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
Vvi3g46 Blo02g00649 . . Bda08g00962 . Bpe12g00095 . . Cmo19g00704 . . . . . . Cpe04g00100 Cpe15g00563 Bhi05g01255 . . . . . . Cla02g00484 Cam02g0492 Cec02g0493 Cco02g0498 Clacu02g0496 Cmu02g0491 Cre02g0824 Cone12ag1189 Cone8ag1236 . Cone10ag1095 . Csa07g00039 . Cme01g01338 Blo04g00541 Blo13g00533 Bda15g01063 Bda14g00581 Bpe15g00840 Bpe05g00313 Bma03g00574 . . . . . Cma19g00692 . Car19g00536 . . . . . . . . . . . . . . . . Lsi11g01139 . Chy01g00742 .
Vvi3g47 . . . . . . . . . . Cma02g00361 Cma20g00806 Car02g00228 Car20g00691 . . . . . . . . . . . . . . . . . Cone12ag1190 Cone8ag1237 . . Lsi10g00421 . Chy11g00331 . Blo04g00542 . . Bda14g00582 Bpe15g00839 . Bma03g00575 . Sed01g0255 Cmo02g00364 Cmo20g00814 . . . . Cpe16g00279 Cpe05g01295 Bhi10g01933 Tan05g1231 Cmetu11g1579 . Hepe08g0968 . . . . . . . . . . Csa02g01313 . Cme11g00176
Vvi3g48 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1206 . . Csa07g00040 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy01g00741 .
Vvi3g49 . . Bda06g00973 . . . . . Cmo19g00706 . . . . . Sed04g3899 Cpe04g00098 Cpe15g00565 Bhi05g01785 Tan02g0750 Cmetu05g1372 . Hepe02g0466 . . Cla02g00482 Cam02g0490 Cec02g0491 Cco02g0496 Clacu02g0493 Cmu02g0489 Cre02g0822 . . Cone3ag1205 . . Csa07g00041 . Cme01g01336 . . . . . . . . . . . . Cma19g00697 . Car19g00539 . . . . . . . . . . . . . . . . Lsi11g01141 . Chy01g00740 .
Vvi3g50 . . . . . . . . Cmo19g00707 . Cma02g00360 . Car02g00227 . Sed04g3898 Cpe04g00097 Cpe15g00566 Bhi05g01783 Tan02g0749 Cmetu01g0444 . . . . Cla02g00481 Cam02g0489 Cec02g0490 Cco02g0495 Clacu02g0492 Cmu02g0488 Cre02g0821 Cone12ag1191 Cone8ag1239 . . Lsi10g00422 Csa07g00042 Chy11g00330 Cme01g01333 . . . . . . . Bma08g00779 Sed01g0254 Cmo02g00363 . . Cma19g00698 . Car19g00540 . Cpe05g01296 Bhi10g01932 Tan05g1230 Cmetu11g1599 . Hepe08g0967 . . . . . . . . . Lsi11g01142 Csa02g01314 Chy01g00739 Cme11g00177
Vvi3g51 Blo02g00651 Blo15g00662 Bda06g00971 Bda08g00964 Bpe07g00493 . . Bma12g00535 . . Cma02g00359 Cma20g00804 Car02g00226 Car20g00688 . . . . . . . . . . . . . . . . . Cone12ag1192 Cone8ag1240 . . Lsi10g00424 . Chy11g00329 . . . . . . . . . Sed05g3557 Cmo02g00362 Cmo20g00812 . . . . Cpe16g00280 Cpe05g01297 Bhi10g01930 Tan05g1229 Cmetu11g0754 . Hepe08g0965 . . . . . . . . . . Csa02g01315 . Cme11g00178
Vvi3g52 . . . . . . Bma05g00418 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe05g00312 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g53 . . . . . . . . Cmo19g00708 . . . . . Sed05g2284 . Cpe15g00567 Bhi05g01781 Tan02g0747 Cmetu01g1228 . Hepe02g0463 . . Cla02g00479 Cam02g0487 Cec02g0488 Cco02g0493 Clacu02g0490 Cmu02g0485 Cre02g0819 Cone12ag1195 Cone8ag1243 . . . Csa07g00045 . Cme01g01322 . . . . . . . . . . . . Cma19g00699 . Car19g00541 . . . . . . . . . . . . . . . . Lsi11g01144 . Chy01g00736 .
