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
Vvi5g279 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g280 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g281 . . . . . Bpe14g01073 . . . . . . Car06g01353 . Sed02g1098 Cpe08g00127 . Bhi01g01146 Tan10g1134 Cmetu06g2072 . Hepe05g1336 . Lcy11g1296 . . . . . . . . . . . . . . . Blo02g00456 . . . . . Bma02g00959 . . Cmo06g01588 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g282 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g283 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g284 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g285 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g286 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g287 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g288 . . . . . Bpe14g01079 . . . . . Cma14g01547 . Car14g01365 Sed02g1093 . Cpe03g01293 Bhi01g01151 Tan10g1142 Cmetu06g0925 . Hepe05g1330 . Lcy11g1291 . . . . . . . . . . . Lsi05g01373 . . Cme06g00846 Blo02g00460 . . Bda13g00235 . . . . . . Cmo14g01583 . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
13 2908759 2914315 - Bda001114.2 Bda13g00235 235
1 22328742 22334303 + XM_039042809.1 Bhi01g01146 1146
1 22561062 22571622 - XM_039038224.1 Bhi01g01151 1151
2 6455391 6458986 + BLOR10186 Blo02g00456 456
2 6543752 6549281 + BLOR10190 Blo02g00460 460
2 49595445 49603314 - Bma015757.1 Bma02g00959 959
14 8049208 8051800 + Bpe014447.1 Bpe14g01073 1073
14 8087953 8093459 + Bpe014453.1 Bpe14g01079 1079
6 9685848 9690031 + Carg25662-RA Car06g01353 1353
14 11547508 11553441 + Carg19586-RA Car14g01365 1365
14 11668197 11674970 + CmaCh14G015470.1 Cma14g01547 1547
6 5781047 5789479 - MELO3C006765.2.1 Cme06g00846 846
6 5863602 5872304 - PI0025274.1 Cmetu06g0925 925
6 5818857 5828936 + PI0027387.2 Cmetu06g2072 2072
6 11137553 11141887 + CmoCh06G015880.1 Cmo06g01588 1588
14 12591106 12597061 + CmoCh14G015830.1 Cmo14g01583 1583
3 10523808 10530348 + Cp4.1LG03g12180.1 Cpe03g01293 1293
8 835108 839509 - Cp4.1LG08g05440.1 Cpe08g00127 127
5 61665005 61672387 + Hsped.05g13300.1 Hepe05g1330 1330
5 61750413 61754983 - Hsped.05g13360.1 Hepe05g1336 1336
11 36355016 36362898 + Maker00031480 Lcy11g1291 1291
11 36449617 36460569 - Maker00031663 Lcy11g1296 1296
5 21594476 21603645 + Lsi05G013740.1 Lsi05g01373 1373
2 48287803 48295965 + Sed0021297.2 Sed02g1093 1093
2 48328207 48335446 - Sed0018318.1 Sed02g1098 1098
10 10993594 10998858 + Tan0015690.1 Tan10g1134 1134
10 11181924 11190998 - Tan0015237.1 Tan10g1142 1142
5 2818840 2819414 + Vvi5g279 Vvi5g279 279
5 2824972 2828379 - Vvi5g280 Vvi5g280 280
5 2837644 2844052 - Vvi5g281 Vvi5g281 281
5 2845584 2846772 - Vvi5g282 Vvi5g282 282
5 2853264 2855466 - Vvi5g283 Vvi5g283 283
5 2859891 2863796 + Vvi5g284 Vvi5g284 284
5 2867205 2868567 + Vvi5g285 Vvi5g285 285
5 2869463 2876265 + Vvi5g286 Vvi5g286 286
5 2877561 2880014 + Vvi5g287 Vvi5g287 287
5 2881363 2896617 + Vvi5g288 Vvi5g288 288
       

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