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
Vvi4g682 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda13g01823 Bpe14g00053 . . Bma02g00573 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g683 . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00805 Cam01g0827 Cec01g0825 Cco01g0857 Clacu01g0820 Cmu01g0788 Cre09g1717 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g684 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g685 Blo01g01433 . Bda01g00646 . . Bpe02g00517 . . . . . . Car09g00329 . . . Cpe06g00269 . . . . . . . Cla05g01645 Cam05g1756 Cec05g1763 Cco05g1819 Clacu05g1745 Cmu05g1630 Cre05g1759 . . . . Lsi04g01371 . . . . . . . . . . . . . Cmo09g00381 Cma09g00379 . . . . . . . . . . . . . . . . . . . . . . Cme07g00161
Vvi4g686 . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00822 Cam01g0848 Cec01g0844 Cco01g0872 Clacu01g0835 Cmu01g0807 Cre09g1703 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g687 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g688 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g689 . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00824 Cam01g0850 Cec01g0846 Cco01g0873 Clacu01g0836 Cmu01g0808 Cre09g1701 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g690 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g691 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 33481986 33483287 + Bda002674.1 Bda01g00646 646
13 42169582 42181278 - Bda032827 Bda13g01823 1823
1 53170352 53171795 - BLOR01433 Blo01g01433 1433
2 12190647 12199239 - Bma015106.1 Bma02g00573 573
2 3375221 3376525 + Bpe008357.1 Bpe02g00517 517
14 870097 878041 + Bpe024952 Bpe14g00053 53
1 9331935 9340954 + CaPI482276_01g008270.1 Cam01g0827 827
1 9619564 9621231 + CaPI482276_01g008480.1 Cam01g0848 848
1 9648690 9650363 + CaPI482276_01g008500.1 Cam01g0850 850
5 26199631 26200989 + CaPI482276_05g017560.1 Cam05g1756 1756
9 1810782 1812149 + Carg02808-RA Car09g00329 329
1 9153038 9162615 + CcPI632755_01g008570.1 Cco01g0857 857
1 9441518 9443185 + CcPI632755_01g008720.1 Cco01g0872 872
1 9488553 9490226 + CcPI632755_01g008730.1 Cco01g0873 873
5 26992842 26994200 + CcPI632755_05g018190.1 Cco05g1819 1819
1 9211381 9224148 + CePI673135_01g008250.1 Cec01g0825 825
1 9527775 9529442 + CePI673135_01g008440.1 Cec01g0844 844
1 9559642 9561315 + CePI673135_01g008460.1 Cec01g0846 846
5 29307805 29308998 + CePI673135_05g017630.1 Cec05g1763 1763
1 8991440 9000398 + ClG42_01g0082000.10 Clacu01g0820 820
1 9301383 9303050 + ClG42_01g0083500.10 Clacu01g0835 835
1 9331711 9333384 + ClG42_01g0083600.10 Clacu01g0836 836
5 26422681 26424033 + ClG42_05g0174500.10 Clacu05g1745 1745
1 9447525 9457098 + ClCG01G008180.2 Cla01g00805 805
1 9767520 9775421 + ClCG01G008360.2 Cla01g00822 822
1 9805970 9807643 + ClCG01G008380.1 Cla01g00824 824
5 27914947 27916299 + ClCG05G015930.1 Cla05g01645 1645
9 1584482 1587949 + CmaCh09G003790.1 Cma09g00379 379
7 1058797 1062817 - MELO3C016928.2.1 Cme07g00161 161
9 1666143 1667510 + CmoCh09G003810.1 Cmo09g00381 381
1 8958138 8967097 + CmPI595203_01g007880.1 Cmu01g0788 788
1 9259860 9267740 + CmPI595203_01g008070.1 Cmu01g0807 807
1 9296395 9298068 + CmPI595203_01g008080.1 Cmu01g0808 808
5 26141513 26142865 + CmPI595203_05g016300.1 Cmu05g1630 1630
6 1463732 1465102 + Cp4.1LG06g02640.1 Cpe06g00269 269
5 29395457 29396815 + CrPI670011_05g017590.1 Cre05g1759 1759
9 35056301 35057974 - CrPI670011_09g017010.1 Cre09g1701 1701
9 35090980 35092647 - CrPI670011_09g017030.1 Cre09g1703 1703
9 35361271 35373769 - CrPI670011_09g017170.1 Cre09g1717 1717
4 21508489 21509856 - Lsi04G013710.1 Lsi04g01371 1371
4 9493850 9572196 - Vvi4g682 Vvi4g682 682
4 9601200 9680561 + Vvi4g683 Vvi4g683 683
4 9681072 9687040 - Vvi4g684 Vvi4g684 684
4 9696114 9697625 + Vvi4g685 Vvi4g685 685
4 9766797 9768784 - Vvi4g686 Vvi4g686 686
4 9772422 9772785 - Vvi4g687 Vvi4g687 687
4 9819405 9820188 - Vvi4g688 Vvi4g688 688
4 9836537 9838712 + Vvi4g689 Vvi4g689 689
4 9842032 9842587 + Vvi4g690 Vvi4g690 690
4 9991453 10005125 + Vvi4g691 Vvi4g691 691
       

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