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
Vvi4g132 Blo01g01454 . . . . . . . . . Cma01g01713 . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g01402 . . . Blo17g00278 . . Bda13g01590 . . . . . . . . . Car01g01331 . . . . . . . . . . . . . . . . . . . . Cme07g00196
Vvi4g133 . . . Bda03g00134 . . Bma04g00119 Bma01g02202 . . . . Car09g00498 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe04g00117 . Bma02g00343 . . . Cma09g00570 . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g134 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g135 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g136 . . . . . . . . Cmo05g00431 . . Cma05g00417 . . Sed11g0850 . . Bhi04g01495 Tan02g1603 Cmetu03g0055 . . . Lcy13g2203 . . . . . . . . . . . . . . . Blo17g00277 Blo18g00268 . . Bpe14g00571 . . Bma02g00541 . . . . . . Car05g00897 Cpe11g00359 . . . . . . . . Cla08g00998 Cam08g1445 Cec08g1023 Cco08g1146 Clacu08g1147 . Cre08g0934 Lsi08g00848 . Chy03g00669 .
Vvi4g137 . . . . . . . . . . . . . . Sed08g1788 . . Bhi04g01497 Tan02g1599 Cmetu03g0638 . Hepe08g1418 . Lcy13g2206 . . . . . . . . . . . . . . . . Blo18g00266 . . . . . Bma02g00544 . . . . . . . . . . . . . . . . . . . . . . . Lsi08g00846 . Chy03g00665 .
Vvi4g138 Blo01g01453 . Bda01g00634 Bda03g00133 . . Bma04g00118 . . . Cma01g01712 . Car09g00305 . . . Cpe06g00253 . . . . . . . Cla05g01857 Cam05g1984 Cec05g1996 Cco05g2054 Clacu05g1976 Cmu05g1857 Cre05g1982 . . Cone7ag1234 . Lsi04g01400 . . . . . . . . Bpe04g00116 . . . . Cmo09g00356 Cma09g00357 . Car01g01330 . . Cpe02g00281 Bhi09g03098 . . . . . . . . . . . . . . . . Cme07g00195
Vvi4g139 Blo01g01452 Blo12g01023 . . . Bpe02g00502 . Bma01g02201 Cmo05g00430 Cmo12g00597 . Cma05g00416 . Car12g00605 Sed08g1791 Cpe07g00574 . Bhi04g01504 Tan02g1591 Cmetu03g1113 . Hepe08g1423 . Lcy13g2215 . . . . . . . . . . . . . . . Blo17g00276 . . Bda13g01589 Bpe14g00276 . . Bma02g00545 . . . . Cma12g00657 . Car05g00354 Cpe11g00358 . . . . . . . . Cla08g00996 Cam08g1443 Cec08g1020 Cco08g1144 . . Cre08g0932 Lsi08g00842 . Chy03g00663 .
Vvi4g140 . Blo12g01025 . Bda03g00132 . . Bma04g00117 . . . Cma01g01711 . . . . . . . . . . . . . Cla05g01858 Cam05g1986 Cec05g1998 Cco05g2055 Clacu05g1977 Cmu05g1858 Cre05g1983 . . . . Lsi04g01399 . . . . . . . . . . . Sed13g1892 Cmo01g01801 . . . Car01g01328 . . Cpe02g00282 Bhi09g03095 Tan01g4589 Cmetu07g2158 . Hepe01g1908 Mch11g0441 . . . . . . . . . . . Cme07g00194
Vvi4g141 . . . . Bpe02g01554 . . . . . Cma01g01709 . Car09g00306 . . . Cpe06g00254 . . . . . . . Cla05g01615 Cam05g1728 Cec05g1731 Cco05g1789 Clacu05g1717 Cmu05g1601 Cre05g1725 Cone4ag1690 Cone7ag1609 . Cone20ag0282 Lsi04g01397 . . . Blo17g00275 Blo18g00264 Bda01g01342 Bda13g01588 Bpe14g00277 . . Bma02g00546 Sed06g0788 Cmo01g01803 Cmo09g00357 Cma09g00358 . Car01g01327 . . Cpe02g00284 Bhi09g03094 Tan01g3460 Cmetu01g2122 . Hepe01g1910 Mch11g0442 . . . . . . . . . . . Cme07g00191
