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
Vvi19g764 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g765 . . . . . . . . . . . . . . Sed07g2769 . . Bhi09g01829 Tan01g3238 Cmetu01g0398 . . Mch11g1316 . . . . . . . . . . . . . . . . . . . . . . Bma07g01126 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g766 . . . . . . . . . . . . . . Sed07g2770 . . Bhi09g01830 Tan01g3239 Cmetu01g2171 . . Mch11g1317 . . . . . . . . . . . . . Csa07g01054 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g767 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g768 . . . . . . . . . . . . . . . . . Bhi09g01831 Tan01g3240 . . . Mch11g1321 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g769 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa07g01053 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme01g01101
Vvi19g770 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g771 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g772 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa07g01052 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme01g01099
Vvi19g773 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
9 49571617 49573296 - XM_039043821.1 Bhi09g01829 1829
9 49571620 49573296 - XM_039043819.1 Bhi09g01830 1830
9 49571785 49573296 - XM_039043822.1 Bhi09g01831 1831
7 45034231 45035335 + Bma026349.1 Bma07g01126 1126
1 13809460 13810347 - MELO3C013209.2.1 Cme01g01099 1099
1 13836380 13837374 - MELO3C013211.2.1 Cme01g01101 1101
1 9891624 9893244 - PI0007525.1 Cmetu01g0398 398
1 9920309 9921448 - PI0007962.1 Cmetu01g2171 2171
7 10041912 10042500 + CsaV3_7G021410.1 Csa07g01052 1052
7 10046823 10047820 + CsaV3_7G021420.1 Csa07g01053 1053
7 10051800 10053234 + CsaV3_7G021430.1 Csa07g01054 1054
11 9322990 9324581 - MC11g1091 Mch11g1316 1316
11 9326356 9327184 - MC11g1092 Mch11g1317 1317
11 9340113 9341669 - MC11g1093 Mch11g1321 1321
7 42724016 42726591 - Sed0019745.1 Sed07g2769 2769
7 42728965 42730953 - Sed0002708.1 Sed07g2770 2770
1 86953570 86960956 - Tan0016744.1 Tan01g3238 3238
1 87007014 87009156 - Tan0005047.1 Tan01g3239 3239
1 87029542 87030138 - Tan0000100.1 Tan01g3240 3240
19 9975326 9975818 - Vvi19g764 Vvi19g764 764
19 10028796 10030110 - Vvi19g765 Vvi19g765 765
19 10049238 10052163 - Vvi19g766 Vvi19g766 766
19 10110446 10113213 - Vvi19g767 Vvi19g767 767
19 10156335 10158496 - Vvi19g768 Vvi19g768 768
19 10189015 10190518 - Vvi19g769 Vvi19g769 769
19 10195355 10195601 + Vvi19g770 Vvi19g770 770
19 10267543 10270507 - Vvi19g771 Vvi19g771 771
19 10275338 10301902 - Vvi19g772 Vvi19g772 772
19 10302481 10305368 - Vvi19g773 Vvi19g773 773
       

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