Vvi3g54 . . . . . Bpe12g00097 . . . . . . . . Sed05g2282 Cpe04g00096 . Bhi05g01779 Tan02g0746 Cmetu01g1015 . Hepe02g0462 . . Cla02g00477 Cam02g0485 Cec02g0487 Cco02g0492 Clacu02g0487 Cmu02g0483 Cre02g0818 . . . . . Csa07g00047 . . . Blo13g00532 Bda15g01062 . . . . Bma08g00778 . . . . . . . . . . . . . . . . . . . . . . . Lsi11g01146 . Chy01g00733 .
Vvi3g55 . . . . . Bpe12g00098 . . Cmo19g00710 . . . . . Sed11g1487 Cpe04g00095 Cpe15g00568 Bhi05g01776 Tan02g2047 Cmetu03g1142 . . . . Cla02g00476 Cam02g0483 Cec02g0485 Cco02g0490 Clacu02g0486 Cmu02g0481 Cre02g0816 Cone12ag1196 Cone8ag1244 . . . Csa07g00049 . Cme01g01320 . Blo13g00531 Bda15g01061 . . . . Bma08g00777 . . . . Cma19g00701 . Car19g00543 . . . . . . . . . . . . . . . . Lsi11g01148 . Chy01g00732 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 29277506 29279674 + Bda022627.1 Bda06g00971 971
6 29349705 29353641 - Bda022631.1 Bda06g00973 973
8 18886273 18891261 + Bda029628.1 Bda08g00962 962
8 18920377 18922542 + Bda029631.1 Bda08g00964 964
14 4445971 4451715 + Bda027333.1 Bda14g00581 581
14 4459937 4461718 + Bda027334.1 Bda14g00582 582
15 19733767 19734576 - Bda013053.1 Bda15g01061 1061
15 19738887 19741100 + Bda013054.2 Bda15g01062 1062
15 19766821 19772816 - Bda013056.2 Bda15g01063 1063
5 45477325 45486191 - XM_039032094.1 Bhi05g01255 1255
5 56579211 56582678 - XM_039032733.1 Bhi05g01776 1776
5 56609252 56613746 + XM_039032452.1 Bhi05g01779 1779
5 56615247 56618876 - XM_039032454.1 Bhi05g01781 1781
5 56751499 56756796 + XM_039031815.1 Bhi05g01783 1783
5 56756702 56765959 - XM_039031813.1 Bhi05g01785 1785
10 48232307 48235535 + XM_039044449.1 Bhi10g01930 1930
10 48241312 48254890 + XM_039045337.1 Bhi10g01932 1932
10 48258530 48268360 - XM_039046835.1 Bhi10g01933 1933
2 15695885 15701000 + BLOR10379 Blo02g00649 649
2 15972672 15974840 + BLOR10381 Blo02g00651 651
4 4650155 4656204 + BLOR13453 Blo04g00541 541
4 4662139 4663935 + BLOR13454 Blo04g00542 542
13 27086332 27087141 - BLOR05812 Blo13g00531 531
13 27096627 27104147 + BLOR05813 Blo13g00532 532
13 27105998 27118751 - BLOR05814 Blo13g00533 533
15 19259644 19260735 + BLOR07056 Blo15g00662 662
3 4810665 4816462 + Bma016864.2 Bma03g00574 574
3 4817054 4818255 + Bma016865.1 Bma03g00575 575
5 13219011 13221084 - Bma021258.1 Bma05g00418 418
8 45094657 45095466 - Bma028158.1 Bma08g00777 777
8 45099092 45101319 + Bma028159.1 Bma08g00778 778
8 45104199 45106027 + Bma028160.2 Bma08g00779 779
12 20093748 20095919 - Bma007653.1 Bma12g00535 535
