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
Vvi5g1259 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1260 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1261 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1262 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1263 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1264 . . . . . . . . . . . . . . . . . Bhi01g02657 . . . Hepe05g1252 . Lcy11g1192 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1265 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1266 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1267 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1268 Blo01g00193 . . Bda08g00158 . . . Bma05g01166 . . . Cma14g01519 . Car14g01343 Sed12g0692 . Cpe03g01278 Bhi01g01188 Tan10g1201 Cmetu06g1782 . Hepe05g1300 . Lcy11g1259 . . . . . . . . . Cone18ag0851 . . . . . . . . Bda13g00549 Bpe05g00974 . . . . . Cmo14g01554 . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 1463114 1469978 + Bda024565.3 Bda08g00158 158
13 6468389 6469554 + Bda001461.1 Bda13g00549 549
1 23399353 23409207 + XM_039018677.1 Bhi01g01188 1188
1 66061764 66070558 - XM_039039487.1 Bhi01g02657 2657
1 2595600 2603092 - BLOR00193 Blo01g00193 193
5 50708449 50717481 - Bma022355.1 Bma05g01166 1166
5 22583343 22599542 - Bpe018386.1 Bpe05g00974 974
14 11341265 11347280 - Carg24796-RA Car14g01343 1343
14 11491518 11500902 - CmaCh14G015190.1 Cma14g01519 1519
6 6055733 6066017 + PI0014974.1 Cmetu06g1782 1782
14 12400386 12410183 - CmoCh14G015540.1 Cmo14g01554 1554
18 5824870 5841287 + Conep18aG0087700.1 Cone18ag0851 851
3 10346637 10355952 - Cp4.1LG03g12330.1 Cpe03g01278 1278
5 59559477 59562518 + Hsped.05g12520.1 Hepe05g1252 1252
5 61097200 61106830 - Hsped.05g13000.1 Hepe05g1300 1300
11 34345570 34349643 + Maker00005247 Lcy11g1192 1192
11 35788775 35799782 - Maker00005289 Lcy11g1259 1259
12 4130370 4146267 - Sed0000993.1 Sed12g0692 692
10 12068565 12082907 + Tan0022615.1 Tan10g1201 1201
5 22996374 23004692 + Vvi5g1259 Vvi5g1259 1259
5 23035015 23036755 + Vvi5g1260 Vvi5g1260 1260
5 23045984 23046335 + Vvi5g1261 Vvi5g1261 1261
5 23048308 23049583 + Vvi5g1262 Vvi5g1262 1262
5 23102729 23104466 + Vvi5g1263 Vvi5g1263 1263
5 23134188 23149240 + Vvi5g1264 Vvi5g1264 1264
5 23190811 23192169 + Vvi5g1265 Vvi5g1265 1265
5 23192257 23192899 + Vvi5g1266 Vvi5g1266 1266
5 23193192 23196309 - Vvi5g1267 Vvi5g1267 1267
5 23203329 23224286 + Vvi5g1268 Vvi5g1268 1268
       

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