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
Vvi1g811 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0630 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g812 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g813 . . . Bda11g01243 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0996 Cone19ag0987 . . . . . . . . . Bda11g01243 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g814 Blo01g00412 . Bda01g02247 Bda11g01242 Bpe13g00471 . Bma14g01759 . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0995 Cone19ag0986 . . . . . . . Blo11g00894 . Bda11g01242 . . Bma01g00077 . . . . . . . . . Cpe07g00608 . . . . . . . . . . . . . . . . . .
Vvi1g815 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g816 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g817 . . . . . . Bma14g01758 . . . . . . . Sed06g1586 . Cpe01g01427 Bhi07g01643 Tan04g1149 Cmetu10g1826 Lac13g0255 Hepe10g1694 . . Cla05g02494 Cam05g2679 Cec05g2713 Cco05g2748 Clacu05g2681 Cmu05g2536 Cre05g2651 Cone13ag0994 . . . . Csa05g02391 Chy10g00953 . . Blo11g00893 . . . . . . . Cmo04g02874 . Cma04g01613 . Car04g01654 . Cpe13g00933 . . . . . . . . . . . . . . . . . Chy09g00284 .
Vvi1g818 . . . . . . . . . . . . . . . . . . . . . . . . Cla05g02493 Cam05g2678 Cec05g2712 Cco05g2747 Clacu05g2680 Cmu05g2535 Cre05g2650 . . . . Lsi04g00493 Csa05g02392 Chy10g00954 Cme10g00472 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g819 . . . . . . Bma14g01757 . . . . . . . . . . . . . . . . . Cla05g02492 Cam05g2677 Cec05g2711 Cco05g2746 Clacu05g2679 Cmu05g2534 Cre05g2649 Cone14ag0364 Cone15ag0400 . . Lsi04g00491 . . . . Blo11g00892 Bda07g01578 . Bpe11g01750 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g820 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 58264061 58265518 - Bda004592.1 Bda01g02247 2247
7 29249402 29251142 - Bda033979 Bda07g01578 1578
11 12947673 12948952 + Bda007753.1 Bda11g01242 1242
11 12950094 12952307 - Bda007754.1 Bda11g01243 1243
7 46303106 46306745 - XM_039036171.1 Bhi07g01643 1643
1 4665092 4666506 - BLOR00412 Blo01g00412 412
11 17784476 17786376 - BLOR03768 Blo11g00892 892
11 17787831 17791654 - BLOR03769 Blo11g00893 893
11 17912638 17914158 + BLOR03770 Blo11g00894 894
1 746806 748063 - Bma000243.1 Bma01g00077 77
14 37799609 37801279 - Bma030736 Bma14g01757 1757
14 37808055 37812869 - Bma012528.1 Bma14g01758 1758
14 37842115 37843890 + Bma012530.1 Bma14g01759 1759
11 13838977 13840672 - Bpe005067.1 Bpe11g01750 1750
13 12200788 12202250 + Bpe010183.2 Bpe13g00471 471
5 34184941 34187324 + CaPI482276_05g026770.1 Cam05g2677 2677
5 34188983 34190908 + CaPI482276_05g026780.1 Cam05g2678 2678
5 34191122 34194328 - CaPI482276_05g026790.1 Cam05g2679 2679
4 9540352 9544758 + Carg01746-RA Car04g01654 1654
5 35313281 35315538 + CcPI632755_05g027460.1 Cco05g2746 2746
5 35317091 35319013 + CcPI632755_05g027470.1 Cco05g2747 2747