5 16688258 16695079 - Bpe017726.1 Bpe05g00312 312
5 16718708 16723711 - Bpe017727.1 Bpe05g00313 313
7 9502214 9504382 - Bpe021335.1 Bpe07g00493 493
12 689152 695318 + Bpe005335.1 Bpe12g00095 95
12 697312 703995 - Bpe005337.1 Bpe12g00097 97
12 706631 707449 + Bpe005338.1 Bpe12g00098 98
15 18424369 18426147 - Bpe001763.1 Bpe15g00839 839
15 18426817 18432598 - Bpe001764.1 Bpe15g00840 840
2 5496013 5497520 - CaPI482276_02g004830.1 Cam02g0483 483
2 5504910 5508497 + CaPI482276_02g004850.1 Cam02g0485 485
2 5517399 5521983 - CaPI482276_02g004870.1 Cam02g0487 487
2 5554235 5558550 + CaPI482276_02g004890.1 Cam02g0489 489
2 5558877 5568651 - CaPI482276_02g004900.1 Cam02g0490 490
2 5578170 5585039 - CaPI482276_02g004920.1 Cam02g0492 492
2 1473595 1475715 + Carg27201-RA Car02g00226 226
2 1479008 1486112 + Carg27200-RA Car02g00227 227
2 1487388 1491395 - Carg27199-RA Car02g00228 228
19 6933998 6939904 + Carg19384-RA Car19g00536 536
19 6945212 6952080 + Carg19381-RA Car19g00539 539
19 6951700 6955435 - Carg19380-RA Car19g00540 540
19 6957358 6961120 + Carg19379-RA Car19g00541 541
19 6962433 6965718 + Carg19377-RA Car19g00543 543
20 3944861 3947011 + Carg25958-RA Car20g00688 688
20 3953264 3954093 - Carg25955-RA Car20g00691 691
2 4529086 4529952 - CcPI632755_02g004900.1 Cco02g0490 490
2 4537353 4540660 + CcPI632755_02g004920.1 Cco02g0492 492
2 4542021 4555239 - CcPI632755_02g004930.1 Cco02g0493 493
2 4590020 4594923 + CcPI632755_02g004950.1 Cco02g0495 495
2 4595224 4605050 - CcPI632755_02g004960.1 Cco02g0496 496
2 4620805 4629023 - CcPI632755_02g004980.1 Cco02g0498 498
2 4527389 4528426 - CePI673135_02g004850.1 Cec02g0485 485
2 4535773 4539277 + CePI673135_02g004870.1 Cec02g0487 487
2 4541763 4544870 - CePI673135_02g004880.1 Cec02g0488 488
2 4567661 4572117 + CePI673135_02g004900.1 Cec02g0490 490
2 4572420 4579900 - CePI673135_02g004910.1 Cec02g0491 491
2 4590264 4597279 - CePI673135_02g004930.1 Cec02g0493 493
1 5369410 5370445 - Chy1G007320.1 Chy01g00732 732
1 5374346 5377469 + Chy1G007330.1 Chy01g00733 733
1 5390747 5394749 - Chy1G007360.1 Chy01g00736 736
1 5428474 5432212 + Chy1G007390.1 Chy01g00739 739
1 5432512 5438685 - Chy1G007400.1 Chy01g00740 740
1 5439860 5440452 + Chy1G007410.1 Chy01g00741 741
1 5441917 5448191 - Chy1G007420.1 Chy01g00742 742
11 2956100 2958253 + Chy11G189090.1 Chy11g00329 329
11 2968651 2973047 + Chy11G189100.1 Chy11g00330 330
11 2974517 2980553 - Chy11G189110.1 Chy11g00331 331
2 4368423 4369814 - ClG42_02g0048600.10 Clacu02g0486 486
