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
Vvi18g1690 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g01260 . . . . . . Bhi06g00165 . . . . . . . . . . . . . . . . .
Vvi18g1691 . . . . . . . . . . . . . . Sed05g2505 . . Bhi04g02557 Tan11g0037 Cmetu03g0795 . Hepe02g3470 . Lcy10g2364 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla11g00803 Cam11g0839 Cec11g0825 . Clacu11g1018 Cmu11g0881 Cre11g1284 . . . .
Vvi18g1692 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1693 Blo01g01678 . . . Bpe02g00263 . . Bma01g02446 . . Cma01g00863 Cma09g01302 Car01g00792 . . Cpe06g00982 . . . . . . . . Cla08g00080 Cam08g0077 Cec08g0174 Cco08g0134 Clacu08g0090 Cmu08g0089 Cre08g0078 Cone4ag1158 . . . . . . Cme09g00077 . . Bda11g00925 . . . . . . Cmo01g00908 . . . . Car09g01114 . Cpe02g00993 . . . . . . . . . . . . . . Lsi08g00097 . . .
Vvi18g1694 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi06g00164 . . . . . . . . . . . . . . . . .
Vvi18g1695 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1696 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1697 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1698 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi06g00159 . . . . . . . . . . . . . . . . .
Vvi18g1699 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 9049494 9059224 - Bda005680.1 Bda11g00925 925
4 68689566 68691408 + XM_039030466.1 Bhi04g02557 2557
6 3789033 3798954 - XM_039034602.1 Bhi06g00159 159
6 3879119 3883884 + XM_039034070.1 Bhi06g00164 164
6 3879120 3883884 + XM_039034068.1 Bhi06g00165 165
1 56507043 56518179 + BLOR01678 Blo01g01678 1678
1 82077392 82086302 + Bma003316.1 Bma01g02446 2446
2 1778310 1788436 - Bpe008108.1 Bpe02g00263 263
8 1380931 1414406 + CaPI482276_08g000770.1 Cam08g0077 77
11 10963029 10964513 + CaPI482276_11g008390.1 Cam11g0839 839
1 5174317 5192426 + Carg26288-RA Car01g00792 792
9 11515265 11530430 - Carg24123-RA Car09g01114 1114
8 2095190 2129126 + CcPI632755_08g001340.1 Cco08g0134 134
8 3372269 3405909 - CePI673135_08g001740.1 Cec08g0174 174
11 10031297 10032781 + CePI673135_11g008250.1 Cec11g0825 825
8 1784625 1806488 + ClG42_08g0009000.10 Clacu08g0090 90
11 12360316 12361800 - ClG42_11g0101800.10 Clacu11g1018 1018
8 1644569 1678348 + ClCG08G000780.1 Cla08g00080 80
11 11838160 11844911 + ClCG11G008390.2 Cla11g00803 803
1 4864357 4883000 + CmaCh01G008630.1 Cma01g00863 863
9 9068457 9084292 - CmaCh09G013020.1 Cma09g01302 1302
9 585657 596244 + MELO3C022164.2.1 Cme09g00077 77
3 26118227 26120463 + PI0023575.1 Cmetu03g0795 795
1 5095353 5114432 + CmoCh01G009080.1 Cmo01g00908 908
9 10975798 10979424 - CmoCh09G012600.1 Cmo09g01260 1260
8 1710056 1736507 + CmPI595203_08g000890.1 Cmu08g0089 89
11 11689537 11691021 - CmPI595203_11g008810.1 Cmu11g0881 881
4 9911720 9920203 - Conep04aG0120400.1 Cone4ag1158 1158
2 9008315 9026864 - Cp4.1LG02g10940.1 Cpe02g00993 993
6 9841838 9860447 - Cp4.1LG06g09890.1 Cpe06g00982 982
8 1639000 1672808 + CrPI670011_08g000780.1 Cre08g0078 78
11 11645747 11647165 + CrPI670011_11g012840.1 Cre11g1284 1284
2 84012124 84014624 + Hsped.02g34700.1 Hepe02g3470 3470
10 47222577 47223992 + Maker00039219 Lcy10g2364 2364
8 2051577 2058973 + Lsi08G000970.1 Lsi08g00097 97
5 37128156 37140181 + Sed0020384.2 Sed05g2505 2505
11 705604 707341 - Tan0004505.1 Tan11g0037 37
18 27641231 27643249 + Vvi18g1690 Vvi18g1690 1690
18 27667978 27672909 - Vvi18g1691 Vvi18g1691 1691
18 27675109 27678094 - Vvi18g1692 Vvi18g1692 1692
18 27682644 27701721 + Vvi18g1693 Vvi18g1693 1693
18 27705193 27721484 - Vvi18g1694 Vvi18g1694 1694
18 27722033 27730799 + Vvi18g1695 Vvi18g1695 1695
18 27762783 27764096 - Vvi18g1696 Vvi18g1696 1696
18 27764433 27771795 - Vvi18g1697 Vvi18g1697 1697
18 27779525 27785293 - Vvi18g1698 Vvi18g1698 1698
18 27828675 27848734 - Vvi18g1699 Vvi18g1699 1699
       

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