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
Vvi17g336 . . . Bda15g00520 Bpe12g00688 . . . . . Cma10g00242 Cma11g00266 Car10g00228 Car11g00242 . . Cpe04g01409 . . . . . . . Cla06g01477 Cam06g1631 Cec06g1694 Cco06g1688 Clacu06g1597 Cmu06g1546 Cre06g2358 . . . . . . . . Blo13g00163 . . . . . . Bma08g00067 . Cmo10g00260 Cmo11g00271 . . . . . Cpe18g00751 . . . . . . . . . . . . . . Lsi06g01340 Csa01g00374 Chy02g02371 Cme02g01754
Vvi17g337 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g338 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g339 . . . . . Bpe13g00343 Bma06g00033 . Cmo13g01071 . . . . . . Cpe20g00114 . . . . . . . . . . . . . . . Cone2ag0698 . . . Lsi02g00172 Csa01g00655 Chy12g01445 Cme12g01885 . . . . . . . . Sed01g1713 . . Cma13g01031 . Car13g00865 . . . Bhi08g01222 Tan05g2279 Cmetu12g0397 Lac10g0224 Hepe07g2405 . . Cla04g01102 Cam04g1155 Cec01g1665 Cco01g1711 Clacu04g1182 Cmu04g1162 Cre01g1460 . . . .
Vvi17g340 . . Bda06g00800 . . . . Bma12g01225 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g341 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo13g00162 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa01g00284 . .
Vvi17g342 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g343 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g344 . . . . . Bpe13g00342 Bma06g00001 . Cmo13g01072 . . . . . . Cpe20g00113 . . . . . . . . . . . . . . . Cone2ag0645 . . . Lsi02g00171 Csa01g00654 Chy12g01446 Cme12g01886 . . . . . . . . Sed08g2171 . . Cma13g01032 . Car13g00866 . . . Bhi08g01221 Tan05g2280 Cmetu12g2040 Lac10g0223 Hepe07g2408 . . Cla04g01103 Cam04g1156 Cec01g1666 Cco01g1712 Clacu04g1183 Cmu04g1163 Cre01g1461 . . . .
Vvi17g345 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0291 Cone19ag0273 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 11142117 11143576 - Bda024125.1 Bda06g00800 800
15 8275586 8278841 + Bda012350.2 Bda15g00520 520
8 37791571 37820171 - XM_039037935.1 Bhi08g01221 1221
8 37849520 37855710 + XM_039039098.1 Bhi08g01222 1222
13 5616985 5617761 + BLOR05443 Blo13g00162 162
13 5655694 5658764 - BLOR05444 Blo13g00163 163
6 154053 170889 + Bma022602.1 Bma06g00001 1
6 639026 642278 + Bma022640.1 Bma06g00033 33
8 844797 848020 + Bma027066.1 Bma08g00067 67
12 45133014 45155865 - Bma008588.1 Bma12g01225 1225
12 12467610 12470815 - Bpe005947.2 Bpe12g00688 688
13 11251842 11266213 - Bpe006469.1 Bpe13g00342 342
13 11274604 11277780 + Bpe006470.1 Bpe13g00343 343
4 25602173 25609120 - CaPI482276_04g011550.1 Cam04g1155 1155
4 25609239 25622045 + CaPI482276_04g011560.1 Cam04g1156 1156
6 27749223 27752072 + CaPI482276_06g016310.1 Cam06g1631 1631
10 1082415 1086145 + Carg17915-RA Car10g00228 228
11 1363145 1365869 - Carg09147-RA Car11g00242 242
13 9175626 9179685 - Carg04807-RA Car13g00865 865
13 9180097 9195518 + Carg04806-RA Car13g00866 866
1 29849851 29855081 - CcPI632755_01g017110.1 Cco01g1711 1711
1 29856943 29869778 + CcPI632755_01g017120.1 Cco01g1712 1712
6 27431639 27434455 + CcPI632755_06g016880.1 Cco06g1688 1688
1 31283839 31290718 - CePI673135_01g016650.1 Cec01g1665 1665
1 31290862 31303617 + CePI673135_01g016660.1 Cec01g1666 1666
6 30500588 30503696 + CePI673135_06g016940.1 Cec06g1694 1694
2 27551742 27554518 + Chy2G046380.1 Chy02g02371 2371
