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
Vvi1g231 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g232 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g233 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g234 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g235 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g236 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g237 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g238 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g239 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g240 . Blo16g01044 . . Bpe13g01320 . . . Cmo04g01619 . . . Car04g01598 . . . Cpe01g01375 . . . . . . . . . . . . . . Cone13ag0868 . Cone6ag0480 . . . . . . . . . . . . Bma06g00780 . . . . Cma15g01421 . . Cpe13g00026 . Bhi12g01423 . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
12 45603737 45606719 + XM_039020362.1 Bhi12g01423 1423
16 38888401 38891186 - BLOR21831 Blo16g01044 1044
6 40129602 40131818 + Bma023785.1 Bma06g00780 780
13 18315576 18317676 - Bpe010983.1 Bpe13g01320 1320
4 9239197 9241469 + Carg01802-RA Car04g01598 1598
15 8992647 8995992 + CmaCh15G014210.1 Cma15g01421 1421
4 8259671 8261943 + CmoCh04G016190.1 Cmo04g01619 1619
6 2378456 2381029 + Conep06aG0049000.1 Cone6ag0480 480
13 7728841 7732180 + Conep13aG0089500.1 Cone13ag0868 868
1 8263886 8266448 + Cp4.1LG01g13380.1 Cpe01g01375 1375
13 215796 218549 - Cp4.1LG13g00290.1 Cpe13g00026 26
1 2369605 2370258 + Vvi1g231 Vvi1g231 231
1 2371302 2371826 + Vvi1g232 Vvi1g232 232
1 2374460 2375324 + Vvi1g233 Vvi1g233 233
1 2383590 2384528 + Vvi1g234 Vvi1g234 234
1 2395308 2400043 + Vvi1g235 Vvi1g235 235
1 2402401 2404621 - Vvi1g236 Vvi1g236 236
1 2408593 2409466 + Vvi1g237 Vvi1g237 237
1 2410020 2422646 + Vvi1g238 Vvi1g238 238
1 2427681 2428209 - Vvi1g239 Vvi1g239 239
1 2429293 2433043 - Vvi1g240 Vvi1g240 240
       

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