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
Vvi5g1239 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1240 . . . . . Bpe14g01056 . . . . Cma06g01631 . Car06g01386 . . . . . . . . . . . . . . . . . . . . . . . . . Cme07g01851 Blo02g00442 Blo07g00111 Bda11g00475 . . . Bma02g00975 . . Cmo06g01629 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1241 Blo01g00195 . Bda03g00975 . Bpe04g00902 . . . Cmo08g00198 Cmo17g00588 . . . . . . . . . . . . . . Cla06g00088 Cam06g0132 . . Clacu06g0097 Cmu06g0095 Cre06g0866 . . Cone18ag0848 . . . . . . Blo07g00112 . . Bpe05g00975 . . Bma06g01437 . . . . Cma17g00607 Car08g00177 Car17g00573 . Cpe17g01088 . . . . . . . . . . . . . . . . . Cme11g02456
Vvi5g1242 Blo01g00194 Blo12g00263 Bda03g00974 Bda08g00157 Bpe04g00901 . . . . Cmo17g00589 . . . . . . . . . . . . . . Cla06g00089 Cam06g0131 Cec06g0098 Cco06g0094 Clacu06g0098 Cmu06g0096 Cre06g0867 . . Cone18ag0849 . . . . . . . . . . . . . . . . . Cma17g00608 . Car17g00574 . . . . . . . . . . . . . . . . . . . Cme11g02455
Vvi5g1243 . . . . . Bpe14g01057 . . . . Cma06g01619 Cma14g01515 Car06g01375 Car14g01339 . Cpe08g00107 Cpe03g01274 . . . . . . . . . . . . . . . . . . . . . . Blo02g00443 . . Bda13g00256 . . Bma02g00974 . . Cmo06g01614 Cmo14g01549 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1244 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1245 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1246 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1247 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1248 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 8808980 8809797 - Bda016984.1 Bda03g00974 974
3 8813827 8814805 + Bda016986.2 Bda03g00975 975
8 1460937 1461752 + Bda033795 Bda08g00157 157
11 4988289 4990081 + Bda005213.1 Bda11g00475 475
13 3235746 3236672 + Bda032842 Bda13g00256 256
1 2606055 2606861 - BLOR00194 Blo01g00194 194
1 2610431 2612165 + BLOR00195 Blo01g00195 195
2 6068640 6075646 + BLOR10172 Blo02g00442 442
2 6078019 6078984 - BLOR10173 Blo02g00443 443
7 1560232 1561983 + BLOR18043 Blo07g00111 111
7 1568502 1570078 - BLOR18044 Blo07g00112 112
12 16009576 16010388 + BLOR04282 Blo12g00263 263
2 50041086 50042033 + Bma030916 Bma02g00974 974
2 50043022 50044779 - Bma030917 Bma02g00975 975
6 51082648 51083906 - Bma024552.1 Bma06g01437 1437
4 6040469 6041284 - Bpe015565.1 Bpe04g00901 901
4 6044861 6045833 + Bpe025668 Bpe04g00902 902
5 22602529 22604204 + Bpe018387.1 Bpe05g00975 975
14 7917750 7919448 + Bpe014430.1 Bpe14g01056 1056
14 7920519 7921460 - Bpe014431.1 Bpe14g01057 1057
6 3277148 3278464 - CaPI482276_06g001310.1 Cam06g0131 131
6 3281083 3283669 + CaPI482276_06g001320.1 Cam06g0132 132
6 9890940 9893309 - Carg15501-RA Car06g01375 1375
6 9958634 9962748 + Carg15490-RA Car06g01386 1386
8 1086956 1089889 + Carg05023-RA Car08g00177 177
14 11326711 11327487 + Carg24800-RA Car14g01339 1339
17 5416293 5417865 + Carg28166-RA Car17g00573 573
17 5444343 5445158 + Carg18906-RA Car17g00574 574
6 871302 872117 + CcPI632755_06g000940.1 Cco06g0094 94
6 902971 903786 + CePI673135_06g000980.1 Cec06g0098 98
6 1063289 1068641 - ClG42_06g0009700.10 Clacu06g0097 97
6 1068985 1069800 + ClG42_06g0009800.10 Clacu06g0098 98
6 893819 899716 - ClCG06G000940.1 Cla06g00088 88
6 899559 900874 + ClCG06G000950.2 Cla06g00089 89
6 10080422 10081261 - CmaCh06G016190.1 Cma06g01619 1619
6 10145311 10149679 + CmaCh06G016310.1 Cma06g01631 1631
14 11476130 11476906 + CmaCh14G015150.1 Cma14g01515 1515
17 5142890 5145943 + CmaCh17G006070.1 Cma17g00607 607
17 5149240 5151396 + CmaCh17G006080.1 Cma17g00608 608
7 23962051 23969596 + MELO3C017680.2.1 Cme07g01851 1851
11 31275152 31277056 - MELO3C022444.2.1 Cme11g02455 2455
11 31278052 31281429 + MELO3C022445.2.1 Cme11g02456 2456
6 11276959 11292810 - CmoCh06G016140.1 Cmo06g01614 1614
6 11358320 11362819 + CmoCh06G016290.1 Cmo06g01629 1629
8 1172012 1174978 + CmoCh08G001980.1 Cmo08g00198 198
14 12384828 12385604 + CmoCh14G015490.1 Cmo14g01549 1549
17 6236889 6240061 + CmoCh17G005880.1 Cmo17g00588 588
17 6254340 6255155 + CmoCh17G005890.1 Cmo17g00589 589
6 852900 858227 - CmPI595203_06g000950.1 Cmu06g0095 95
6 858571 859386 + CmPI595203_06g000960.1 Cmu06g0096 96
18 5803138 5806119 - Conep18aG0087400.1 Cone18ag0848 848
18 5808613 5810369 + Conep18aG0087500.1 Cone18ag0849 849
3 10328770 10331858 + Cp4.1LG03g12410.1 Cpe03g01274 1274
8 682834 683673 + Cp4.1LG08g05810.1 Cpe08g00107 107
17 8252826 8256144 + Cp4.1LG17g10890.1 Cpe17g01088 1088
6 1955119 1957675 - CrPI670011_06g008660.1 Cre06g0866 866
6 1960806 1961621 + CrPI670011_06g008670.1 Cre06g0867 867
5 22621137 22635498 - Vvi5g1239 Vvi5g1239 1239
5 22635812 22642663 + Vvi5g1240 Vvi5g1240 1240
5 22643831 22646892 - Vvi5g1241 Vvi5g1241 1241
5 22653579 22654859 + Vvi5g1242 Vvi5g1242 1242
5 22669084 22679702 - Vvi5g1243 Vvi5g1243 1243
5 22722238 22724013 + Vvi5g1244 Vvi5g1244 1244
5 22724542 22745577 - Vvi5g1245 Vvi5g1245 1245
5 22753526 22755877 - Vvi5g1246 Vvi5g1246 1246
5 22774640 22779289 - Vvi5g1247 Vvi5g1247 1247
5 22803232 22809231 - Vvi5g1248 Vvi5g1248 1248
       

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