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
Vvi18g1150 . . . . . . . . . . . . . . Sed11g1102 . . Bhi04g00123 Tan02g2833 Cmetu03g0369 . . . Lcy13g1897 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1151 . . . . . . . . Cmo05g00323 Cmo12g00348 . . . Car12g00375 Sed08g0406 . Cpe07g00352 Bhi04g00121 Tan02g2832 Cmetu03g2049 . Hepe10g0170 . Lcy13g1896 Cla08g01407 Cam08g1887 Cec08g1464 Cco08g1597 Clacu08g1579 . Cre08g1362 . . . . . . . . . . Bda08g01209 . . Bpe05g00149 . Bma05g00181 . . . Cma12g00397 Cma05g00320 Car05g00267 . Cpe11g00268 . . . . . . . . . . . . . . . Lsi08g01303 . . .
Vvi18g1152 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1419 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1153 . Blo12g00878 Bda01g00473 . Bpe02g00338 Bpe04g00253 Bma04g00253 Bma01g02381 . . Cma01g01984 Cma09g00093 Car01g01555 . . Cpe06g00055 . . . . . . . . . . . . . . . . . . . Lsi04g01762 Csa03g04294 Chy04g00402 . . . . . . . . . Sed01g2478 Cmo01g02042 . . . . Car09g00080 . Cpe02g00061 Bhi09g02071 Tan01g5041 Cmetu04g2661 . Hepe01g1602 Mch11g0101 . . . . . . . . . . . Cme04g00455
Vvi18g1154 Blo01g01608 . . . . . . . Cmo05g00327 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma05g00324 Car05g00271 . . . . . . . . . . . . . . . . . . . . .
Vvi18g1155 . . . . . . . Bma01g02382 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1156 Blo01g01609 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag1904 . Cone20ag0063 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1157 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1158 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi09g01519 . . . . . . . . . . . . . Lsi08g01297 . Chy03g00639 .
Vvi18g1159 . . . . . . . . . . . . . . . . Cpe07g00344 . . . . . . . Cla08g01400 Cam08g1880 Cec08g1457 Cco08g1590 Clacu08g1572 . Cre08g1355 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 31808588 31813406 - Bda002475.1 Bda01g00473 473
8 49615821 49617431 - Bda030190.1 Bda08g01209 1209
4 3164858 3167638 - XM_039030451.1 Bhi04g00121 121
4 3169129 3171431 + XM_039029521.1 Bhi04g00123 123
9 40221207 40252044 - XM_039041749.1 Bhi09g01519 1519
9 59105306 59110944 - XM_039042650.1 Bhi09g02071 2071
1 55967121 55976006 + BLOR01608 Blo01g01608 1608
1 55988055 55990070 + BLOR01609 Blo01g01609 1609
12 26978764 26989993 - BLOR04897 Blo12g00878 878
1 81431861 81436590 + Bma003252.1 Bma01g02381 2381
1 81438679 81441181 + Bma003253.1 Bma01g02382 2382
4 2147807 2154800 + Bma018705.1 Bma04g00253 253
5 5112644 5114260 + Bma020907.1 Bma05g00181 181
2 2200872 2218613 - Bpe008179.1 Bpe02g00338 338
4 1687923 1692610 + Bpe014966.1 Bpe04g00253 253
5 4267887 4269499 + Bpe017536.2 Bpe05g00149 149
8 24809646 24813879 + CaPI482276_08g018800.1 Cam08g1880 1880
8 24862239 24864704 - CaPI482276_08g018870.1 Cam08g1887 1887
1 12989243 12993673 + Carg17210-RA Car01g01555 1555
5 1476149 1478985 + Carg09392-RA Car05g00267 267
5 1495141 1496856 - Carg09388-RA Car05g00271 271
9 402960 407402 - Carg08663-RA Car09g00080 80
12 2389695 2392138 - Carg03982-RA Car12g00375 375
8 27469172 27480217 + CcPI632755_08g015900.1 Cco08g1590 1590
