498260 - XM_039036259.1 Bhi07g01596 1596
7 45516608 45519595 - XM_039036809.1 Bhi07g01598 1598
1 4731886 4733635 + BLOR00420 Blo01g00420 420
16 39821002 39829267 - BLOR21916 Blo16g01129 1129
1 974020 975569 + Bma000252.1 Bma01g00086 86
6 35672082 35673556 + Bma031291 Bma06g00663 663
14 34493193 34512146 + Bma012345.3 Bma14g01634 1634
15 1794749 1796614 + Bma013149.2 Bma15g00168 168
15 2494171 2498912 + Bma013235.1 Bma15g00250 250
2 24028699 24030250 - Bpe010174.1 Bpe02g02356 2356
10 14463417 14465282 - Bpe003161.2 Bpe10g00857 857
10 14465764 14468450 - Bpe003162.1 Bpe10g00858 858
11 12429987 12431746 + Bpe004944.1 Bpe11g01631 1631
13 19563870 19565321 - Bpe011091.1 Bpe13g01427 1427
5 33986997 33990901 + CaPI482276_05g026500.1 Cam05g2650 2650
5 33991350 34004052 - CaPI482276_05g026510.1 Cam05g2651 2651
5 34004462 34008460 - CaPI482276_05g026520.1 Cam05g2652 2652
4 9645363 9647263 + Carg01722-RA Car04g01677 1677
4 9647376 9649220 - Carg01721-RA Car04g01678 1678
4 9651375 9654837 + Carg01720-RA Car04g01679 1679
18 10930947 10933778 + Carg17253-RA Car18g01077 1077
18 10933900 10942326 - Carg17252-RA Car18g01078 1078
18 10942750 10946055 - Carg17251-RA Car18g01079 1079
5 35097951 35109486 + CcPI632755_05g027190.1 Cco05g2719 2719
5 35109934 35122787 - CcPI632755_05g027200.1 Cco05g2720 2720
5 35123194 35127249 - CcPI632755_05g027210.1 Cco05g2721 2721
5 37429297 37432008 + CePI673135_05g026850.1 Cec05g2685 2685
5 37432080 37447324 - CePI673135_05g026860.1 Cec05g2686 2686
5 37447635 37451710 - CePI673135_05g026870.1 Cec05g2687 2687
10 15269231 15277271 + Chy10G181730.1 Chy10g00979 979
10 15277536 15282954 + Chy10G181740.1 Chy10g00980 980
10 15283436 15287440 - Chy10G181750.1 Chy10g00981 981
5 34190098 34192822 + ClG42_05g0265400.10 Clacu05g2654 2654
5 34193271 34205976 - ClG42_05g0265500.10 Clacu05g2655 2655
5 34206386 34210356 - ClG42_05g0265600.10 Clacu05g2656 2656
5 36090831 36093555 + ClCG05G024490.1 Cla05g02463 2463
5 36093997 36106711 - ClCG05G024500.1 Cla05g02464 2464
5 36107121 36109154 - ClCG05G024530.1 Cla05g02467 2467
4 8253751 8255857 + CmaCh04G016360.1 Cma04g01636 1636
4 8255972 8257816 - CmaCh04G016370.1 Cma04g01637 1637
4 8259093 8263376 + CmaCh04G016380.1 Cma04g01638 1638
18 9362452 9366436 + CmaCh18G011680.1 Cma18g01168 1168
18 9366702 9375092 - CmaCh18G011690.1 Cma18g01169 1169
18 9376211 9378818 - CmaCh18G011700.1 Cma18g01170 1170
10 2796559 2799613 + MELO3C012075.2.1 Cme10g00438 438
10 2800027 2802201 - MELO3C012074.2.1 Cme10g00439 439
10 2810793 2813584 - MELO3C012073.2.1 Cme10g00442 442
