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
Vvi18g1280 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1509 . . . . . . . . . . . . . . . . . . . . . . . . Bhi09g01475 . . . . Mch11g1405 . . . . . . . . . . . .
Vvi18g1281 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag1442 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1282 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1283 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo17g00126 . . Bda13g01409 . . . Bma02g00148 . . . . . . Car15g00556 . . . . . . . . . . . . . . . . . . . .
Vvi18g1284 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1285 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1286 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1287 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1288 Blo01g01755 . . . Bpe02g00187 . . Bma01g02538 . . . Cma09g01151 Car01g00842 . . Cpe06g00926 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g01162 . . . . . . Bhi09g01574 Tan01g3001 . . . . . Cla09g00968 Cam09g1019 Cec09g1023 Cco09g1034 . . Cre09g0985 . . . Cme01g00744
Vvi18g1289 Blo01g01754 Blo12g00765 . Bda03g00417 Bpe02g00188 . . Bma01g02537 . . Cma01g00941 . . . . Cpe06g00921 . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00847 . . . . . . Cmo01g00981 . . . . . . . Bhi09g01565 Tan01g2974 . . . . . Cla09g00961 Cam09g1013 Cec09g1016 Cco09g1028 . . Cre09g0976 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 3617756 3620443 - Bda016382.1 Bda03g00417 417
11 8350731 8354006 + Bda033063 Bda11g00847 847
13 36811282 36813087 + Bda000236.1 Bda13g01409 1409
9 37954817 37959954 + XM_039040829.1 Bhi09g01475 1475
9 42052015 42060975 + XM_039041414.1 Bhi09g01565 1565
9 42477382 42486643 + XM_039041213.1 Bhi09g01574 1574
1 57310293 57313719 - BLOR01754 Blo01g01754 1754
1 57317978 57320198 + BLOR01755 Blo01g01755 1755
12 26011874 26014561 + BLOR04784 Blo12g00765 765
17 1161328 1163120 + BLOR15947 Blo17g00126 126
1 83065994 83068904 - Bma030308 Bma01g02537 2537
1 83084689 83086450 + Bma003418.1 Bma01g02538 2538
2 1309261 1311065 + Bma014604.1 Bma02g00148 148
2 1302369 1304240 - Bpe008038.4 Bpe02g00187 187
2 1306943 1310273 + Bpe008039.1 Bpe02g00188 188
9 10532652 10541586 + CaPI482276_09g010130.1 Cam09g1013 1013
9 10598619 10603627 + CaPI482276_09g010190.1 Cam09g1019 1019
1 6640738 6644039 - Carg28125-RA Car01g00842 842
15 3068417 3071114 - Carg01599-RA Car15g00556 556
9 9830686 9839397 + CcPI632755_09g010280.1 Cco09g1028 1028
9 9906958 9912077 + CcPI632755_09g010340.1 Cco09g1034 1034
9 9841398 9848770 + CePI673135_09g010160.1 Cec09g1016 1016
9 9909315 9914357 + CePI673135_09g010230.1 Cec09g1023 1023
9 10100819 10108253 + ClCG09G010290.2 Cla09g00961 961
9 10165843 10171275 + ClCG09G010360.1 Cla09g00968 968
1 5965176 5968659 - CmaCh01G009410.1 Cma01g00941 941
9 6606694 6611559 - CmaCh09G011510.1 Cma09g01151 1151
1 7323798 7334635 - MELO3C023658.2.1 Cme01g00744 744
1 6475213 6478766 - CmoCh01G009810.1 Cmo01g00981 981
9 7342644 7347940 - CmoCh09G011620.1 Cmo09g01162 1162
4 11725811 11726716 - Conep04aG0156100.1 Cone4ag1509 1509
7 10210622 10212134 + Conep07aG0148400.1 Cone7ag1442 1442
6 6603037 6604623 + Cp4.1LG06g09260.1 Cpe06g00921 921
6 6826002 6831032 + Cp4.1LG06g09190.1 Cpe06g00926 926
9 10040706 10048161 + CrPI670011_09g009760.1 Cre09g0976 976
9 10118295 10123360 + CrPI670011_09g009850.1 Cre09g0985 985
11 10301687 10308094 + MC11g1160 Mch11g1405 1405
1 69766956 69781471 + Tan0000628.4 Tan01g2974 2974
1 73527717 73534364 + Tan0014700.5 Tan01g3001 3001
18 16218962 16221368 + Vvi18g1280 Vvi18g1280 1280
18 16231735 16233196 + Vvi18g1281 Vvi18g1281 1281
18 16234067 16271237 - Vvi18g1282 Vvi18g1282 1282
18 16285606 16288125 - Vvi18g1283 Vvi18g1283 1283
18 16288124 16293527 - Vvi18g1284 Vvi18g1284 1284
18 16296858 16297513 + Vvi18g1285 Vvi18g1285 1285
18 16302856 16307318 + Vvi18g1286 Vvi18g1286 1286
18 16506972 16507131 - Vvi18g1287 Vvi18g1287 1287
18 17293486 17296105 + Vvi18g1288 Vvi18g1288 1288
18 17367996 17396611 + Vvi18g1289 Vvi18g1289 1289
       

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