8 27527628 27530090 - CcPI632755_08g015970.1 Cco08g1597 1597
8 26337609 26341853 + CePI673135_08g014570.1 Cec08g1457 1457
8 26390246 26392708 - CePI673135_08g014640.1 Cec08g1464 1464
3 8898338 8910247 - Chy3G056190.1 Chy03g00639 639
4 3572259 3577068 - Chy4G071200.1 Chy04g00402 402
8 25557354 25561582 + ClG42_08g0157200.10 Clacu08g1572 1572
8 25609382 25611860 - ClG42_08g0157900.10 Clacu08g1579 1579
8 26905267 26916350 + ClCG08G014050.2 Cla08g01400 1400
8 26965766 26968244 - ClCG08G014130.2 Cla08g01407 1407
1 12762108 12767746 + CmaCh01G019840.1 Cma01g01984 1984
5 1387024 1390194 + CmaCh05G003200.1 Cma05g00320 320
5 1401541 1410609 - CmaCh05G003240.1 Cma05g00324 324
9 403869 408274 - CmaCh09G000930.1 Cma09g00093 93
12 2050309 2052782 - CmaCh12G003970.1 Cma12g00397 397
4 3597750 3603026 - MELO3C003739.2.1 Cme04g00455 455
3 4988451 4990712 + PI0017061.1 Cmetu03g0369 369
3 4985227 4987969 - PI0006471.1 Cmetu03g2049 2049
4 29764188 29769862 + PI0025063.1 Cmetu04g2661 2661
1 14303409 14307802 + CmoCh01G020420.1 Cmo01g02042 2042
5 1430392 1433477 + CmoCh05G003230.1 Cmo05g00323 323
5 1450515 1452217 - CmoCh05G003270.1 Cmo05g00327 327
12 2160520 2162905 - CmoCh12G003480.1 Cmo12g00348 348
7 12207104 12208577 + Conep07aG0196100.1 Cone7ag1904 1904
17 9730656 9731529 + Conep17aG0145700.1 Cone17ag1419 1419
20 300786 302127 - Conep20aG0006500.1 Cone20ag0063 63
2 314506 319226 - Cp4.1LG02g08100.1 Cpe02g00061 61
6 280661 285356 - Cp4.1LG06g00520.1 Cpe06g00055 55
7 2236455 2239882 + Cp4.1LG07g03330.1 Cpe07g00344 344
7 2282500 2286544 - Cp4.1LG07g03540.1 Cpe07g00352 352
11 1444007 1447472 + Cp4.1LG11g02630.1 Cpe11g00268 268
8 26607329 26618442 + CrPI670011_08g013550.1 Cre08g1355 1355
8 26664275 26669508 - CrPI670011_08g013620.1 Cre08g1362 1362
3 37603443 37608770 + CsaV3_3G046000.1 Csa03g04294 4294
1 81297883 81303205 - Hsped.01g16020.1 Hepe01g1602 1602
10 1731078 1736891 + Hsped.10g01700.1 Hepe10g0170 170
13 37913619 37919688 - Maker00033718 Lcy13g1896 1896
13 37920704 37923156 + Maker00033758 Lcy13g1897 1897
4 24874254 24879119 + Lsi04G017620.1 Lsi04g01762 1762
8 21344753 21355256 + Lsi08G012970.1 Lsi08g01297 1297
8 21392617 21405863 - Lsi08G013030.1 Lsi08g01303 1303
11 665523 670256 - MC11g0090 Mch11g0101 101
1 18535811 18541725 - Sed0016624.1 Sed01g2478 2478
8 2458973 2463485 - Sed0005025.1 Sed08g0406 406
11 26721310 26723337 - Sed0007913.1 Sed11g1102 1102
1 115982957 115988577 + Tan0017631.1 Tan01g5041 5041
2 96607861 96616050 - Tan0008719.1 Tan02g2832 2832
2 96616741 96619109 + Tan0007643.1 Tan02g2833 2833
18 12767384 12770597 - Vvi18g1150 Vvi18g1150 1150
18 12776645 12781444 + Vvi18g1151 Vvi18g1151 1151
18 12783607 12784590 + Vvi18g1152 Vvi18g1152 1152
18 12787198 12810091 + Vvi18g1153 Vvi18g1153 1153
18 12821111 12823055 + Vvi18g1154 Vvi18g1154 1154
18 12823490 12836197 + Vvi18g1155 Vvi18g1155 1155
18 12838653 12840711 + Vvi18g1156 Vvi18g1156 1156
18 12841217 12848327 + Vvi18g1157 Vvi18g1157 1157
18 12853193 12856039 + Vvi18g1158 Vvi18g1158 1158
18 12859116 12862545 + Vvi18g1159 Vvi18g1159 1159
       

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