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 33332162 33333196 + Bda002659.1 Bda01g00634 634
1 49118127 49144445 + Bda003579.1 Bda01g01342 1342
3 1161469 1162873 + Bda016072.1 Bda03g00132 132
3 1171354 1172376 - Bda016074.1 Bda03g00133 133
3 1173842 1174309 + Bda033473 Bda03g00134 134
13 39415398 39419591 - Bda000456.1 Bda13g01588 1588
13 39420346 39422898 + Bda000457.1 Bda13g01589 1589
13 39486566 39487033 + Bda000460.1 Bda13g01590 1590
4 36879380 36885710 - XM_039028606.1 Bhi04g01495 1495
4 36946928 36948872 + XM_039029639.1 Bhi04g01497 1497
4 37051316 37056009 - XM_039028997.1 Bhi04g01504 1504
9 79788454 79793084 - XM_039042970.1 Bhi09g03094 3094
9 79813601 79815237 + XM_039040733.1 Bhi09g03095 3095
9 79813877 79819932 - XM_039041850.1 Bhi09g03098 3098
1 53610034 53622421 + BLOR01452 Blo01g01452 1452
1 53630259 53630957 - BLOR01453 Blo01g01453 1453
1 53632238 53632708 + BLOR01454 Blo01g01454 1454
12 28150001 28151545 - BLOR05042 Blo12g01023 1023
12 28155355 28156809 - BLOR05044 Blo12g01025 1025
17 2892978 2902124 - BLOR16096 Blo17g00275 275
17 2903439 2905954 + BLOR16097 Blo17g00276 276
17 2922355 2923786 + BLOR16098 Blo17g00277 277
17 2948956 2949426 + BLOR16099 Blo17g00278 278
18 2809754 2814667 - BLOR08752 Blo18g00264 264
18 2831418 2837510 + BLOR08754 Blo18g00266 266
18 2858190 2859593 + BLOR08756 Blo18g00268 268
1 78932295 78933950 + Bma003047.1 Bma01g02201 2201
1 78938120 78938587 + Bma030286 Bma01g02202 2202
2 5547897 5548364 + Bma014813.1 Bma02g00343 343
2 10665532 10666371 - Bma015048.1 Bma02g00541 541
2 11053046 11054496 - Bma015058.1 Bma02g00544 544
2 11058348 11060903 - Bma015059.1 Bma02g00545 545
2 11061726 11065701 + Bma015060.1 Bma02g00546 546
4 934851 935924 + Bma018563.1 Bma04g00117 117
4 954175 955197 - Bma018565.1 Bma04g00118 118
4 956479 956967 + Bma018566.1 Bma04g00119 119
2 3263991 3265646 - Bpe008342.2 Bpe02g00502 502
2 18565810 18569863 + Bpe009406.1 Bpe02g01554 1554
4 804176 805198 - Bpe014838.3 Bpe04g00116 116
4 806647 807114 + Bpe025576 Bpe04g00117 117
14 2783384 2785911 - Bpe006929.1 Bpe14g00276 276
14 2787197 2791469 + Bpe006930.1 Bpe14g00277 277
14 4858122 4861548 + Bpe007220.1 Bpe14g00571 571
5 25823392 25827313 + CaPI482276_05g017280.1 Cam05g1728 1728
5 28661642 28662694 + CaPI482276_05g019840.1 Cam05g1984 1984
5 28665319 28666968 - CaPI482276_05g019860.1 Cam05g1986 1986
8 20765589 20772297 + CaPI482276_08g014430.1 Cam08g1443 1443
8 20781278 20784018 - CaPI482276_08g014450.1 Cam08g1445 1445
1 11841689 11845547 - Carg10710-RA Car01g01327 1327
1 11846354 11850878 + Carg10709-RA Car01g01328 1328
1 11852113 11853150 - Carg10707-RA Car01g01330 1330
1 11854911 11855390 + Carg10706-RA Car01g01331 1331
5 2043992 2049236 + Carg09305-RA Car05g00354 354
5 8744271 8748333 + Carg11953-RA Car05g00897 897
9 1693339 1694385 + Carg02784-RA Car09g00305 305
