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
Vvi1g691 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g692 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g693 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag1033 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g694 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g695 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g696 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g697 Blo01g00396 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g02335 . Cme10g00524 . . . . . . . . . . . Cma04g01734 . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g698 . . . . . . . . . . . . . . Sed04g0627 . Cpe01g01533 Bhi07g01732 Tan04g1237 Cmetu10g1279 . . . . Cla05g02543 Cam05g2733 Cec05g2764 Cco05g2804 Clacu05g2734 Cmu05g2587 Cre05g2701 . . . . Lsi04g00551 . Chy10g00903 . . . Bda07g01603 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g699 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g700 . . . . . Bpe10g00839 Bma14g01795 Bma15g00184 . Cmo18g00802 . Cma18g00798 . Car18g00729 . Cpe09g00505 . Bhi07g01730 . . . . . . Cla05g02542 . . . . . . Cone13ag1041 . Cone8ag0663 . Lsi04g00550 . Chy10g00904 . Blo06g00877 Blo11g00916 Bda07g01602 . . . . . . . . Cma04g01733 . Car04g01766 . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 29691199 29694577 + Bda028471.1 Bda07g01602 1602
7 29694986 29696131 - Bda028472.1 Bda07g01603 1603
7 47816903 47820833 + XM_039037025.1 Bhi07g01730 1730
7 47821049 47823806 - XM_039037110.1 Bhi07g01732 1732
1 4479393 4481637 - BLOR00396 Blo01g00396 396
6 32056340 32063431 + BLOR17460 Blo06g00877 877
11 19000087 19003468 + BLOR03792 Blo11g00916 916
14 38539221 38541935 + Bma012566.4 Bma14g01795 1795
15 1925429 1927807 - Bma013166.2 Bma15g00184 184
10 14356868 14360030 + Bpe003144.1 Bpe10g00839 839
5 34629720 34631885 - CaPI482276_05g027330.1 Cam05g2733 2733
4 10109406 10112635 + Carg14339-RA Car04g01766 1766
18 8428061 8430982 - Carg14469-RA Car18g00729 729
5 35772790 35774954 - CcPI632755_05g028040.1 Cco05g2804 2804
5 38087012 38089177 - CePI673135_05g027640.1 Cec05g2764 2764
10 14732787 14739000 + Chy10G180970.1 Chy10g00903 903
10 14739630 14742678 - Chy10G180980.1 Chy10g00904 904
5 34837709 34839875 - ClG42_05g0273400.10 Clacu05g2734 2734
5 36770135 36773591 + ClCG05G025350.2 Cla05g02542 2542
5 36774438 36776657 - ClCG05G025360.2 Cla05g02543 2543
4 8715449 8718864 + CmaCh04G017330.1 Cma04g01733 1733
4 8718800 8721463 - CmaCh04G017340.1 Cma04g01734 1734
18 7019254 7022362 - CmaCh18G007980.1 Cma18g00798 798
10 3374659 3377528 - MELO3C011994.2.1 Cme10g00524 524
10 18634293 18636976 + PI0023920.1 Cmetu10g1279 1279
18 9482250 9485173 - CmoCh18G008020.1 Cmo18g00802 802
5 34575696 34577862 - CmPI595203_05g025870.1 Cmu05g2587 2587
8 6652064 6656044 + Conep08aG0068600.1 Cone8ag0663 663
13 8618068 8620688 + Conep13aG0107200.1 Cone13ag1041 1041
19 7677626 7680275 + Conep19aG0106500.1 Cone19ag1033 1033
1 9174100 9178935 - Cp4.1LG01g15300.1 Cpe01g01533 1533
9 3353628 3356703 + Cp4.1LG09g04970.1 Cpe09g00505 505
5 37936977 37939142 - CrPI670011_05g027010.1 Cre05g2701 2701
5 25725825 25732273 + CsaV3_5G031540.1 Csa05g02335 2335
4 5048319 5051647 + Lsi04G005500.1 Lsi04g00550 550
4 5051242 5054880 - Lsi04G005520.1 Lsi04g00551 551
4 4844927 4847554 + Sed0004702.1 Sed04g0627 627
4 11756536 11759771 - Tan0021846.4 Tan04g1237 1237
1 7941993 7942663 + Vvi1g691 Vvi1g691 691
1 7942710 7943176 + Vvi1g692 Vvi1g692 692
1 7943321 7945676 - Vvi1g693 Vvi1g693 693
1 7946356 7960766 - Vvi1g694 Vvi1g694 694
1 7963566 7968686 + Vvi1g695 Vvi1g695 695
1 7972479 7972665 - Vvi1g696 Vvi1g696 696
1 7987553 7987940 + Vvi1g697 Vvi1g697 697
1 7989002 7990113 + Vvi1g698 Vvi1g698 698
1 7999868 8002071 - Vvi1g699 Vvi1g699 699
1 8004149 8007646 - Vvi1g700 Vvi1g700 700
       

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