10 19191612 19194297 + PI0028487.1 Cmetu10g1744 1744
4 8686405 8688772 + CmoCh04G017140.1 Cmo04g01714 1714
4 8688745 8690589 - CmoCh04G017150.1 Cmo04g01715 1715
4 8691817 8696264 + CmoCh04G017160.1 Cmo04g01716 1716
18 11957083 11961249 + CmoCh18G011920.1 Cmo18g01192 1192
18 11965570 11970334 - CmoCh18G011940.1 Cmo18g01194 1194
18 11970852 11973545 - CmoCh18G011950.1 Cmo18g01195 1195
5 33927862 33930586 + CmPI595203_05g025060.1 Cmu05g2506 2506
5 33931035 33943742 - CmPI595203_05g025070.1 Cmu05g2507 2507
5 33944152 33946167 - CmPI595203_05g025080.1 Cmu05g2508 2508
6 3008911 3011379 - Conep06aG0062600.1 Cone6ag0608 608
9 2902721 2905026 - Conep09aG0062600.1 Cone9ag0612 612
13 8296659 8299791 + Conep13aG0100400.1 Cone13ag0974 974
13 8299845 8302099 - Conep13aG0100500.1 Cone13ag0975 975
19 7336213 7339375 + Conep19aG0099600.1 Cone19ag0964 964
19 7339466 7341741 - Conep19aG0099700.1 Cone19ag0965 965
19 7342332 7346184 + Conep19aG0099800.1 Cone19ag0966 966
19 7344339 7346137 - Conep19aG0099900.1 Cone19ag0967 967
1 8672029 8675348 + Cp4.1LG01g12660.1 Cpe01g01449 1449
1 8677627 8686595 + Cp4.1LG01g12700.1 Cpe01g01450 1450
9 913931 916622 + Cp4.1LG09g01560.1 Cpe09g00157 157
9 923729 926920 + Cp4.1LG09g01600.1 Cpe09g00159 159
9 926037 929800 - Cp4.1LG09g01640.1 Cpe09g00160 160
5 37291690 37294413 + CrPI670011_05g026220.1 Cre05g2622 2622
5 37294860 37307190 - CrPI670011_05g026230.1 Cre05g2623 2623
5 37307600 37311561 - CrPI670011_05g026240.1 Cre05g2624 2624
5 26237422 26240604 + CsaV3_5G032420.1 Csa05g02423 2423
5 26248586 26252437 + CsaV3_5G032450.1 Csa05g02426 2426
5 26252158 26255448 - CsaV3_5G032460.1 Csa05g02427 2427
13 2065814 2067929 + Lag0040086.1 Lac13g0290 290
13 2072339 2076468 + Lag0040088.1 Lac13g0292 292
13 2085332 2088126 - Lag0040090.1 Lac13g0294 294
4 4296077 4300344 + Lsi04G004460.1 Lsi04g00446 446
4 4306573 4311123 - Lsi04G004510.1 Lsi04g00451 451
4 4314156 4317377 - Lsi04G004520.1 Lsi04g00452 452
8 149452 152289 - Sed0021117.3 Sed08g0035 35
4 10129432 10137430 - Tan0011940.1 Tan04g1110 1110
4 10182451 10185479 - Tan0006826.1 Tan04g1112 1112
1 10977205 10982423 + Vvi1g861 Vvi1g861 861
1 10983755 10987218 + Vvi1g862 Vvi1g862 862
1 10987352 10989206 - Vvi1g863 Vvi1g863 863
1 10991458 11002007 - Vvi1g864 Vvi1g864 864
1 11008740 11013679 + Vvi1g865 Vvi1g865 865
1 11013834 11016961 - Vvi1g866 Vvi1g866 866
1 11028168 11033705 + Vvi1g867 Vvi1g867 867
1 11042153 11042492 - Vvi1g868 Vvi1g868 868
1 11080252 11083113 + Vvi1g869 Vvi1g869 869
1 11124689 11127549 + Vvi1g870 Vvi1g870 870
       

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