9 1696023 1699725 + Carg02785-RA Car09g00306 306
9 2782126 2786284 - Carg02980-RA Car09g00498 498
12 4025006 4028482 + Carg23942-RA Car12g00605 605
5 26592054 26595963 + CcPI632755_05g017890.1 Cco05g1789 1789
5 29585425 29587072 + CcPI632755_05g020540.1 Cco05g2054 2054
5 29589647 29591286 - CcPI632755_05g020550.1 Cco05g2055 2055
8 23295016 23301660 + CcPI632755_08g011440.1 Cco08g1144 1144
8 23312216 23314993 - CcPI632755_08g011460.1 Cco08g1146 1146
5 28881727 28885637 + CePI673135_05g017310.1 Cec05g1731 1731
5 31957681 31959328 + CePI673135_05g019960.1 Cec05g1996 1996
5 31962145 31963604 - CePI673135_05g019980.1 Cec05g1998 1998
8 22143498 22148503 + CePI673135_08g010200.1 Cec08g1020 1020
8 22160476 22163259 - CePI673135_08g010230.1 Cec08g1023 1023
3 9234183 9240496 + Chy3G056430.1 Chy03g00663 663
3 9248192 9249713 - Chy3G056450.1 Chy03g00665 665
3 9277725 9279475 + Chy3G056490.1 Chy03g00669 669
5 26026790 26030705 + ClG42_05g0171700.10 Clacu05g1717 1717
5 28864369 28865421 + ClG42_05g0197600.10 Clacu05g1976 1976
5 28868044 28869690 - ClG42_05g0197700.10 Clacu05g1977 1977
8 21554892 21557509 - ClG42_08g0114700.10 Clacu08g1147 1147
5 27485698 27490595 + ClCG05G015620.1 Cla05g01615 1615
5 30443758 30444810 + ClCG05G018150.1 Cla05g01857 1857
5 30447433 30449079 - ClCG05G018160.1 Cla05g01858 1858
8 22725908 22733142 + ClCG08G009920.2 Cla08g00996 996
8 22740303 22746634 - ClCG08G009940.2 Cla08g00998 998
1 11635605 11639773 - CmaCh01G017090.1 Cma01g01709 1709
1 11642405 11643778 + CmaCh01G017110.1 Cma01g01711 1711
1 11645103 11646140 - CmaCh01G017120.1 Cma01g01712 1712
1 11647579 11648058 + CmaCh01G017130.1 Cma01g01713 1713
5 1869933 1874974 + CmaCh05G004160.1 Cma05g00416 416
5 1876325 1878855 - CmaCh05G004170.1 Cma05g00417 417
9 1469887 1470933 + CmaCh09G003570.1 Cma09g00357 357
9 1472481 1476320 + CmaCh09G003580.1 Cma09g00358 358
9 2580963 2590552 - CmaCh09G005700.1 Cma09g00570 570
12 3506288 3511660 + CmaCh12G006570.1 Cma12g00657 657
7 1296195 1300741 - MELO3C016902.2.1 Cme07g00191 191
7 1304888 1308551 + MELO3C016900.2.1 Cme07g00194 194
7 1306859 1310861 - MELO3C016899.2.1 Cme07g00195 195
7 1312087 1312578 + MELO3C016898.2.1 Cme07g00196 196
1 1666130 1670594 + PI0006614.1 Cmetu01g2122 2122
3 5922765 5925239 - PI0026416.1 Cmetu03g0055 55
3 5946506 5948261 + PI0017027.1 Cmetu03g0638 638
3 5955000 5960396 - PI0016017.1 Cmetu03g1113 1113
7 23490470 23492084 - PI0009686.1 Cmetu07g2158 2158
1 13246474 13247848 - CmoCh01G018010.1 Cmo01g01801 1801
1 13250436 13254041 + CmoCh01G018030.1 Cmo01g01803 1803
5 2007974 2012817 + CmoCh05G004300.1 Cmo05g00430 430
5 2014122 2016953 - CmoCh05G004310.1 Cmo05g00431 431
9 1537744 1538790 + CmoCh09G003560.1 Cmo09g00356 356
9 1540935 1545040 + CmoCh09G003570.1 Cmo09g00357 357
12 3678268 3683907 + CmoCh12G005970.1 Cmo12g00597 597
5 25746216 25750131 + CmPI595203_05g016010.1 Cmu05g1601 1601
5 28589918 28590970 + CmPI595203_05g018570.1 Cmu05g1857 1857
