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
Vvi19g1114 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1115 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1116 . Blo13g00596 . . . . Bma08g00817 . . . . . . . Sed04g3509 . . Bhi05g02009 Tan02g0053 Cmetu01g1368 Lac12g0050 Hepe02g0022 . . . . . . . . . . . . . . Csa07g01198 . . . . . . . . . . . . . . . . . Cpe15g00896 . . . . . . . . . . . . . . . . . Chy01g00865 Cme01g01518
Vvi19g1117 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1118 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1119 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1120 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1121 Blo04g00469 . . . . . . . . . . . . . Sed04g3511 . . Bhi05g02006 Tan02g0051 Cmetu01g2451 Lac12g0048 . . . . . . . . . . . . . . . Csa07g01200 . . . . . . Bpe15g00912 . Bma03g00502 . . . . . . . . . . . . . . . . . . . . . . . . . . Chy01g00863 .
Vvi19g1122 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1123 Blo04g00468 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 61602172 61605127 - XM_039032902.1 Bhi05g02006 2006
5 61608985 61618940 - XM_039031353.1 Bhi05g02009 2009
4 3884204 3889340 - BLOR13380 Blo04g00468 468
4 3890248 3891821 - BLOR13381 Blo04g00469 469
13 28376058 28384802 + BLOR19648 Blo13g00596 596
3 3927935 3929875 - Bma016783.1 Bma03g00502 502
8 45826458 45835453 + Bma028208.1 Bma08g00817 817
15 18929118 18931132 + Bpe001834.1 Bpe15g00912 912
1 7623666 7626094 - Chy1G008630.1 Chy01g00863 863
1 7632890 7644752 - Chy1G008650.1 Chy01g00865 865
1 19976582 19988962 - MELO3C012612.2.1 Cme01g01518 1518
1 7279416 7291610 - PI0025493.1 Cmetu01g1368 1368
1 7271111 7274362 - PI0003716.1 Cmetu01g2451 2451
15 8623328 8634149 + Cp4.1LG15g08910.1 Cpe15g00896 896
7 11775767 11788549 + CsaV3_7G022870.1 Csa07g01198 1198
7 11795368 11798843 + CsaV3_7G022890.1 Csa07g01200 1200
2 341144 351629 - Hsped.02g00220.1 Hepe02g0022 22
12 581294 584210 - Lag0014420.1 Lac12g0048 48
12 588792 599424 - Lag0014422.1 Lac12g0050 50
4 44573044 44584470 + Sed0006880.1 Sed04g3509 3509
4 44589291 44592290 + Sed0008622.1 Sed04g3511 3511
2 679988 683325 - Tan0004703.1 Tan02g0051 51
2 686376 697816 - Tan0005010.1 Tan02g0053 53
19 22386460 22391612 - Vvi19g1114 Vvi19g1114 1114
19 22400679 22412010 + Vvi19g1115 Vvi19g1115 1115
19 22420568 22445496 + Vvi19g1116 Vvi19g1116 1116
19 22472387 22474179 - Vvi19g1117 Vvi19g1117 1117
19 22499712 22500162 - Vvi19g1118 Vvi19g1118 1118
19 22500177 22502622 - Vvi19g1119 Vvi19g1119 1119
19 22505326 22505756 + Vvi19g1120 Vvi19g1120 1120
19 22522287 22530061 + Vvi19g1121 Vvi19g1121 1121
19 22530546 22543278 + Vvi19g1122 Vvi19g1122 1122
19 22546263 22547496 + Vvi19g1123 Vvi19g1123 1123
       

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