5 35319227 35322412 - CcPI632755_05g027480.1 Cco05g2748 2748
5 37630339 37633924 + CePI673135_05g027110.1 Cec05g2711 2711
5 37635637 37637556 + CePI673135_05g027120.1 Cec05g2712 2712
5 37637789 37641006 - CePI673135_05g027130.1 Cec05g2713 2713
9 2388821 2392611 - Chy9G160000.1 Chy09g00284 284
10 15095649 15098666 + Chy10G181470.1 Chy10g00953 953
10 15098842 15100758 - Chy10G181480.1 Chy10g00954 954
5 34392459 34394838 + ClG42_05g0267900.10 Clacu05g2679 2679
5 34396504 34398429 + ClG42_05g0268000.10 Clacu05g2680 2680
5 34398637 34401866 - ClG42_05g0268100.10 Clacu05g2681 2681
5 36301819 36304198 + ClCG05G024790.2 Cla05g02492 2492
5 36306121 36308046 + ClCG05G024800.1 Cla05g02493 2493
5 36310098 36313493 - ClCG05G024810.1 Cla05g02494 2494
4 8147520 8152020 + CmaCh04G016130.1 Cma04g01613 1613
10 2979003 2980960 + MELO3C012046.2.1 Cme10g00472 472
10 19018490 19024194 + PI0008200.1 Cmetu10g1826 1826
4 20441819 20445936 + CmoCh04G028740.1 Cmo04g02874 2874
5 34130367 34132746 + CmPI595203_05g025340.1 Cmu05g2534 2534
5 34134416 34136341 + CmPI595203_05g025350.1 Cmu05g2535 2535
5 34136579 34139810 - CmPI595203_05g025360.1 Cmu05g2536 2536
8 6236468 6239149 - Conep08aG0065100.1 Cone8ag0630 630
13 8378745 8382327 - Conep13aG0102500.1 Cone13ag0994 994
13 8388473 8390698 + Conep13aG0102600.1 Cone13ag0995 995
13 8390773 8392078 - Conep13aG0102700.1 Cone13ag0996 996
14 1686592 1689790 + Conep14aG0037200.1 Cone14ag0364 364
15 1876404 1879445 + Conep15aG0040900.1 Cone15ag0400 400
19 7438204 7440389 + Conep19aG0101800.1 Cone19ag0986 986
19 7440555 7441988 - Conep19aG0101900.1 Cone19ag0987 987
1 8570971 8575546 + Cp4.1LG01g12890.1 Cpe01g01427 1427
7 4169450 4172263 + Cp4.1LG07g05660.1 Cpe07g00608 608
13 7889234 7893761 + Cp4.1LG13g08670.1 Cpe13g00933 933
5 37487519 37488773 + CrPI670011_05g026490.1 Cre05g2649 2649
5 37490412 37492334 + CrPI670011_05g026500.1 Cre05g2650 2650
5 37492571 37495779 - CrPI670011_05g026510.1 Cre05g2651 2651
5 26075372 26081477 + CsaV3_5G032100.1 Csa05g02391 2391
5 26079359 26081275 - CsaV3_5G032110.1 Csa05g02392 2392
10 53662768 53669373 + Hsped.10g16940.1 Hepe10g1694 1694
13 1843749 1846998 + Lag0040051.1 Lac13g0255 255
4 4536199 4538888 + Lsi04G004910.1 Lsi04g00491 491
4 4540822 4542738 + Lsi04G004920.1 Lsi04g00493 493
6 40650294 40654568 - Sed0018449.2 Sed06g1586 1586
4 10702711 10706214 - Tan0004644.1 Tan04g1149 1149
1 10087354 10090494 + Vvi1g811 Vvi1g811 811
1 10114880 10136219 + Vvi1g812 Vvi1g812 812
1 10140471 10145698 + Vvi1g813 Vvi1g813 813
1 10146180 10150591 - Vvi1g814 Vvi1g814 814
1 10164109 10164993 - Vvi1g815 Vvi1g815 815
1 10175844 10178979 + Vvi1g816 Vvi1g816 816
1 10189899 10197800 + Vvi1g817 Vvi1g817 817
1 10197873 10200282 - Vvi1g818 Vvi1g818 818
1 10214816 10216764 - Vvi1g819 Vvi1g819 819
1 10226502 10227418 + Vvi1g820 Vvi1g820 820
       

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