12 18440649 18446492 - Chy12G220450.1 Chy12g01445 1445
12 18448237 18459960 + Chy12G220460.1 Chy12g01446 1446
4 25991351 25998278 - ClG42_04g0118200.10 Clacu04g1182 1182
4 25998422 26011228 + ClG42_04g0118300.10 Clacu04g1183 1183
6 26805628 26808396 + ClG42_06g0159700.10 Clacu06g1597 1597
4 26210713 26216970 - ClCG04G011200.1 Cla04g01102 1102
4 26218568 26232487 + ClCG04G011210.2 Cla04g01103 1103
6 28320444 28323611 + ClCG06G014910.1 Cla06g01477 1477
10 1073605 1076943 + CmaCh10G002420.1 Cma10g00242 242
11 1351488 1354718 - CmaCh11G002660.1 Cma11g00266 266
13 7882834 7887300 - CmaCh13G010310.1 Cma13g01031 1031
13 7887715 7902159 + CmaCh13G010320.1 Cma13g01032 1032
2 24474732 24478065 + MELO3C017298.2.1 Cme02g01754 1754
12 25016381 25022037 - MELO3C002082.2.1 Cme12g01885 1885
12 25023863 25036072 + MELO3C002081.2.1 Cme12g01886 1886
12 1188903 1195407 + PI0017004.1 Cmetu12g0397 397
12 1175397 1187873 - PI0025088.1 Cmetu12g2040 2040
10 1153437 1164787 + CmoCh10G002600.1 Cmo10g00260 260
11 1329735 1332408 - CmoCh11G002710.1 Cmo11g00271 271
13 8887550 8891334 - CmoCh13G010710.1 Cmo13g01071 1071
13 8891765 8906938 + CmoCh13G010720.1 Cmo13g01072 1072
4 26173074 26179993 - CmPI595203_04g011620.1 Cmu04g1162 1162
4 26180137 26192966 + CmPI595203_04g011630.1 Cmu04g1163 1163
6 26708312 26711080 + CmPI595203_06g015460.1 Cmu06g1546 1546
2 31051398 31092607 + Conep02aG0165600.1 Cone2ag0645 645
2 32504692 32510337 - Conep02aG0171100.1 Cone2ag0698 698
13 2182957 2184117 + Conep13aG0030900.1 Cone13ag0291 291
19 1922822 1923573 - Conep19aG0028300.1 Cone19ag0273 273
4 11347102 11350274 + Cp4.1LG04g13960.1 Cpe04g01409 1409
18 7255986 7259466 - Cp4.1LG18g07490.1 Cpe18g00751 751
20 622024 636858 - Cp4.1LG20g01200.1 Cpe20g00113 113
20 637266 643819 + Cp4.1LG20g01110.1 Cpe20g00114 114
1 27818917 27825800 - CrPI670011_01g014600.1 Cre01g1460 1460
1 27825944 27838709 + CrPI670011_01g014610.1 Cre01g1461 1461
6 31506030 31508842 + CrPI670011_06g023580.1 Cre06g2358 2358
1 1788086 1791498 + CsaV3_1G002840.1 Csa01g00284 284
1 2331927 2335214 - CsaV3_1G003740.1 Csa01g00374 374
1 4193518 4206303 - CsaV3_1G006540.1 Csa01g00654 654
1 4207136 4213492 + CsaV3_1G006550.1 Csa01g00655 655
7 68397887 68403252 - Hsped.07g24050.1 Hepe07g2405 2405
7 68413718 68427226 + Hsped.07g24080.1 Hepe07g2408 2408
10 1746834 1761121 - Lag0024268.1 Lac10g0223 223
10 1762493 1767771 + Lag0024269.1 Lac10g0224 224
2 1437763 1451898 - Lsi02G001710.1 Lsi02g00171 171
2 1453899 1457993 + Lsi02G001720.1 Lsi02g00172 172
6 23980808 23983861 + Lsi06G013400.1 Lsi06g01340 1340
1 12458848 12469769 + Sed0007266.1 Sed01g1713 1713
8 35629650 35644845 - Sed0003499.1 Sed08g2171 2171
5 74115598 74120163 - Tan0012272.1 Tan05g2279 2279
5 74147803 74165688 + Tan0009130.1 Tan05g2280 2280
17 3767748 3773002 + Vvi17g336 Vvi17g336 336
17 3774074 3775250 + Vvi17g337 Vvi17g337 337
17 3777807 3798404 + Vvi17g338 Vvi17g338 338
17 3799064 3805978 - Vvi17g339 Vvi17g339 339
17 3817693 3819382 - Vvi17g340 Vvi17g340 340
17 3823247 3831307 - Vvi17g341 Vvi17g341 341
17 3846663 3879071 - Vvi17g342 Vvi17g342 342
17 3886867 3898796 - Vvi17g343 Vvi17g343 343
17 3898801 3949355 - Vvi17g344 Vvi17g344 344
17 3952893 3954545 - Vvi17g345 Vvi17g345 345
       

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