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
Vvi17g166 . . Bda06g00868 . . . . Bma12g01285 . Cmo18g00064 . . . . . . . . . . . . . . . . . . . . . . . . . . Csa01g00733 Chy12g01380 Cme12g01813 . Blo15g00017 . . Bpe07g01089 . . . . . . . Cma18g00085 Car13g00813 Car18g00074 Cpe09g01105 . Bhi08g01329 . . . . . . . . . . . . . . . . .
Vvi17g167 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g168 . . . . . . . . Cmo13g01011 . . . . . . Cpe20g00165 . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01809 . . . . . . . . Cma13g00976 . . . . . Bhi08g01328 . . . . . . Cla04g01028 Cam04g1070 Cec01g1584 Cco01g1633 Clacu04g1097 Cmu04g1081 Cre01g1381 . . . .
Vvi17g169 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g170 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g171 . . . Bda15g00561 Bpe12g00646 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone2ag0776 . . . . . Chy12g01587 . Blo13g00123 . . . . . . Bma08g00108 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g172 . . . . . Bpe13g00381 . . . Cmo18g00062 . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00246 Csa01g00727 Chy12g01586 Cme12g01818 . . Bda11g01808 . . . Bma03g00926 Bma08g00107 . . . . Cma18g00081 Car13g00816 Car18g00071 . . . . . . . . . . . . . . . . . . . .
Vvi17g173 . . Bda06g00866 . . . . Bma12g01283 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy12g01585 . . Blo15g00020 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g174 . . . . . . . . Cmo13g01014 . . . . . . Cpe20g00162 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed08g2771 . . Cma13g00980 . . . . . Bhi08g01315 Tan05g2171 Cmetu12g1926 Lac10g0301 Hepe07g2339 . . Cla04g01033 Cam04g1075 Cec01g1589 Cco01g1638 Clacu04g1103 Cmu04g1086 Cre01g1385 . . . .
Vvi17g175 . . . Bda15g00560 Bpe12g00647 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo13g00124 Blo15g00019 . . Bpe07g01087 . . Bma08g00106 . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 11917897 11926618 - Bda024200.3 Bda06g00866 866
6 11935272 11937525 - Bda024202.1 Bda06g00868 868
11 53163949 53165939 - Bda008737.1 Bda11g01808 1808
11 53177394 53178344 - Bda008738.1 Bda11g01809 1809
15 8733944 8734578 + Bda012398.1 Bda15g00560 560
15 8745370 8746278 - Bda012399.1 Bda15g00561 561
8 39925198 39926957 - XM_039039200.1 Bhi08g01315 1315
8 40376514 40377740 + XM_039040097.1 Bhi08g01328 1328
8 40395617 40398856 + XM_039039260.1 Bhi08g01329 1329
13 3208198 3226862 + BLOR05404 Blo13g00123 123
13 3347391 3348631 - BLOR05405 Blo13g00124 124
15 123474 125984 + BLOR06411 Blo15g00017 17
15 135243 136188 + BLOR06413 Blo15g00019 19
15 137880 143691 + BLOR06414 Blo15g00020 20
3 9604459 9605767 - Bma017251.1 Bma03g00926 926
8 1267007 1268171 + Bma027107.1 Bma08g00106 106
8 1273070 1275202 + Bma027108.1 Bma08g00107 107
8 1284572 1303752 - Bma027109.1 Bma08g00108 108
12 45813729 45818705 - Bma008647.2 Bma12g01283 1283
12 45827083 45829177 - Bma008649.1 Bma12g01285 1285
7 16234319 16235150 - Bpe021927.1 Bpe07g01087 1087
7 16243231 16245479 - Bpe021929.1 Bpe07g01089 1089
