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
Vvi1g1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g2 Blo01g00462 . . . . Bpe10g00911 Bma14g01718 . Cmo04g01798 Cmo18g01113 . Cma18g01089 . Car18g01010 . Cpe09g00233 Cpe01g01517 . . . . . . . . . . . . . . Cone13ag0891 Cone19ag0890 Cone6ag0514 Cone9ag0526 . Csa05g02523 . . Blo06g00939 Blo11g00801 . . . . . . . . . Cma04g01711 . Car04g01745 . . Cpe07g00095 . . . . . . . . . . . . . . . . . .
Vvi1g3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g4 . . . . . . Bma14g01717 Bma15g00110 . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0892 Cone19ag0891 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g5 Blo01g00462 . Bda01g02118 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0893 . . . . . . . . . . . . Bpe02g02306 Bma01g00132 . . . . . . . . . Cpe07g00094 . . . . . . . . . . . . . . . . . .
Vvi1g6 . . . . . . Bma14g01716 . Cmo04g01798 Cmo18g01118 . Cma18g01096 . Car18g01011 Sed07g2036 Cpe09g00230 . Bhi07g01468 Tan04g0973 Cmetu10g0107 Lac13g0388 Hepe10g1807 . . Cla05g02384 Cam05g2556 Cec05g2588 Cco05g2629 Clacu05g2557 Cmu05g2414 Cre05g2531 Cone13ag0894 . . Cone9ag0527 Lsi04g00353 Csa05g02523 Chy10g01067 Cme10g00347 . . . . . . . Bma06g00744 . . . Cma04g01711 . Car04g01745 . . . . . . . . . . . . . . . . . . . . .
Vvi1g7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme09g00694
Vvi1g8 . . Bda01g02119 . . . Bma14g01715 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe02g02307 Bma01g00131 Bma06g00742 . . . . . . . . Cpe07g00093 . . . . . . . . . . . . . . . . . .
Vvi1g9 Blo01g00461 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g10 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0515 Cone9ag0528 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57219088 57225281 - Bda004449.1 Bda01g02118 2118
1 57227731 57230188 - Bda004450.1 Bda01g02119 2119
7 43086139 43087655 - XM_039036910.1 Bhi07g01468 1468
1 5098214 5105922 + BLOR00461 Blo01g00461 461
1 5108512 5114287 + BLOR00462 Blo01g00462 462
6 32609995 32618417 + BLOR17522 Blo06g00939 939
11 12495951 12497827 + BLOR03677 Blo11g00801 801
1 1275757 1278266 + Bma000296.1 Bma01g00131 131
1 1289506 1295941 + Bma000297.2 Bma01g00132 132
6 38543749 38547162 - Bma023731.1 Bma06g00742 742
6 38621157 38623961 - Bma023734.2 Bma06g00744 744
14 36348830 36350457 + Bma012464.1 Bma14g01715 1715
14 36358926 36364233 + Bma012466.1 Bma14g01716 1716
14 36386548 36389180 + Bma012468.1 Bma14g01717 1717
14 36390395 36392526 - Bma030735 Bma14g01718 1718
15 1190260 1191689 - Bma013085.1 Bma15g00110 110
2 23745007 23752369 - Bpe010122.1 Bpe02g02306 2306
2 23754926 23757415 - Bpe010123.1 Bpe02g02307 2307
10 14766742 14768857 + Bpe003214.1 Bpe10g00911 911
