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
Vvi18g570 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g571 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g572 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g573 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g574 . . . . . . . . Cmo05g00594 Cmo12g00181 . . . Car12g00207 Sed01g1237 . . Bhi04g00898 Tan02g2514 Cmetu03g1714 . Hepe10g0400 . Lcy13g1451 Cla08g01188 Cam08g1653 Cec08g1229 Cco08g1348 Clacu08g1349 . Cre08g1135 . . Cone17ag1153 Cone20ag0575 . . . Cme03g01775 Blo17g00082 Blo18g00092 . Bda13g01343 Bpe02g01171 Bpe14g00502 Bma01g01360 Bma02g00097 . . . Cma12g00226 Cma05g00568 Car05g00512 . Cpe11g00497 . . . . . . . . . . . . . . . Lsi08g01051 Csa02g02235 Chy03g01282 .
Vvi18g575 Blo01g01786 . . . Bpe02g00155 . . Bma01g02572 . Cmo12g00183 . . . Car12g00209 Sed08g1987 . Cpe07g00193 Bhi04g00897 Tan02g2516 Cmetu03g0103 . Hepe10g0399 . Lcy13g1450 Cla08g01190 Cam08g1654 Cec08g1231 Cco08g1350 Clacu08g1351 . Cre08g1137 . . . . . . . Cme03g01774 . . Bda11g00815 . . . . Bma02g00169 . . . Cma12g00228 . Car05g00514 . . . . . . . . . . . . . . . . . Lsi08g01052 Csa02g02236 Chy03g01280 .
Vvi18g576 Blo01g01785 . . Bda03g00445 . Bpe04g00409 . Bma01g02569 Cmo05g00597 Cmo12g00184 Cma01g01455 Cma09g00611 . Car12g00210 . Cpe06g00472 Cpe07g00194 Bhi04g00891 . . . . . Lcy13g1799 . . . . . . . Cone4ag1266 Cone7ag0878 Cone17ag1151 Cone20ag0577 Lsi04g02309 Csa03g04527 Chy04g00175 Cme03g01772 . . . Bda13g01341 . Bpe14g00504 . Bma02g00096 . Cmo01g01507 Cmo09g00599 Cma12g00230 Cma05g00571 Car05g00517 Car09g00542 Cpe11g00500 Cpe02g00496 Bhi09g02546 . . . . . . . . . . . . . . Csa02g02237 Chy03g01278 Cme04g00205
Vvi18g577 . . Bda01g00928 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo17g00080 Blo18g00091 . . Bpe02g01727 Bpe14g00506 Bma01g00727 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g578 . . Bda01g00929 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1150 . . . . . . Blo18g00090 . . Bpe02g01173 . Bma01g01358 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g579 . Blo12g00745 . Bda03g00444 . . Bma04g00421 . . . Cma01g01453 . . . . . . . . . . . . . . . . . . . . . . Cone17ag1148 Cone20ag0579 Lsi04g02310 Csa03g04529 Chy04g00174 . . . . . . . . Bma02g00208 Sed05g1524 Cmo01g01506 . . . . . . Cpe02g00497 Bhi09g02547 Tan01g3894 Cmetu04g2782 . Hepe01g2199 Mch11g0749 . Cla11g01459 Cam11g1512 Cec11g1550 Cco11g1545 Clacu11g1677 Cmu11g1493 Cre11g1914 . . . Cme04g00202
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 42584690 42585672 + Bda003076.1 Bda01g00928 928
1 42609801 42613233 - Bda003078.1 Bda01g00929 929
3 3804220 3807057 - Bda016412.1 Bda03g00444 444
3 3813730 3821004 - Bda016413.2 Bda03g00445 445
11 8075579 8078281 - Bda005566.1 Bda11g00815 815
13 35721352 35723691 - Bda000154.1 Bda13g01341 1341
13 35793749 35795344 + Bda000158.1 Bda13g01343 1343
4 22428998 22432904 - XM_039028632.1 Bhi04g00891 891
4 22565562 22573911 + XM_039028803.1 Bhi04g00897 897
4 22574059 22577557 + XM_039028802.1 Bhi04g00898 898
9 69210818 69214263 + XM_039042395.1 Bhi09g02546 2546
9 69346735 69353374 + XM_039040823.1 Bhi09g02547 2547
1 57580477 57583482 - BLOR01785 Blo01g01785 1785
1 57590023 57592726 + BLOR01786 Blo01g01786 1786
12 25802759 25806121 + BLOR04764 Blo12g00745 745
17 598165 613301 - BLOR15901 Blo17g00080 80
