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
Vvi4g1252 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1253 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1254 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1255 . . . . . . . . . Cmo20g01078 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma20g01071 . . . . Bhi10g02336 . . . Hepe08g1255 . . Cla02g00070 Cam02g0071 Cec02g0072 Cco02g0065 Clacu02g0069 Cmu02g0068 Cre02g0408 Lsi10g00711 . . Cme11g00074
Vvi4g1256 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1257 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1258 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1259 . Blo16g00527 . . . . Bma09g00237 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1260 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1261 . Blo16g00530 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
10 60910031 60913653 - XM_039046172.1 Bhi10g02336 2336
16 21743462 21745777 + BLOR07775 Blo16g00527 527
16 21840838 21843195 + BLOR07778 Blo16g00530 530
9 10202898 10205219 - Bma029015.1 Bma09g00237 237
2 1803902 1805459 - CaPI482276_02g000710.1 Cam02g0071 71
2 671065 674999 - CcPI632755_02g000650.1 Cco02g0065 65
2 670524 674191 - CePI673135_02g000720.1 Cec02g0072 72
2 689986 693624 - ClG42_02g0006900.10 Clacu02g0069 69
2 684987 688625 - ClCG02G000660.2 Cla02g00070 70
20 8096025 8099627 - CmaCh20G010710.1 Cma20g01071 1071
11 594682 596271 - MELO3C023262.2.1 Cme11g00074 74
20 10211910 10215038 - CmoCh20G010780.1 Cmo20g01078 1078
2 689016 692850 - CmPI595203_02g000680.1 Cmu02g0068 68
2 1227226 1230916 - CrPI670011_02g004080.1 Cre02g0408 408
8 13427544 13429495 - Hsped.08g12550.1 Hepe08g1255 1255
10 9946389 9948698 + Lsi10G007110.1 Lsi10g00711 711
4 21784490 21800688 + Vvi4g1252 Vvi4g1252 1252
4 21801183 21807342 - Vvi4g1253 Vvi4g1253 1253
4 21807684 21809320 + Vvi4g1254 Vvi4g1254 1254
4 21857376 21863191 + Vvi4g1255 Vvi4g1255 1255
4 21881936 21882484 + Vvi4g1256 Vvi4g1256 1256
4 21882920 21884724 + Vvi4g1257 Vvi4g1257 1257
4 21924473 21924838 + Vvi4g1258 Vvi4g1258 1258
4 21928993 21930032 - Vvi4g1259 Vvi4g1259 1259
4 21941208 21942857 + Vvi4g1260 Vvi4g1260 1260
4 21957770 21968697 - Vvi4g1261 Vvi4g1261 1261
       

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