2 4377428 4380762 + ClG42_02g0048700.10 Clacu02g0487 487
2 4428355 4460282 - ClG42_02g0049000.10 Clacu02g0490 490
2 4506418 4510828 + ClG42_02g0049200.10 Clacu02g0492 492
2 4511097 4518310 - ClG42_02g0049300.10 Clacu02g0493 493
2 4529874 4536444 - ClG42_02g0049600.10 Clacu02g0496 496
2 4638088 4641885 - ClCG02G004470.1 Cla02g00476 476
2 4647452 4653306 + ClCG02G004480.1 Cla02g00477 477
2 4672181 4675282 - ClCG02G004510.2 Cla02g00479 479
2 4711631 4717008 + ClCG02G004530.1 Cla02g00481 481
2 4717106 4724319 - ClCG02G004540.2 Cla02g00482 482
2 4739362 4748040 - ClCG02G004570.2 Cla02g00484 484
2 1765533 1767653 + CmaCh02G003590.1 Cma02g00359 359
2 1771256 1778237 + CmaCh02G003600.1 Cma02g00360 360
2 1778931 1783187 - CmaCh02G003610.1 Cma02g00361 361
19 7154378 7160435 + CmaCh19G006920.1 Cma19g00692 692
19 7165039 7170635 + CmaCh19G006970.1 Cma19g00697 697
19 7171526 7175490 - CmaCh19G006980.1 Cma19g00698 698
19 7178458 7181843 + CmaCh19G006990.1 Cma19g00699 699
19 7189965 7191589 + CmaCh19G007010.1 Cma19g00701 701
20 3785981 3788137 + CmaCh20G008040.1 Cma20g00804 804
20 3791944 3796036 - CmaCh20G008060.1 Cma20g00806 806
1 16583620 16586761 - MELO3C013409.2.1 Cme01g01320 1320
1 16602697 16609505 - MELO3C013411.2.1 Cme01g01322 1322
1 16734509 16739521 + MELO3C013417.2.1 Cme01g01333 1333
1 16761110 16765907 - MELO3C028749.2.1 Cme01g01336 1336
1 16769128 16777591 - MELO3C013420.2.1 Cme01g01338 1338
11 2010131 2015370 + MELO3C023357.2.1 Cme11g00176 176
11 2016003 2022155 - MELO3C023358.2.1 Cme11g00177 177
11 2027153 2030463 - MELO3C023359.2.1 Cme11g00178 178
1 5700194 5706934 + PI0005077.1 Cmetu01g0444 444
1 5663024 5666429 + PI0006588.1 Cmetu01g1015 1015
1 5676369 5681285 - PI0026308.1 Cmetu01g1228 1228
3 2254853 2258548 + PI0022328.2 Cmetu03g1142 1142
5 18770549 18771439 - PI0025329.1 Cmetu05g1372 1372
11 27997174 28001003 - PI0007685.1 Cmetu11g0754 754
11 27979740 27985133 + PI0024567.1 Cmetu11g1579 1579
11 27986152 27990970 - PI0028700.1 Cmetu11g1599 1599
2 1824731 1826848 + CmoCh02G003620.1 Cmo02g00362 362
2 1831044 1837775 + CmoCh02G003630.1 Cmo02g00363 363
2 1839039 1842916 - CmoCh02G003640.1 Cmo02g00364 364
19 7419246 7426212 + CmoCh19G007040.1 Cmo19g00704 704
19 7430191 7437488 + CmoCh19G007060.1 Cmo19g00706 706
19 7437329 7441865 - CmoCh19G007070.1 Cmo19g00707 707
19 7444257 7447750 + CmoCh19G007080.1 Cmo19g00708 708
19 7451316 7452505 + CmoCh19G007100.1 Cmo19g00710 710
20 4019182 4021332 + CmoCh20G008120.1 Cmo20g00812 812
