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
Vvi1g891 . . . Bda11g01223 Bpe13g01417 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01223 . . . . . . . . . . . . Cpe07g00205 . . . . . . . . . . . . . . . . . .
Vvi1g892 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g893 . . . . . Bpe10g00865 . Bma15g00162 . . . . . Car18g01069 Sed04g0698 Cpe09g00169 . Bhi07g01578 Tan04g1092 Cmetu10g1278 . . . . Cla05g02452 Cam05g2638 Cec05g2671 . Clacu05g2641 Cmu05g2495 Cre05g2608 Cone13ag0962 Cone19ag0953 . . Lsi04g00435 Csa05g02439 Chy10g00991 Cme10g00426 Blo06g00903 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g894 . Blo16g01121 . Bda11g01222 Bpe13g01416 . . Bma15g00272 Cmo04g01729 Cmo18g01183 . Cma18g01160 . Car18g01068 Sed06g1538 . Cpe01g01458 Bhi07g01576 Tan04g1091 Cmetu10g1669 Lac13g0309 Hepe10g1732 . . Cla05g02451 Cam05g2637 Cec05g2670 Cco05g2708 Clacu05g2640 Cmu05g2494 Cre05g2607 . Cone19ag0952 . . Lsi04g00434 Csa05g02440 Chy10g00992 Cme10g00425 . . . Bda11g01222 . . . Bma06g00680 . . . . . Car04g01690 . . . . . . . . . . . . . . . . . . . . .
Vvi1g895 . . . . . . . . Cmo04g01730 . . . . . Sed06g1537 . Cpe01g01459 Bhi07g01575 Tan04g1090 Cmetu10g1591 Lac13g0310 Hepe10g1733 . . Cla05g02450 Cam05g2636 Cec05g2669 Cco05g2707 Clacu05g2639 Cmu05g2493 Cre05g2606 . . Cone6ag0596 Cone9ag0599 Lsi04g00433 Csa05g02441 Chy10g00993 Cme10g00424 . . . . . . . . . . . Cma04g01650 . Car04g01691 . . . . . . . . . . . . . . . . . . . . .
Vvi1g896 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g897 . Blo16g01120 . Bda11g01221 Bpe13g01415 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0595 Cone9ag0598 . . . . . . . Bda11g01221 . . . . . . . . . . . . Cpe07g00653 . . . . . . . . . . . . . . . . . .
Vvi1g898 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone9ag0597 . . . . . . . . . . . . . . . . . . . . Cpe07g00652 . . . . . . . . . . . . . . . . . .
Vvi1g899 Blo01g00424 . Bda01g02163 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0960 Cone19ag0950 . . . . . . . . . . . Bpe02g02349 Bma01g00092 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g900 . . Bda01g02162 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag0949 . . . . . . . . . . . Bpe02g02348 Bma01g00093 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57548472 57550292 - Bda004500.1 Bda01g02162 2162
1 57551596 57554400 - Bda004501.1 Bda01g02163 2163
11 12575226 12578744 + Bda007727.2 Bda11g01221 1221
11 12583633 12584694 + Bda007728.1 Bda11g01222 1222
11 12603990 12608628 + Bda007729.1 Bda11g01223 1223
7 45060673 45064622 + XM_039036422.1 Bhi07g01575 1575
7 45137800 45139563 + XM_039037358.1 Bhi07g01576 1576
7 45141080 45143500 + XM_039037244.1 Bhi07g01578 1578
1 4789418 4803612 + BLOR00424 Blo01g00424 424
6 32283539 32287930 + BLOR17486 Blo06g00903 903
16 39683740 39686604 + BLOR21907 Blo16g01120 1120
16 39702350 39717226 + BLOR21908 Blo16g01121 1121
1 1022599 1025747 + Bma000257.1 Bma01g00092 92
1 1026840 1028801 + Bma000258.2 Bma01g00093 93
6 36519399 36520442 - Bma023656.1 Bma06g00680 680
15 1721000 1721948 - Bma013143.1 Bma15g00162 162
15 2657284 2658138 - Bma013251.1 Bma15g00272 272
2 23979277 23981246 - Bpe010166.1 Bpe02g02348 2348
2 23982546 23985390 - Bpe010167.1 Bpe02g02349 2349
10 14520812 14521738 + Bpe024720 Bpe10g00865 865
13 19389120 19397562 + Bpe011077.1 Bpe13g01415 1415
13 19402438 19403481 + Bpe011078.1 Bpe13g01416 1416
13 19418907 19425911 + Bpe011080.1 Bpe13g01417 1417
5 33828273 33838076 + CaPI482276_05g026360.1 Cam05g2636 2636
5 33849672 33850733 + CaPI482276_05g026370.1 Cam05g2637 2637
5 33854712 33856305 + CaPI482276_05g026380.1 Cam05g2638 2638
4 9711586 9712725 - Carg01709-RA Car04g01690 1690
4 9716338 9720622 - Carg01708-RA Car04g01691 1691
18 10862749 10863822 + Carg17262-RA Car18g01068 1068
18 10865345 10866962 + Carg17261-RA Car18g01069 1069
5 34952649 34957781 + CcPI632755_05g027070.1 Cco05g2707 2707
5 34968929 34969990 + CcPI632755_05g027080.1 Cco05g2708 2708
