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
Vvi18g1060 . . . . . . . . Cmo05g00298 Cmo12g00369 . . . Car12g00396 . . Cpe07g00376 Bhi04g00239 . . . . . . . . . . . . . . . . . . . . . Blo17g00751 . Bda08g01227 Bda01g01528 Bpe02g01724 Bpe05g00134 . . . . . . Cma05g00293 Car05g00242 . Cpe11g00243 . . . . . . . . . . . . . . . . Csa02g02118 . .
Vvi18g1061 . . . . . . . . . . . . . . . . . Bhi04g00240 . . . Hepe10g0135 . . Cla08g01437 Cam08g1917 Cec08g1493 . . . Cre08g1393 Cone4ag1956 Cone7ag1869 . . . . . Cme03g01896 . Blo18g00782 . . . . Bma01g00731 . . . . Cma12g00420 . . Car15g00648 . . . . . . . . . . . . . . . . Lsi08g01338 . Chy03g01399 .
Vvi18g1062 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1388 Cone20ag0093 . . . . Blo17g00749 . Bda08g01226 . . . . Bma05g00160 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1063 . . Bda01g00500 . Bpe02g00362 . . Bma01g02357 . . Cma01g01953 . Car01g01525 . . . . . . . . . . . . . . . . . . . . Cone17ag1389 Cone20ag0092 Lsi04g01721 Csa03g04257 Chy04g00438 . . . . . . . . . . Cmo01g02012 . . . . . . Cpe02g00088 Bhi09g02117 Tan01g4990 . . Hepe01g1636 Mch11g0139 . . . . . . . . . . . Cme04g00492
Vvi18g1064 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1065 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1066 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1067 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1068 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1069 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 31992077 31996821 - Bda002503.1 Bda01g00500 500
1 51168262 51169396 + Bda003789.1 Bda01g01528 1528
8 50159097 50161318 - Bda030215.1 Bda08g01226 1226
8 50167744 50168868 - Bda030216.1 Bda08g01227 1227
4 5910249 5913537 + XM_039029786.1 Bhi04g00239 239
4 5910249 5913537 + XM_039029785.1 Bhi04g00240 240
9 60018544 60024693 - XM_039042866.1 Bhi09g02117 2117
17 23503188 23505481 - BLOR08295 Blo17g00749 749
17 23579358 23580492 - BLOR08297 Blo17g00751 751
18 22560307 22576017 - BLOR09270 Blo18g00782 782
1 6715976 6717110 - Bma000944.1 Bma01g00731 731
1 81264624 81269338 + Bma003228.1 Bma01g02357 2357
5 4667359 4669611 + Bma020875.1 Bma05g00160 160
2 2366204 2370894 - Bpe008203.1 Bpe02g00362 362
2 19697508 19698642 + Bpe009555.1 Bpe02g01724 1724
5 3101954 3103075 + Bpe025792 Bpe05g00134 134
8 25126617 25134507 - CaPI482276_08g019170.1 Cam08g1917 1917
1 12859050 12863716 + Carg17180-RA Car01g01525 1525
5 1349930 1352123 + Carg09417-RA Car05g00242 242
12 2531359 2532480 - Carg04004-RA Car12g00396 396
15 3574832 3579405 + Carg01507-RA Car15g00648 648
8 26663655 26671454 - CePI673135_08g014930.1 Cec08g1493 1493
3 16759840 16769247 - Chy3G063790.1 Chy03g01399 1399
4 3897179 3902900 - Chy4G071560.1 Chy04g00438 438
8 27243380 27247790 - ClCG08G014430.1 Cla08g01437 1437
1 12632208 12637751 + CmaCh01G019530.1 Cma01g01953 1953
5 1258878 1260679 + CmaCh05G002930.1 Cma05g00293 293
12 2178482 2179603 - CmaCh12G004200.1 Cma12g00420 420
3 27107833 27111774 - MELO3C010996.2.1 Cme03g01896 1896
4 3922226 3927763 - MELO3C003774.2.1 Cme04g00492 492
1 14167521 14172807 + CmoCh01G020120.1 Cmo01g02012 2012
5 1301051 1303185 + CmoCh05G002980.1 Cmo05g00298 298
12 2297281 2298833 - CmoCh12G003690.1 Cmo12g00369 369
4 13769816 13772297 + Conep04aG0201800.1 Cone4ag1956 1956
7 12059704 12060847 + Conep07aG0192400.1 Cone7ag1869 1869
17 9607920 9610554 + Conep17aG0142400.1 Cone17ag1388 1388
17 9611031 9615280 + Conep17aG0142500.1 Cone17ag1389 1389
20 421203 425422 - Conep20aG0009500.1 Cone20ag0092 92
20 425791 428608 - Conep20aG0009600.1 Cone20ag0093 93
2 444817 450174 - Cp4.1LG02g07710.1 Cpe02g00088 88
7 2428775 2433363 - Cp4.1LG07g03700.1 Cpe07g00376 376
11 1314902 1315956 + Cp4.1LG11g02390.1 Cpe11g00243 243
8 26934633 26942497 - CrPI670011_08g013930.1 Cre08g1393 1393
2 19227774 19232675 + CsaV3_2G029370.1 Csa02g02118 2118
3 37313213 37319161 + CsaV3_3G045630.1 Csa03g04257 4257
1 81571361 81577514 - Hsped.01g16360.1 Hepe01g1636 1636
10 1366617 1370209 + Hsped.10g01350.1 Hepe10g0135 135
4 24547985 24555133 + Lsi04G017210.1 Lsi04g01721 1721
8 21684989 21689048 - Lsi08G013380.1 Lsi08g01338 1338
11 890042 897119 - MC11g0125 Mch11g0139 139
1 115663581 115670053 + Tan0018581.2 Tan01g4990 4990
18 11741874 11742625 + Vvi18g1060 Vvi18g1060 1060
18 11742625 11743871 + Vvi18g1061 Vvi18g1061 1061
18 11745490 11746340 - Vvi18g1062 Vvi18g1062 1062
18 11749842 11761172 + Vvi18g1063 Vvi18g1063 1063
18 11761769 11763902 - Vvi18g1064 Vvi18g1064 1064
18 11764400 11773531 - Vvi18g1065 Vvi18g1065 1065
18 11774359 11775955 - Vvi18g1066 Vvi18g1066 1066
18 11778506 11781055 - Vvi18g1067 Vvi18g1067 1067
18 11784343 11786072 - Vvi18g1068 Vvi18g1068 1068
18 11789355 11791909 + Vvi18g1069 Vvi18g1069 1069
       

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