20 4024363 4028206 - CmoCh20G008140.1 Cmo20g00814 814
2 4364250 4365641 - CmPI595203_02g004810.1 Cmu02g0481 481
2 4373257 4376593 + CmPI595203_02g004830.1 Cmu02g0483 483
2 4395373 4398473 - CmPI595203_02g004850.1 Cmu02g0485 485
2 4444176 4448585 + CmPI595203_02g004880.1 Cmu02g0488 488
2 4448854 4456248 - CmPI595203_02g004890.1 Cmu02g0489 489
2 4467633 4474205 - CmPI595203_02g004910.1 Cmu02g0491 491
3 30766050 30771864 - Conep03aG0171200.1 Cone3ag1205 1205
3 30772032 30773194 + Conep03aG0171300.1 Cone3ag1206 1206
8 10394395 10399914 + Conep08aG0127400.1 Cone8ag1236 1236
8 10400119 10401976 + Conep08aG0127500.1 Cone8ag1237 1237
8 10403124 10406008 - Conep08aG0127700.1 Cone8ag1239 1239
8 10406820 10409798 - Conep08aG0127800.1 Cone8ag1240 1240
8 10418665 10420711 + Conep08aG0128100.1 Cone8ag1243 1243
8 10422942 10423955 + Conep08aG0128200.1 Cone8ag1244 1244
10 7662580 7668807 - Conep10aG0112400.1 Cone10ag1095 1095
12 9374447 9380031 + Conep12aG0122900.1 Cone12ag1189 1189
12 9381461 9383323 + Conep12aG0123000.1 Cone12ag1190 1190
12 9383982 9386241 - Conep12aG0123100.1 Cone12ag1191 1191
12 9387845 9390927 - Conep12aG0123200.1 Cone12ag1192 1192
12 9398940 9401213 + Conep12aG0123500.1 Cone12ag1195 1195
12 9401432 9404455 + Conep12aG0123600.1 Cone12ag1196 1196
4 874267 878691 - Cp4.1LG04g01130.1 Cpe04g00095 95
4 880146 883476 + Cp4.1LG04g01230.1 Cpe04g00096 96
4 885096 891659 + Cp4.1LG04g01220.1 Cpe04g00097 97
4 891156 896717 - Cp4.1LG04g01160.1 Cpe04g00098 98
4 900943 911097 - Cp4.1LG04g01150.1 Cpe04g00100 100
5 9037500 9041587 + Cp4.1LG05g12860.1 Cpe05g01295 1295
5 9042386 9049459 - Cp4.1LG05g12910.1 Cpe05g01296 1296
5 9052331 9054448 - Cp4.1LG05g12970.1 Cpe05g01297 1297
15 6454530 6462792 + Cp4.1LG15g05550.1 Cpe15g00563 563
15 6467735 6474388 + Cp4.1LG15g05700.1 Cpe15g00565 565
15 6473877 6477139 - Cp4.1LG15g05720.1 Cpe15g00566 566
15 6482943 6485964 + Cp4.1LG15g05680.1 Cpe15g00567 567
15 6487237 6490895 + Cp4.1LG15g05690.1 Cpe15g00568 568
16 4779564 4783786 + Cp4.1LG16g02720.1 Cpe16g00279 279
16 4787666 4789816 - Cp4.1LG16g02820.1 Cpe16g00280 280
2 4957734 4958771 - CrPI670011_02g008160.1 Cre02g0816 816
2 4966425 4969752 + CrPI670011_02g008180.1 Cre02g0818 818
2 4972185 4975295 - CrPI670011_02g008190.1 Cre02g0819 819
2 4993831 4998423 + CrPI670011_02g008210.1 Cre02g0821 821
2 4998744 5007642 - CrPI670011_02g008220.1 Cre02g0822 822
2 5018745 5025812 - CrPI670011_02g008240.1 Cre02g0824 824
2 12761790 12766438 + CsaV3_2G015290.1 Csa02g01313 1313
