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
Vvi18g170 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1426 Cone20ag0057 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g171 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g172 . Blo12g00875 . . . Bpe04g00258 Bma04g00259 . . . . Cma09g00088 . . . Cpe06g00051 . . . . . . . . . . . . . . . . . . . Lsi04g01774 . Chy04g00395 . . . . . . . . . . . Cmo09g00086 . . . Car09g00076 . . . . . . . . . Cla05g01601 Cam05g1712 Cec05g1712 Cco05g1769 Clacu05g1699 Cmu05g1588 Cre05g1707 . . . .
Vvi18g173 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g174 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g175 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g176 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g177 Blo01g01610 Blo12g00876 . Bda03g00296 . Bpe04g00256 Bma04g00257 Bma01g02384 . . Cma01g01987 Cma09g00089 Car01g01558 . . Cpe06g00052 . . . . . . . . Cla08g01406 Cam08g1886 Cec08g1463 Cco08g1596 Clacu08g1578 . Cre08g1361 . Cone7ag1910 . . Lsi04g01771 . Chy04g00397 . . . . . . . . . . Cmo01g02045 Cmo09g00087 . . . Car09g00077 . Cpe02g00058 . . . . . . . Cla05g01603 Cam05g1716 Cec05g1717 Cco05g1777 Clacu05g1705 Cmu05g1592 Cre05g1711 Lsi08g01303 . . .
Vvi18g178 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g179 . . . . . . . Bma01g02703 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00911 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 2619072 2623948 - Bda016254.2 Bda03g00296 296
11 8930645 8932531 + Bda005666.1 Bda11g00911 911
1 55990548 56001759 - BLOR01610 Blo01g01610 1610
12 26955640 26957050 - BLOR04894 Blo12g00875 875
12 26959119 26973069 + BLOR04895 Blo12g00876 876
1 81445187 81447730 - Bma003255.1 Bma01g02384 2384
1 84448129 84450131 + Bma003585.1 Bma01g02703 2703
4 2166944 2169458 - Bma018709.1 Bma04g00257 257
4 2174774 2175723 + Bma018711.1 Bma04g00259 259
4 1707017 1709576 - Bpe025589 Bpe04g00256 256
4 1714774 1715976 + Bpe014969.1 Bpe04g00258 258
5 25486299 25492209 - CaPI482276_05g017120.1 Cam05g1712 1712
5 25630859 25634410 + CaPI482276_05g017160.1 Cam05g1716 1716
8 24855449 24858711 - CaPI482276_08g018860.1 Cam08g1886 1886
1 13005016 13008546 - Carg17213-RA Car01g01558 1558
9 368137 372406 - Carg08659-RA Car09g00076 76
9 380746 384457 + Carg08660-RA Car09g00077 77
5 26147308 26152850 - CcPI632755_05g017690.1 Cco05g1769 1769
5 26404662 26407475 + CcPI632755_05g017770.1 Cco05g1777 1777
8 27520929 27524207 - CcPI632755_08g015960.1 Cco08g1596 1596
5 28442184 28447738 - CePI673135_05g017120.1 Cec05g1712 1712
5 28688691 28691509 + CePI673135_05g017170.1 Cec05g1717 1717
8 26383422 26386699 - CePI673135_08g014630.1 Cec08g1463 1463
4 3492611 3497365 - Chy4G071130.1 Chy04g00395 395
4 3521161 3523903 + Chy4G071150.1 Chy04g00397 397
5 25678929 25684340 - ClG42_05g0169900.10 Clacu05g1699 1699
5 25830655 25836406 + ClG42_05g0170500.10 Clacu05g1705 1705
8 25602604 25605885 - ClG42_08g0157800.10 Clacu08g1578 1578
5 27131737 27137753 - ClCG05G015450.2 Cla05g01601 1601
5 27286690 27290265 + ClCG05G015480.1 Cla05g01603 1603
8 26958988 26962383 - ClCG08G014120.1 Cla08g01406 1406
1 12778619 12782199 - CmaCh01G019870.1 Cma01g01987 1987
9 374715 379188 - CmaCh09G000880.1 Cma09g00088 88
9 379098 388693 + CmaCh09G000890.1 Cma09g00089 89
1 14319916 14323597 - CmoCh01G020450.1 Cmo01g02045 2045
9 388605 393156 - CmoCh09G000860.1 Cmo09g00086 86
9 396893 400263 + CmoCh09G000870.1 Cmo09g00087 87
5 25400595 25406095 - CmPI595203_05g015880.1 Cmu05g1588 1588
5 25549933 25555704 + CmPI595203_05g015920.1 Cmu05g1592 1592
7 12237096 12241735 - Conep07aG0196700.1 Cone7ag1910 1910
17 9756747 9759377 + Conep17aG0146400.1 Cone17ag1426 1426
20 279156 281902 - Conep20aG0005900.1 Cone20ag0057 57
2 301105 304652 + Cp4.1LG02g08220.1 Cpe02g00058 58
6 251154 255753 - Cp4.1LG06g00490.1 Cpe06g00051 51
6 258950 262574 + Cp4.1LG06g00420.1 Cpe06g00052 52
5 28576218 28585741 - CrPI670011_05g017070.1 Cre05g1707 1707
5 28800970 28803789 + CrPI670011_05g017110.1 Cre05g1711 1711
8 26660759 26663529 - CrPI670011_08g013610.1 Cre08g1361 1361
4 24933702 24938426 - Lsi04G017710.1 Lsi04g01771 1771
4 24963360 24969239 + Lsi04G017740.1 Lsi04g01774 1774
8 21392617 21405863 - Lsi08G013030.1 Lsi08g01303 1303
18 1698713 1706243 - Vvi18g170 Vvi18g170 170
18 1711993 1712514 + Vvi18g171 Vvi18g171 171
18 1712532 1714096 - Vvi18g172 Vvi18g172 172
18 1714246 1715403 - Vvi18g173 Vvi18g173 173
18 1721215 1721614 + Vvi18g174 Vvi18g174 174
18 1727183 1728333 - Vvi18g175 Vvi18g175 175
18 1729782 1732607 - Vvi18g176 Vvi18g176 176
18 1743054 1758026 + Vvi18g177 Vvi18g177 177
18 1758025 1758094 - Vvi18g178 Vvi18g178 178
18 1761928 1765473 + Vvi18g179 Vvi18g179 179
       

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