5 33332403 33333309 - CaPI482276_05g025560.1 Cam05g2556 2556
4 10002835 10004073 + Carg14360-RA Car04g01745 1745
18 10523842 10528271 + Carg17320-RA Car18g01010 1010
18 10548340 10549817 - Carg17319-RA Car18g01011 1011
5 34437282 34438167 - CcPI632755_05g026290.1 Cco05g2629 2629
5 36772815 36773706 - CePI673135_05g025880.1 Cec05g2588 2588
10 15828094 15829056 + Chy10G182610.1 Chy10g01067 1067
5 33539958 33540855 - ClG42_05g0255700.10 Clacu05g2557 2557
5 35389710 35390636 - ClCG05G023590.1 Cla05g02384 2384
4 8609437 8610719 + CmaCh04G017110.1 Cma04g01711 1711
18 8958712 8963762 + CmaCh18G010890.1 Cma18g01089 1089
18 8982094 8983456 - CmaCh18G010960.1 Cma18g01096 1096
9 7878110 7883649 + MELO3C002930.2.1 Cme09g00694 694
10 2245316 2247190 - MELO3C012161.2.1 Cme10g00347 347
10 19767986 19769366 + PI0005702.1 Cmetu10g0107 107
4 9043364 9044646 + CmoCh04G017980.1 Cmo04g01798 1798
18 11530764 11533621 + CmoCh18G011130.1 Cmo18g01113 1113
18 11556233 11558457 - CmoCh18G011180.1 Cmo18g01118 1118
5 33277792 33278689 - CmPI595203_05g024140.1 Cmu05g2414 2414
6 2553284 2555846 + Conep06aG0052600.1 Cone6ag0514 514
6 2575701 2576858 + Conep06aG0052700.1 Cone6ag0515 515
9 2511926 2513120 + Conep09aG0053600.1 Cone9ag0526 526
9 2517356 2518379 - Conep09aG0053700.1 Cone9ag0527 527
9 2532276 2533357 + Conep09aG0053800.1 Cone9ag0528 528
13 7892887 7895420 + Conep13aG0091900.1 Cone13ag0891 891
13 7896834 7900052 + Conep13aG0092000.1 Cone13ag0892 892
13 7905100 7911039 - Conep13aG0092100.1 Cone13ag0893 893
13 7911605 7912185 - Conep13aG0092200.1 Cone13ag0894 894
19 6964192 6967143 + Conep19aG0091500.1 Cone19ag0890 890
19 6969203 6972720 + Conep19aG0091600.1 Cone19ag0891 891
1 9066361 9082704 - Cp4.1LG01g15190.1 Cpe01g01517 1517
7 459230 470274 + Cp4.1LG07g00830.1 Cpe07g00093 93
7 471999 479147 + Cp4.1LG07g00820.1 Cpe07g00094 94
7 481898 484626 - Cp4.1LG07g00910.1 Cpe07g00095 95
9 1323882 1325462 + Cp4.1LG09g02260.1 Cpe09g00230 230
9 1345306 1350049 - Cp4.1LG09g02380.1 Cpe09g00233 233
5 36628326 36629201 - CrPI670011_05g025310.1 Cre05g2531 2531
5 26770880 26773822 + CsaV3_5G033420.1 Csa05g02523 2523
10 54864264 54866015 + Hsped.10g18070.1 Hepe10g1807 1807
13 2767276 2768127 + Lag0040184.1 Lac13g0388 388
4 3515932 3517212 - Lsi04G003530.1 Lsi04g00353 353
7 35449463 35451480 - Sed0023361.1 Sed07g2036 2036
4 8804105 8806939 - Tan0003687.1 Tan04g0973 973
1 10730 27033 + Vvi1g1 Vvi1g1 1
1 32354 36097 + Vvi1g2 Vvi1g2 2
1 46793 47258 - Vvi1g3 Vvi1g3 3
1 48573 58015 + Vvi1g4 Vvi1g4 4
1 92039 107832 - Vvi1g5 Vvi1g5 5
1 109278 110282 - Vvi1g6 Vvi1g6 6
1 112284 118695 + Vvi1g7 Vvi1g7 7
1 150381 175544 - Vvi1g8 Vvi1g8 8
1 194106 206538 - Vvi1g9 Vvi1g9 9
1 220861 222178 + Vvi1g10 Vvi1g10 10
       

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