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
Vvi3g576 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g577 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g578 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g579 . . . . . . . . Cmo19g00671 . . . . . . . Cpe15g00532 Bhi05g01108 . . . . . . Cla02g00530 Cam02g0548 Cec02g0549 Cco02g0555 Clacu02g0549 Cmu02g0544 Cre02g0875 Cone12ag1145 Cone8ag1193 . . . . . . Blo04g00506 . . Bda14g00547 . . Bma03g00547 . . . . . Cma19g00658 . Car19g00501 . . . . . . . . . . . . . . . . Lsi11g01094 . Chy01g00796 .
Vvi3g580 . . . . . Bpe12g00077 . . Cmo19g00673 . . . . . . . Cpe15g00533 Bhi05g01223 Tan02g0809 . . Hepe02g0515 . . Cla02g00529 Cam02g0547 Cec02g0548 Cco02g0554 Clacu02g0548 Cmu02g0543 Cre02g0874 Cone12ag1146 Cone8ag1194 Cone3ag1157 Cone10ag1166 Lsi10g00673 . . Cme01g01430 Blo04g00507 Blo13g00556 Bda15g00017 Bda14g00548 . . . . . . . . Cma19g00659 . Car19g00502 . Cpe01g00429 . . . . . . . . . . . . . . Lsi11g01095 . Chy01g00795 Cme11g00207
Vvi3g581 Blo02g00798 . . Bda08g00923 . . Bma05g00474 . . . Cma02g00405 Cma20g00855 Car02g00265 . . . . . . . . . . . . . . . . . . . . . . . . Chy11g00389 . . . . . . . . . . Cmo02g00410 Cmo20g00866 . . . . . Cpe05g01252 Bhi10g02022 . . . . . . . . . . . . . . Csa02g01248 . .
Vvi3g582 Blo02g00800 . . Bda08g00925 . Bpe12g00078 . . Cmo19g00674 . Cma02g00404 . Car02g00264 Car20g00739 Sed05g2322 Cpe04g00125 Cpe15g00534 Bhi05g01224 Tan02g0807 Cmetu01g1965 . Hepe02g0514 . . Cla02g00528 Cam02g0546 Cec02g0547 Cco02g0553 Clacu02g0547 Cmu02g0542 Cre02g0873 Cone12ag1147 Cone8ag1195 Cone3ag1158 . Lsi10g00358 . Chy11g00388 Cme01g01429 Blo04g00508 Blo13g00555 . Bda14g00549 Bpe15g00871 . . . Sed01g0309 Cmo02g00409 Cmo20g00865 . Cma19g00660 . Car19g00503 . Cpe05g01253 Bhi10g02020 Tan05g1319 Cmetu11g0171 . Hepe08g1023 . . . . . . . . . Lsi11g01096 Csa02g01249 Chy01g00794 .
Vvi3g583 . . . . . . . . . . . . . . . Cpe04g00251 . . . . . . . . . . . . . . . . . . . . Csa07g00824 . . . . . . . . . . . . . . . Car11g01067 . . . . . . . . . . . . . . . . . . . . .
Vvi3g584 Blo02g00801 . . Bda08g00926 . . . . Cmo19g00675 . . . . . Sed05g2321 Cpe04g00124 Cpe15g00535 Bhi05g01225 Tan02g0806 Cmetu01g2025 . Hepe02g0513 . . Cla02g00527 Cam02g0545 Cec02g0546 Cco02g0552 Clacu02g0546 Cmu02g0541 Cre02g0872 Cone12ag1148 Cone8ag1196 . . . . . Cme01g01428 Blo04g00509 . . Bda14g00550 Bpe15g00870 . Bma03g00548 . . . . . Cma19g00661 . Car19g00504 . . . . . . . . . . . . . . . . Lsi11g01098 . Chy01g00793 .