5 28593593 28595240 - CmPI595203_05g018580.1 Cmu05g1858 1858
4 12585296 12588035 + Conep04aG0174400.1 Cone4ag1690 1690
7 9152009 9153742 + Conep07aG0127100.1 Cone7ag1234 1234
7 10950477 10953306 + Conep07aG0165700.1 Cone7ag1609 1609
20 1259341 1261562 + Conep20aG0029500.1 Cone20ag0282 282
2 1456039 1457076 + Cp4.1LG02g05950.1 Cpe02g00281 281
2 1458353 1461164 - Cp4.1LG02g05830.1 Cpe02g00282 282
2 1462221 1470258 + Cp4.1LG02g05940.1 Cpe02g00284 284
6 1347418 1348464 + Cp4.1LG06g02420.1 Cpe06g00253 253
6 1350021 1361194 + Cp4.1LG06g02500.1 Cpe06g00254 254
7 3810000 3813620 + Cp4.1LG07g06120.1 Cpe07g00574 574
11 1957860 1962761 + Cp4.1LG11g03490.1 Cpe11g00358 358
11 1964445 1966844 - Cp4.1LG11g03610.1 Cpe11g00359 359
5 28965134 28969032 + CrPI670011_05g017250.1 Cre05g1725 1725
5 31905459 31908542 + CrPI670011_05g019820.1 Cre05g1982 1982
5 31909735 31911385 - CrPI670011_05g019830.1 Cre05g1983 1983
8 22526059 22535512 + CrPI670011_08g009320.1 Cre08g0932 932
8 22542923 22545702 - CrPI670011_08g009340.1 Cre08g0934 934
1 83890121 83890546 - Hsped.01g19080.1 Hepe01g1908 1908
1 83894764 83899067 + Hsped.01g19100.1 Hepe01g1910 1910
8 16770378 16773489 + Hsped.08g14180.1 Hepe08g1418 1418
8 16817032 16820562 - Hsped.08g14230.1 Hepe08g1423 1423
13 40931755 40934334 - Maker00025417 Lcy13g2203 2203
13 40950039 40952489 + Maker00025293 Lcy13g2206 2206
13 41017907 41022781 - Maker00025414 Lcy13g2215 2215
4 21769234 21774378 - Lsi04G013970.1 Lsi04g01397 1397
4 21780036 21781656 + Lsi04G013990.1 Lsi04g01399 1399
4 21784232 21785284 - Lsi04G014000.1 Lsi04g01400 1400
4 21787742 21788215 + Lsi04G014020.1 Lsi04g01402 1402
8 16868547 16871158 + Lsi08G008420.1 Lsi08g00842 842
8 16892001 16895950 + Lsi08G008460.1 Lsi08g00846 846
8 16907764 16910608 - Lsi08G008480.1 Lsi08g00848 848
11 2765876 2768430 - MC11g0355 Mch11g0441 441
11 2771709 2775734 + MC11g0356 Mch11g0442 442
6 8410790 8415200 + Sed0001289.1 Sed06g0788 788
8 32634676 32637044 + Sed0013407.1 Sed08g1788 1788
8 32644505 32649106 - Sed0017786.3 Sed08g1791 1791
11 19527112 19529668 - Sed0000310.1 Sed11g0850 850
13 23897906 23900142 - Sed0013137.1 Sed13g1892 1892
1 99918555 99923380 + Tan0016075.1 Tan01g3460 3460
1 111929040 111931152 + Tan0013683.1 Tan01g4589 4589
2 73711944 73716596 + Tan0017994.1 Tan02g1591 1591
2 74110624 74113946 - Tan0009879.1 Tan02g1599 1599
2 74434042 74435696 + Tan0018728.1 Tan02g1603 1603
4 1246996 1249312 - Vvi4g132 Vvi4g132 132
4 1251912 1252699 - Vvi4g133 Vvi4g133 133
4 1255449 1257661 - Vvi4g134 Vvi4g134 134
4 1262052 1262217 + Vvi4g135 Vvi4g135 135
4 1266806 1275745 - Vvi4g136 Vvi4g136 136
4 1280893 1283643 - Vvi4g137 Vvi4g137 137
4 1288745 1290719 + Vvi4g138 Vvi4g138 138
4 1292382 1296907 - Vvi4g139 Vvi4g139 139
4 1298296 1304140 - Vvi4g140 Vvi4g140 140
4 1307400 1313986 + Vvi4g141 Vvi4g141 141
       

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