5 37274206 37279628 + CePI673135_05g026690.1 Cec05g2669 2669
5 37290645 37291715 + CePI673135_05g026700.1 Cec05g2670 2670
5 37295652 37297225 + CePI673135_05g026710.1 Cec05g2671 2671
10 15392926 15396804 - Chy10G181850.1 Chy10g00991 991
10 15398882 15399979 - Chy10G181860.1 Chy10g00992 992
10 15410565 15414030 - Chy10G181870.1 Chy10g00993 993
5 34038407 34043659 + ClG42_05g0263900.10 Clacu05g2639 2639
5 34054604 34055671 + ClG42_05g0264000.10 Clacu05g2640 2640
5 34059508 34061098 + ClG42_05g0264100.10 Clacu05g2641 2641
5 35926211 35930864 + ClCG05G024360.2 Cla05g02450 2450
5 35942771 35943838 + ClCG05G024370.1 Cla05g02451 2451
5 35947549 35949827 + ClCG05G024380.2 Cla05g02452 2452
4 8326301 8330369 - CmaCh04G016500.1 Cma04g01650 1650
18 9296551 9300881 + CmaCh18G011600.1 Cma18g01160 1160
10 2670682 2674716 + MELO3C012087.2.1 Cme10g00424 424
10 2683489 2685269 + MELO3C012086.2.1 Cme10g00425 425
10 2686262 2688182 + MELO3C012085.2.1 Cme10g00426 426
10 19325893 19328062 - PI0000594.1 Cmetu10g1278 1278
10 19340890 19345642 - PI0005912.1 Cmetu10g1591 1591
10 19329286 19330898 - PI0022715.1 Cmetu10g1669 1669
4 8756861 8757991 - CmoCh04G017290.1 Cmo04g01729 1729
4 8761524 8765795 - CmoCh04G017300.1 Cmo04g01730 1730
18 11881839 11882906 + CmoCh18G011830.1 Cmo18g01183 1183
5 33776339 33780655 + CmPI595203_05g024930.1 Cmu05g2493 2493
5 33792540 33793604 + CmPI595203_05g024940.1 Cmu05g2494 2494
5 33797451 33799023 + CmPI595203_05g024950.1 Cmu05g2495 2495
6 2915284 2916502 + Conep06aG0060800.1 Cone6ag0595 595
6 2917740 2920145 + Conep06aG0060900.1 Cone6ag0596 596
9 2821847 2824533 + Conep09aG0060700.1 Cone9ag0597 597
9 2824874 2826775 + Conep09aG0060800.1 Cone9ag0598 598
9 2827271 2829517 + Conep09aG0060900.1 Cone9ag0599 599
13 8216449 8219604 - Conep13aG0098800.1 Cone13ag0960 960
13 8229745 8230688 + Conep13aG0099000.1 Cone13ag0962 962
19 7248453 7250421 - Conep19aG0097700.1 Cone19ag0949 949
19 7251278 7253668 - Conep19aG0097800.1 Cone19ag0950 950
19 7261477 7263182 + Conep19aG0098000.1 Cone19ag0952 952
19 7264785 7265360 + Conep19aG0098100.1 Cone19ag0953 953
1 8738376 8740054 - Cp4.1LG01g12420.1 Cpe01g01458 1458
1 8743874 8748127 - Cp4.1LG01g12400.1 Cpe01g01459 1459
7 1319496 1326267 + Cp4.1LG07g02440.1 Cpe07g00205 205
7 4807099 4821439 + Cp4.1LG07g06380.1 Cpe07g00652 652
7 4822850 4834813 - Cp4.1LG07g06360.1 Cpe07g00653 653
9 994575 996470 - Cp4.1LG09g01850.1 Cpe09g00169 169
5 37136143 37141405 + CrPI670011_05g026060.1 Cre05g2606 2606
5 37152907 37153962 + CrPI670011_05g026070.1 Cre05g2607 2607
5 37157817 37159355 + CrPI670011_05g026080.1 Cre05g2608 2608
5 26361306 26363721 - CsaV3_5G032580.1 Csa05g02439 2439
5 26363833 26366348 - CsaV3_5G032590.1 Csa05g02440 2440
5 26374588 26379022 - CsaV3_5G032600.1 Csa05g02441 2441
10 54154477 54156877 - Hsped.10g17320.1 Hepe10g1732 1732
10 54169953 54173539 - Hsped.10g17330.1 Hepe10g1733 1733
13 2216427 2217554 - Lag0040105.1 Lac13g0309 309
13 2227230 2232905 - Lag0040106.1 Lac13g0310 310
4 4121267 4126185 + Lsi04G004330.1 Lsi04g00433 433
4 4137810 4138877 + Lsi04G004340.1 Lsi04g00434 434
4 4139967 4144473 + Lsi04G004350.1 Lsi04g00435 435
4 5642966 5645017 - Sed0019025.1 Sed04g0698 698
6 40108307 40113245 + Sed0027317.2 Sed06g1537 1537
6 40133483 40135487 + Sed0003260.1 Sed06g1538 1538
4 9795492 9800901 + Tan0022423.2 Tan04g1090 1090
4 9812635 9816185 + Tan0019206.1 Tan04g1091 1091
4 9817840 9819907 + Tan0005161.1 Tan04g1092 1092
1 11577723 11584830 - Vvi1g891 Vvi1g891 891
1 11585229 11597948 - Vvi1g892 Vvi1g892 892
1 11599813 11601818 - Vvi1g893 Vvi1g893 893
1 11610080 11611375 - Vvi1g894 Vvi1g894 894
1 11618114 11623032 - Vvi1g895 Vvi1g895 895
1 11680567 11687175 + Vvi1g896 Vvi1g896 896
1 11714600 11721062 - Vvi1g897 Vvi1g897 897
1 11722266 11730200 - Vvi1g898 Vvi1g898 898
1 11757627 11766675 + Vvi1g899 Vvi1g899 899
1 11767828 11770802 + Vvi1g900 Vvi1g900 900
       

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