Vvi3g585 . . . Bda08g00927 . . Bma05g00472 . . . . Cma20g00854 . Car20g00738 . . . . . . . . . . . . . . . . . . . Cone3ag1159 Cone10ag1167 Lsi10g00361 . Chy11g00387 . . . . Bda14g01407 . . . . . . Cmo20g00864 . . . . . . Bhi10g02019 . . . Hepe08g1022 . . . . . . . . . . Csa02g01250 . Cme11g00190
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 16984613 16987258 - Bda029555.1 Bda08g00923 923
8 17046261 17052502 + Bda029558.1 Bda08g00925 925
8 17053550 17057228 - Bda029559.1 Bda08g00926 926
8 17081843 17083517 - Bda029560.1 Bda08g00927 927
14 4006287 4011319 + Bda027293.1 Bda14g00547 547
14 4012532 4015537 - Bda027294.1 Bda14g00548 548
14 4019125 4019337 + Bda027295.1 Bda14g00549 549
14 4023619 4031462 - Bda033938 Bda14g00550 550
14 17567012 17568388 + Bda011126.1 Bda14g01407 1407
15 1325082 1328499 - Bda011767.1 Bda15g00017 17
5 40053228 40056222 - XM_039032478.1 Bhi05g01108 1108
5 43799169 43802379 - XM_039032998.1 Bhi05g01223 1223
5 43856407 43862750 + XM_039032337.1 Bhi05g01224 1224
5 43866597 43870945 - XM_039033038.1 Bhi05g01225 1225
10 50564816 50571149 + XM_039045064.1 Bhi10g02019 2019
10 50585978 50596881 - XM_039045803.1 Bhi10g02020 2020
10 50654272 50660401 - XM_039046045.1 Bhi10g02022 2022
2 27198106 27200077 + BLOR10528 Blo02g00798 798
2 27287626 27293404 + BLOR10530 Blo02g00800 800
2 27309510 27312487 - BLOR10531 Blo02g00801 801
4 4295460 4300376 + BLOR13418 Blo04g00506 506
4 4302716 4305437 - BLOR13419 Blo04g00507 507
4 4305496 4311823 + BLOR13420 Blo04g00508 508
4 4313096 4320180 - BLOR13421 Blo04g00509 509
13 27526283 27533997 - BLOR05836 Blo13g00555 555
13 27536561 27538972 + BLOR05837 Blo13g00556 556
3 4497182 4502234 + Bma016833.2 Bma03g00547 547
3 4503480 4511591 - Bma016834.1 Bma03g00548 548
5 17263995 17266583 - Bma021362.1 Bma05g00472 472
5 17633591 17635678 - Bma021367.1 Bma05g00474 474
12 532018 535359 - Bpe005316.1 Bpe12g00077 77
12 535779 542040 + Bpe005317.1 Bpe12g00078 78
15 18655836 18665223 + Bpe001792.2 Bpe15g00870 870
15 18666462 18685269 - Bpe001793.1 Bpe15g00871 871
2 6227547 6231387 + CaPI482276_02g005450.1 Cam02g0545 545
2 6236796 6242809 - CaPI482276_02g005460.1 Cam02g0546 546
2 6247964 6250652 + CaPI482276_02g005470.1 Cam02g0547 547
2 6251805 6261398 - CaPI482276_02g005480.1 Cam02g0548 548
2 1793824 1801733 - Carg22949-RA Car02g00264 264
2 1803418 1806232 - Carg22950-RA Car02g00265 265
11 8244294 8245118 - Carg26485-RA Car11g01067 1067
19 6690362 6698354 + Carg19419-RA Car19g00501 501
19 6698569 6701966 - Carg19418-RA Car19g00502 502
19 6703542 6711151 + Carg19417-RA Car19g00503 503
19 6712698 6717135 - Carg19416-RA Car19g00504 504
20 4324467 4328431 + Carg27534-RA Car20g00738 738