17 632629 634412 + BLOR15903 Blo17g00082 82
18 740861 753279 + BLOR08578 Blo18g00090 90
18 755381 756810 - BLOR08579 Blo18g00091 91
18 775345 777119 + BLOR08580 Blo18g00092 92
1 6655160 6657991 + Bma000937.1 Bma01g00727 727
1 20320033 20323471 + Bma001690.1 Bma01g01358 1358
1 20470050 20471510 + Bma001692.1 Bma01g01360 1360
1 83310675 83312921 - Bma003451.1 Bma01g02569 2569
1 83321177 83327665 + Bma003454.1 Bma01g02572 2572
2 841950 844676 - Bma014551.2 Bma02g00096 96
2 865439 867034 + Bma014552.1 Bma02g00097 97
2 1489160 1490919 + Bma014624.1 Bma02g00169 169
2 2248767 2250372 - Bma014665.1 Bma02g00208 208
4 3396600 3402416 - Bma018886.1 Bma04g00421 421
2 1078796 1081509 - Bpe008006.1 Bpe02g00155 155
2 15376890 15378239 - Bpe009032.1 Bpe02g01171 1171
2 15415872 15419291 - Bpe009034.1 Bpe02g01173 1173
2 19721057 19723884 - Bpe009558.1 Bpe02g01727 1727
4 2573605 2576543 - Bpe015093.1 Bpe04g00409 409
14 4454734 4456194 - Bpe007152.1 Bpe14g00502 502
14 4473160 4476156 + Bpe007154.1 Bpe14g00504 504
14 4482137 4484325 + Bpe007156.1 Bpe14g00506 506
8 22775197 22777072 - CaPI482276_08g016530.1 Cam08g1653 1653
8 22778996 22786279 - CaPI482276_08g016540.1 Cam08g1654 1654
11 27998628 28005004 + CaPI482276_11g015120.1 Cam11g1512 1512
5 2989119 2990982 - Carg08255-RA Car05g00512 512
5 2996463 2998237 - Carg08257-RA Car05g00514 514
5 3004746 3007872 + Carg08260-RA Car05g00517 517
9 3080351 3083356 + Carg03024-RA Car09g00542 542
12 1311924 1313717 - Carg22487-RA Car12g00207 207
12 1317264 1322342 - Carg22485-RA Car12g00209 209
12 1325059 1328025 + Carg22484-RA Car12g00210 210
8 25411234 25413119 - CcPI632755_08g013480.1 Cco08g1348 1348
8 25417159 25422281 - CcPI632755_08g013500.1 Cco08g1350 1350
11 28363903 28370362 + CcPI632755_11g015450.1 Cco11g1545 1545
8 24254538 24256420 - CePI673135_08g012290.1 Cec08g1229 1229
8 24260491 24265595 - CePI673135_08g012310.1 Cec08g1231 1231
11 29807860 29814286 + CePI673135_11g015500.1 Cec11g1550 1550
3 15810150 15813065 - Chy3G062580.1 Chy03g01278 1278
3 15820581 15826004 + Chy3G062600.1 Chy03g01280 1280
3 15830402 15832210 + Chy3G062620.1 Chy03g01282 1282
4 1511759 1517067 - Chy4G068920.1 Chy04g00174 174
4 1542431 1544926 - Chy4G068930.1 Chy04g00175 175
8 23548145 23550008 - ClG42_08g0134900.10 Clacu08g1349 1349
8 23554121 23559235 - ClG42_08g0135100.10 Clacu08g1351 1351
11 28028838 28035268 + ClG42_11g0167700.10 Clacu11g1677 1677
8 24821208 24823292 - ClCG08G011920.1 Cla08g01188 1188
8 24829466 24834987 - ClCG08G011940.2 Cla08g01190 1190
11 28274052 28281639 + ClCG11G014920.1 Cla11g01459 1459
1 10211150 10214651 - CmaCh01G014530.1 Cma01g01453 1453
1 10221745 10224951 - CmaCh01G014550.1 Cma01g01455 1455
5 2803558 2805690 - CmaCh05G005680.1 Cma05g00568 568
5 2824500 2827474 + CmaCh05G005710.1 Cma05g00571 571
9 2889430 2892531 + CmaCh09G006110.1 Cma09g00611 611
12 1117637 1119616 - CmaCh12G002260.1 Cma12g00226 226
12 1123406 1128040 - CmaCh12G002280.1 Cma12g00228 228
12 1131420 1134780 + CmaCh12G002300.1 Cma12g00230 230
3 26199097 26202542 - MELO3C011117.2.1 Cme03g01772 1772
3 26210062 26218818 + MELO3C011115.2.1 Cme03g01774 1774
3 26219739 26222112 + MELO3C011114.2.1 Cme03g01775 1775
4 1478709 1482958 - MELO3C003485.2.1 Cme04g00202 202
4 1506131 1510192 - MELO3C003486.2.1 Cme04g00205 205
3 3203774 3210445 - PI0028895.1 Cmetu03g0103 103