2 12767206 12773839 - CsaV3_2G015300.1 Csa02g01314 1314
2 12777266 12781041 - CsaV3_2G015310.1 Csa02g01315 1315
7 486158 492545 + CsaV3_7G000390.1 Csa07g00039 39
7 493878 494408 - CsaV3_7G000400.1 Csa07g00040 40
7 495414 502372 + CsaV3_7G000410.1 Csa07g00041 41
7 502278 507438 - CsaV3_7G000420.1 Csa07g00042 42
7 536232 539360 + CsaV3_7G000450.1 Csa07g00045 45
7 545371 549380 - CsaV3_7G000470.1 Csa07g00047 47
7 550696 554122 + CsaV3_7G000490.1 Csa07g00049 49
2 4536787 4540143 + Hsped.02g04620.1 Hepe02g0462 462
2 4541062 4544982 - Hsped.02g04630.1 Hepe02g0463 463
2 4563276 4570645 - Hsped.02g04660.1 Hepe02g0466 466
8 9073950 9076109 + Hsped.08g09650.1 Hepe08g0965 965
8 9083533 9089429 + Hsped.08g09670.1 Hepe08g0967 967
8 9090607 9094881 - Hsped.08g09680.1 Hepe08g0968 968
10 6373968 6375245 + Lsi10G004210.1 Lsi10g00421 421
10 6379533 6387051 - Lsi10G004220.1 Lsi10g00422 422
10 6394005 6396158 - Lsi10G004240.1 Lsi10g00424 424
11 19905923 19913818 + Lsi11G011390.1 Lsi11g01139 1139
11 19922566 19929718 + Lsi11G011410.1 Lsi11g01141 1141
11 19929495 19934866 - Lsi11G011420.1 Lsi11g01142 1142
11 19958705 19962958 + Lsi11G011440.1 Lsi11g01144 1144
11 19992854 19998015 - Lsi11G011460.1 Lsi11g01146 1146
11 20002856 20004687 + Lsi11G011480.1 Lsi11g01148 1148
1 1982473 1994280 + Sed0009657.1 Sed01g0254 254
1 1995675 2000232 - Sed0023703.1 Sed01g0255 255
4 47137806 47143620 + Sed0026809.1 Sed04g3898 3898
4 47143686 47150549 - Sed0012779.1 Sed04g3899 3899
5 35391571 35396073 + Sed0011434.1 Sed05g2282 2282
5 35402699 35409905 - Sed0005024.1 Sed05g2284 2284
5 44141000 44144635 - Sed0015136.1 Sed05g3557 3557
11 30621009 30623927 - Sed0006417.1 Sed11g1487 1487
2 7031467 7035304 + Tan0022723.1 Tan02g0746 746
2 7036619 7039531 - Tan0015235.1 Tan02g0747 747
2 7072517 7076658 + Tan0020732.1 Tan02g0749 749
2 7077017 7084577 - Tan0018101.1 Tan02g0750 750
2 89901216 89907369 + Tan0011901.1 Tan02g2047 2047
5 12631281 12636826 + Tan0004885.1 Tan05g1229 1229
5 12662543 12669214 + Tan0020285.1 Tan05g1230 1230
5 12679259 12683648 - Tan0001812.1 Tan05g1231 1231
3 607517 613848 + Vvi3g46 Vvi3g46 46
3 615716 620606 + Vvi3g47 Vvi3g47 47
3 623791 624325 - Vvi3g48 Vvi3g48 48
3 624671 632248 + Vvi3g49 Vvi3g49 49
3 632522 639580 - Vvi3g50 Vvi3g50 50
3 644717 647153 - Vvi3g51 Vvi3g51 51
3 661990 664840 - Vvi3g52 Vvi3g52 52
3 666617 670971 + Vvi3g53 Vvi3g53 53
3 671035 676607 - Vvi3g54 Vvi3g54 54
3 679189 684422 + Vvi3g55 Vvi3g55 55
       

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