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
Vvi3g266 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1231 . . . . . Blo04g00595 . . . . . Bma03g00628 Bma08g00728 . . . . . . Car19g00599 . . . . . . . . . . . . . . . . . . . .
Vvi3g267 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo04g00594 . . Bda14g00638 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g268 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g269 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone10ag1013 . . . . Blo04g00593 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g270 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g271 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g272 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g273 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1232 . . . . . Blo04g00592 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g274 . . . . . . . Bma12g00866 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi10g01221 Tan05g1085 . . . . . Cla02g01079 Cam02g1159 Cec02g1157 Cco02g1205 Clacu02g1150 Cmu02g1112 Cre02g1415 . . . Cme11g01244
Vvi3g275 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
14 4775534 4777090 + Bda027395.2 Bda14g00638 638
10 26999444 27002706 - XM_039045193.1 Bhi10g01221 1221
4 5095878 5097058 + BLOR13504 Blo04g00592 592
4 5098059 5100977 - BLOR13505 Blo04g00593 593
4 5102690 5104294 + BLOR13506 Blo04g00594 594
4 5104406 5107039 - BLOR13507 Blo04g00595 595
3 5183078 5185052 - Bma016919.1 Bma03g00628 628
8 43117424 43120156 + Bma028092.1 Bma08g00728 728
12 39624347 39626669 + Bma008187.1 Bma12g00866 866
2 22639308 22642013 + CaPI482276_02g011590.1 Cam02g1159 1159
19 7389645 7392923 - Carg25746-RA Car19g00599 599
2 22367693 22370382 + CcPI632755_02g012050.1 Cco02g1205 1205
2 26983784 26986488 + CePI673135_02g011570.1 Cec02g1157 1157
2 22762709 22765416 + ClG42_02g0115000.10 Clacu02g1150 1150
2 22890390 22893344 + ClCG02G011050.2 Cla02g01079 1079
11 19047267 19050864 + MELO3C013654.2.1 Cme11g01244 1244
2 22626633 22629340 + CmPI595203_02g011120.1 Cmu02g1112 1112
3 31093229 31095870 + Conep03aG0173800.1 Cone3ag1231 1231
3 31098919 31101866 + Conep03aG0173900.1 Cone3ag1232 1232
10 7023423 7028799 + Conep10aG0104000.1 Cone10ag1013 1013
2 24630683 24633743 + CrPI670011_02g014150.1 Cre02g1415 1415
5 9539744 9543282 + Tan0017600.2 Tan05g1085 1085
3 2549516 2565520 + Vvi3g266 Vvi3g266 266
3 2568800 2571113 - Vvi3g267 Vvi3g267 267
3 2571164 2580535 + Vvi3g268 Vvi3g268 268
3 2581956 2585281 + Vvi3g269 Vvi3g269 269
3 2585953 2587664 + Vvi3g270 Vvi3g270 270
3 2588923 2591048 + Vvi3g271 Vvi3g271 271
3 2591510 2593945 - Vvi3g272 Vvi3g272 272
3 2595896 2600151 - Vvi3g273 Vvi3g273 273
3 2604332 2609255 + Vvi3g274 Vvi3g274 274
3 2609546 2612364 - Vvi3g275 Vvi3g275 275
       

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