3 3198337 3201032 - PI0017419.1 Cmetu03g1714 1714
4 31920946 31926980 + PI0017602.1 Cmetu04g2782 2782
1 11624955 11628299 - CmoCh01G015060.1 Cmo01g01506 1506
1 11636258 11639682 - CmoCh01G015070.1 Cmo01g01507 1507
5 2953698 2956254 - CmoCh05G005940.1 Cmo05g00594 594
5 2970194 2973161 + CmoCh05G005970.1 Cmo05g00597 597
9 2974990 2978063 + CmoCh09G005990.1 Cmo09g00599 599
12 1188721 1190571 - CmoCh12G001810.1 Cmo12g00181 181
12 1194417 1199124 - CmoCh12G001830.1 Cmo12g00183 183
12 1201778 1204775 + CmoCh12G001840.1 Cmo12g00184 184
11 27281032 27287465 + CmPI595203_11g014930.1 Cmu11g1493 1493
4 10422660 10426023 - Conep04aG0131200.1 Cone4ag1266 1266
7 6807374 6810648 + Conep07aG0090700.1 Cone7ag0878 878
17 8454138 8456752 - Conep17aG0117700.1 Cone17ag1148 1148
17 8472333 8475643 + Conep17aG0117900.1 Cone17ag1150 1150
17 8480964 8484178 - Conep17aG0118000.1 Cone17ag1151 1151
17 8512671 8514660 + Conep17aG0118200.1 Cone17ag1153 1153
20 3298724 3300473 - Conep20aG0059200.1 Cone20ag0575 575
20 3317756 3319819 + Conep20aG0059400.1 Cone20ag0577 577
20 3325197 3328047 + Conep20aG0059600.1 Cone20ag0579 579
2 2888980 2899090 + Cp4.1LG02g03830.1 Cpe02g00496 496
2 2907240 2910731 + Cp4.1LG02g03800.1 Cpe02g00497 497
6 2787761 2790903 + Cp4.1LG06g03970.1 Cpe06g00472 472
7 1211848 1222603 - Cp4.1LG07g02570.1 Cpe07g00193 193
7 1225364 1228620 + Cp4.1LG07g02670.1 Cpe07g00194 194
11 2903394 2913563 - Cp4.1LG11g05070.1 Cpe11g00497 497
11 2919597 2923765 + Cp4.1LG11g05010.1 Cpe11g00500 500
8 24574670 24576551 - CrPI670011_08g011350.1 Cre08g1135 1135
8 24580666 24585778 - CrPI670011_08g011370.1 Cre08g1137 1137
11 30915534 30922022 + CrPI670011_11g019140.1 Cre11g1914 1914
2 20088455 20091320 - CsaV3_2G030540.1 Csa02g02235 2235
2 20093960 20100618 - CsaV3_2G030550.1 Csa02g02236 2236
2 20106593 20111098 + CsaV3_2G030560.1 Csa02g02237 2237
3 39472827 39477113 + CsaV3_3G048330.1 Csa03g04527 4527
3 39498333 39503823 + CsaV3_3G048350.1 Csa03g04529 4529
1 86722075 86725729 + Hsped.01g21990.1 Hepe01g2199 2199
10 4392310 4398397 + Hsped.10g03990.1 Hepe10g0399 399
10 4401690 4403811 + Hsped.10g04000.1 Hepe10g0400 400
13 33002247 33010693 + Maker00034145 Lcy13g1450 1450
13 33012196 33014478 + Maker00033920 Lcy13g1451 1451
13 36968465 36968893 - Maker00033792 Lcy13g1799 1799
4 30282321 30286204 + Lsi04G023090.1 Lsi04g02309 2309
4 30312610 30318744 + Lsi04G023100.1 Lsi04g02310 2310
8 19131850 19134151 - Lsi08G010510.1 Lsi08g01051 1051
8 19137124 19144520 - Lsi08G010520.1 Lsi08g01052 1052
11 5047888 5051662 + MC11g0628 Mch11g0749 749
1 9191869 9193637 - Sed0021913.1 Sed01g1237 1237
5 28881241 28886590 - Sed0021509.1 Sed05g1524 1524
8 34226962 34229812 + Sed0002671.1 Sed08g1987 1987
1 103964504 103970128 + Tan0000725.1 Tan01g3894 3894
2 93769751 93772489 - Tan0017165.1 Tan02g2514 2514
2 93776094 93781350 - Tan0006166.1 Tan02g2516 2516
18 6648783 6649030 - Vvi18g570 Vvi18g570 570
18 6649029 6651798 - Vvi18g571 Vvi18g571 571
18 6652255 6660443 + Vvi18g572 Vvi18g572 572
18 6661616 6681884 + Vvi18g573 Vvi18g573 573
18 6688298 6690573 - Vvi18g574 Vvi18g574 574
18 6693572 6703325 - Vvi18g575 Vvi18g575 575
18 6723749 6733513 + Vvi18g576 Vvi18g576 576
18 6747125 6750253 + Vvi18g577 Vvi18g577 577
18 6751782 6760147 - Vvi18g578 Vvi18g578 578
18 6771377 6774993 + Vvi18g579 Vvi18g579 579
       

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