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
Vvi4g782 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g783 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g784 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe14g00006 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g785 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g786 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g787 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g788 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g789 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g790 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0913 Cone1ag1670 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla03g01090 Cam03g1136 Cec03g1151 Cco03g1133 Clacu03g1113 Cmu03g1692 Cre03g1400 Lsi06g00751 . . .
Vvi4g791 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone10ag0625 . . . . Cme05g01074 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
14 158941 160329 - Bpe006665.1 Bpe14g00006 6
3 22115534 22119057 - CaPI482276_03g011360.1 Cam03g1136 1136
3 21525938 21529458 - CcPI632755_03g011330.1 Cco03g1133 1133
3 25192501 25197411 - CePI673135_03g011510.1 Cec03g1151 1151
3 20887113 20891795 - ClG42_03g0111300.10 Clacu03g1113 1113
3 21791948 21796208 - ClCG03G011330.1 Cla03g01090 1090
5 16603013 16605456 + MELO3C008669.2.1 Cme05g01074 1074
3 21272451 21277524 - CmPI595203_03g016920.1 Cmu03g1692 1692
1 57848316 57852260 - Conep01aG0173300.1 Cone1ag1670 1670
5 3907344 3910068 - Conep05aG0093900.1 Cone5ag0913 913
10 2978931 2981431 - Conep10aG0064200.1 Cone10ag0625 625
3 26259326 26264401 - CrPI670011_03g014000.1 Cre03g1400 1400
6 13871865 13881265 - Lsi06G007510.1 Lsi06g00751 751
4 14878674 14882905 - Vvi4g782 Vvi4g782 782
4 14943619 14962982 + Vvi4g783 Vvi4g783 783
4 14964960 14966325 - Vvi4g784 Vvi4g784 784
4 14992017 14993981 + Vvi4g785 Vvi4g785 785
4 15011614 15039726 - Vvi4g786 Vvi4g786 786
4 15084284 15085366 - Vvi4g787 Vvi4g787 787
4 15108282 15109209 + Vvi4g788 Vvi4g788 788
4 15123327 15124227 - Vvi4g789 Vvi4g789 789
4 15167438 15175571 + Vvi4g790 Vvi4g790 790
4 15210733 15213343 + Vvi4g791 Vvi4g791 791
       

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