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
Vvi2g772 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g773 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g774 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g775 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g776 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g777 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g778 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g779 . . . . . . Bma07g00905 . . Cmo16g01248 Cma02g01644 . Car02g01402 . . . Cpe05g00149 . . . . . . . . . . . . . . . . . . Lsi07g01150 . . Cme06g02430 Blo03g00891 . Bda07g00068 . . Bpe11g00307 . . Sed01g4150 Cmo02g01690 Cmo19g00223 . Cma16g01201 . Car16g01131 . Cpe15g00181 Bhi05g00425 Tan07g2037 Cmetu06g0105 Lac11g2460 Hepe06g0978 . Lcy12g1984 . . . . . . . . Csa03g00122 Chy06g02183 .
Vvi2g780 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g781 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 909236 911988 - Bda025126.1 Bda07g00068 68
5 8957179 8963013 - XM_039031955.1 Bhi05g00425 425
3 34844958 34847671 + BLOR12072 Blo03g00891 891
7 32075150 32077153 + Bma025995.1 Bma07g00905 905
11 2237773 2240762 - Bpe003681.1 Bpe11g00307 307
2 9228457 9231002 + Carg08869-RA Car02g01402 1402
16 9680398 9683508 + Carg23578-RA Car16g01131 1131
6 26081373 26084652 + Chy6G127110.1 Chy06g02183 2183
2 9321347 9324211 + CmaCh02G016440.1 Cma02g01644 1644
16 9129085 9132389 + CmaCh16G012010.1 Cma16g01201 1201
6 31380803 31384721 - MELO3C013811.2.1 Cme06g02430 2430
6 30025508 30029682 + PI0022958.1 Cmetu06g0105 105
2 9697160 9701573 + CmoCh02G016900.1 Cmo02g01690 1690
16 8908808 8912490 + CmoCh16G012480.1 Cmo16g01248 1248
19 1500529 1504484 - CmoCh19G002230.1 Cmo19g00223 223
5 778357 781562 - Cp4.1LG05g00330.1 Cpe05g00149 149
15 1480746 1484326 - Cp4.1LG15g01750.1 Cpe15g00181 181
3 959760 964611 - CsaV3_3G001220.1 Csa03g00122 122
6 57503862 57508067 - Hsped.06g09780.1 Hepe06g0978 978
11 40789991 40794088 + Lag0033098.1 Lac11g2460 2460
12 41224286 41228727 + Maker00038024 Lcy12g1984 1984
7 16976219 16980936 - Lsi07G011500.1 Lsi07g01150 1150
1 70273663 70281087 + Sed0013554.1 Sed01g4150 4150
7 71930560 71935568 + Tan0020384.1 Tan07g2037 2037
2 11576141 11579157 - Vvi2g772 Vvi2g772 772
2 11660107 11663331 + Vvi2g773 Vvi2g773 773
2 11773713 11774120 - Vvi2g774 Vvi2g774 774
2 11781087 11782139 - Vvi2g775 Vvi2g775 775
2 11785461 11786162 + Vvi2g776 Vvi2g776 776
2 11835674 11847570 + Vvi2g777 Vvi2g777 777
2 11847578 11848204 + Vvi2g778 Vvi2g778 778
2 12236134 12239970 + Vvi2g779 Vvi2g779 779
2 12280961 12281208 - Vvi2g780 Vvi2g780 780
2 12445348 12445839 + Vvi2g781 Vvi2g781 781
       

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