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
Vvi5g1249 . . . . . . . . . . . . . . Sed02g1027 . . Bhi01g02658 Tan10g1276 Cmetu07g1550 . . . Lcy11g1190 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1250 . . . . . Bpe14g01059 . . . . . Cma14g01516 . Car14g01340 . . . . . . . . . . . . . . . . . . . Cone18ag0850 . . . . . Blo02g00445 . . . . . . . . . Cmo14g01550 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1251 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1252 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1253 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1254 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1255 . . . . . . Bma04g00863 . . . . . . . Sed02g1078 . . Bhi01g01169 Tan10g1170 Cmetu09g1097 . Hepe05g1313 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1256 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1257 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1258 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone11ag1088 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 22891829 22897003 - XM_039036832.1 Bhi01g01169 1169
1 66066498 66070558 - XM_039039481.1 Bhi01g02658 2658
2 6098413 6099934 + BLOR10175 Blo02g00445 445
4 11345912 11346727 - Bma019414.1 Bma04g00863 863
14 7927690 7929261 + Bpe014433.1 Bpe14g01059 1059
14 11328587 11330560 + Carg24799-RA Car14g01340 1340
14 11477786 11479994 + CmaCh14G015160.1 Cma14g01516 1516
7 2778975 2782455 + PI0027079.1 Cmetu07g1550 1550
9 3370741 3372065 - PI0021171.1 Cmetu09g1097 1097
14 12386879 12388857 + CmoCh14G015500.1 Cmo14g01550 1550
11 8499372 8502132 - Conep11aG0112300.1 Cone11ag1088 1088
18 5813702 5815334 + Conep18aG0087600.1 Cone18ag0850 850
5 61295399 61300891 + Hsped.05g13130.1 Hepe05g1313 1313
11 34322227 34325840 + Maker00005273 Lcy11g1190 1190
2 47653193 47656779 + Sed0025891.1 Sed02g1027 1027
2 48116849 48121587 + Sed0008554.1 Sed02g1078 1078
10 11775043 11782942 - Tan0007289.2 Tan10g1170 1170
10 14524903 14528408 + Tan0012945.1 Tan10g1276 1276
5 22819170 22824151 - Vvi5g1249 Vvi5g1249 1249
5 22843171 22845524 + Vvi5g1250 Vvi5g1250 1250
5 22856750 22862502 - Vvi5g1251 Vvi5g1251 1251
5 22865111 22878894 + Vvi5g1252 Vvi5g1252 1252
5 22881864 22883976 - Vvi5g1253 Vvi5g1253 1253
5 22907017 22908789 + Vvi5g1254 Vvi5g1254 1254
5 22918210 22919944 + Vvi5g1255 Vvi5g1255 1255
5 22924188 22924772 - Vvi5g1256 Vvi5g1256 1256
5 22951894 22973624 - Vvi5g1257 Vvi5g1257 1257
5 22974127 22989011 + Vvi5g1258 Vvi5g1258 1258
       

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