12 12105926 12117805 + Bpe005906.1 Bpe12g00646 646
12 12128919 12130003 - Bpe005907.2 Bpe12g00647 647
13 11574495 11576485 - Bpe006505.1 Bpe13g00381 381
4 24856635 24857642 + CaPI482276_04g010700.1 Cam04g1070 1070
4 24898898 24900803 + CaPI482276_04g010750.1 Cam04g1075 1075
13 8900907 8903732 + Carg04859-RA Car13g00813 813
13 8917335 8920068 + Carg04856-RA Car13g00816 816
18 369067 371770 - Carg06636-RA Car18g00071 71
18 387056 391085 - Carg06639-RA Car18g00074 74
1 29063757 29064755 + CcPI632755_01g016330.1 Cco01g1633 1633
1 29106285 29108159 + CcPI632755_01g016380.1 Cco01g1638 1638
1 30477094 30478092 + CePI673135_01g015840.1 Cec01g1584 1584
1 30532652 30534530 + CePI673135_01g015890.1 Cec01g1589 1589
12 17999670 18002312 + Chy12G219800.1 Chy12g01380 1380
12 19351324 19388350 + Chy12G221850.1 Chy12g01585 1585
12 19388379 19389869 + Chy12G221860.1 Chy12g01586 1586
12 19391094 19418918 - Chy12G221870.1 Chy12g01587 1587
4 25222611 25223609 + ClG42_04g0109700.10 Clacu04g1097 1097
4 25264696 25270906 + ClG42_04g0110300.10 Clacu04g1103 1103
4 25428858 25429574 + ClCG04G010440.1 Cla04g01028 1028
4 25471846 25484241 + ClCG04G010500.2 Cla04g01033 1033
13 7605521 7606480 + CmaCh13G009760.1 Cma13g00976 976
13 7620789 7623092 + CmaCh13G009800.1 Cma13g00980 980
18 358045 360757 - CmaCh18G000810.1 Cma18g00081 81
18 374761 379228 - CmaCh18G000850.1 Cma18g00085 85
12 24591716 24594872 + MELO3C002149.2.1 Cme12g01813 1813
12 24622113 24625399 + MELO3C002144.2.1 Cme12g01818 1818
12 1649555 1651169 - PI0009990.1 Cmetu12g1926 1926
13 8596536 8597495 + CmoCh13G010110.1 Cmo13g01011 1011
13 8611519 8612941 + CmoCh13G010140.1 Cmo13g01014 1014
18 402885 405625 - CmoCh18G000620.1 Cmo18g00062 62
18 420869 425062 - CmoCh18G000640.1 Cmo18g00064 64
4 25408940 25409938 + CmPI595203_04g010810.1 Cmu04g1081 1081
4 25451270 25452137 + CmPI595203_04g010860.1 Cmu04g1086 1086
2 33726449 33741896 + Conep02aG0180300.1 Cone2ag0776 776
9 9530435 9539267 + Cp4.1LG09g10960.1 Cpe09g01105 1105
20 912766 914772 - Cp4.1LG20g01690.1 Cpe20g00162 162
20 929013 929972 - Cp4.1LG20g01640.1 Cpe20g00165 165
1 27039926 27040924 + CrPI670011_01g013810.1 Cre01g1381 1381
1 27082633 27084497 + CrPI670011_01g013850.1 Cre01g1385 1385
1 4605115 4609504 - CsaV3_1G007270.1 Csa01g00727 727
1 4633563 4637552 - CsaV3_1G007330.1 Csa01g00733 733
7 67757411 67759486 + Hsped.07g23390.1 Hepe07g2339 2339
10 2321043 2322580 - Lag0024346.1 Lac10g0301 301
2 2085090 2088446 - Lsi02G002460.1 Lsi02g00246 246
8 39301712 39308735 - Sed0026882.1 Sed08g2771 2771
5 72499164 72501459 + Tan0004589.1 Tan05g2171 2171
17 1518273 1526623 - Vvi17g166 Vvi17g166 166
17 1529099 1531743 + Vvi17g167 Vvi17g167 167
17 1537422 1538551 + Vvi17g168 Vvi17g168 168
17 1553718 1569449 + Vvi17g169 Vvi17g169 169
17 1571625 1575393 - Vvi17g170 Vvi17g170 170
17 1582166 1627116 + Vvi17g171 Vvi17g171 171
17 1630708 1633977 - Vvi17g172 Vvi17g172 172
17 1642886 1656845 - Vvi17g173 Vvi17g173 173
17 1659387 1663729 - Vvi17g174 Vvi17g174 174
17 1666196 1668095 - Vvi17g175 Vvi17g175 175
       

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