20 4329500 4340770 - Carg27535-RA Car20g00739 739
2 5277837 5281610 + CcPI632755_02g005520.1 Cco02g0552 552
2 5286851 5295220 - CcPI632755_02g005530.1 Cco02g0553 553
2 5298002 5300676 + CcPI632755_02g005540.1 Cco02g0554 554
2 5301823 5311402 - CcPI632755_02g005550.1 Cco02g0555 555
2 5246152 5249953 + CePI673135_02g005460.1 Cec02g0546 546
2 5255485 5261790 - CePI673135_02g005470.1 Cec02g0547 547
2 5266612 5269272 + CePI673135_02g005480.1 Cec02g0548 548
2 5270400 5280001 - CePI673135_02g005490.1 Cec02g0549 549
1 6365096 6368801 + Chy1G007930.1 Chy01g00793 793
1 6372788 6379216 - Chy1G007940.1 Chy01g00794 794
1 6385005 6387632 + Chy1G007950.1 Chy01g00795 795
1 6388986 6403995 - Chy1G007960.1 Chy01g00796 796
11 3660444 3666840 + Chy11G189670.1 Chy11g00387 387
11 3672186 3681683 - Chy11G189680.1 Chy11g00388 388
11 3684568 3688683 - Chy11G189690.1 Chy11g00389 389
2 5188231 5192050 + ClG42_02g0054600.10 Clacu02g0546 546
2 5197555 5203862 - ClG42_02g0054700.10 Clacu02g0547 547
2 5208666 5211365 + ClG42_02g0054800.10 Clacu02g0548 548
2 5212510 5222058 - ClG42_02g0054900.10 Clacu02g0549 549
2 5433403 5437936 + ClCG02G005070.1 Cla02g00527 527
2 5442824 5449524 - ClCG02G005080.1 Cla02g00528 528
2 5454369 5457565 + ClCG02G005090.1 Cla02g00529 529
2 5458000 5467974 - ClCG02G005100.2 Cla02g00530 530
2 2040301 2048417 - CmaCh02G004040.1 Cma02g00404 404
2 2049807 2053141 - CmaCh02G004050.1 Cma02g00405 405
19 6934953 6945622 + CmaCh19G006580.1 Cma19g00658 658
19 6946081 6948908 - CmaCh19G006590.1 Cma19g00659 659
19 6950096 6956453 + CmaCh19G006600.1 Cma19g00660 660
19 6957032 6961201 - CmaCh19G006610.1 Cma19g00661 661
20 4092253 4102683 + CmaCh20G008540.1 Cma20g00854 854
20 4104105 4121764 - CmaCh20G008550.1 Cma20g00855 855
1 18173811 18178794 + MELO3C012527.2.1 Cme01g01428 1428
1 18180704 18187828 - MELO3C012528.2.1 Cme01g01429 1429
1 18206048 18209194 + MELO3C012529.2.1 Cme01g01430 1430
11 2298198 2304994 - MELO3C020979.2.1 Cme11g00190 190
11 2469099 2471535 - MELO3C020964.2.1 Cme11g00207 207
1 6392081 6398465 - PI0017941.1 Cmetu01g1965 1965
1 6384563 6388248 + PI0002322.1 Cmetu01g2025 2025
11 27348810 27362115 + PI0006628.1 Cmetu11g0171 171
2 2109297 2118234 - CmoCh02G004090.1 Cmo02g00409 409
2 2119774 2122583 - CmoCh02G004100.1 Cmo02g00410 410
19 7166027 7175287 + CmoCh19G006710.1 Cmo19g00671 671
19 7175721 7178885 - CmoCh19G006730.1 Cmo19g00673 673
19 7180685 7187323 + CmoCh19G006740.1 Cmo19g00674 674
19 7188660 7192920 - CmoCh19G006750.1 Cmo19g00675 675
20 4361318 4365252 + CmoCh20G008640.1 Cmo20g00864 864
20 4366036 4378353 - CmoCh20G008650.1 Cmo20g00865 865
20 4382714 4387590 - CmoCh20G008660.1 Cmo20g00866 866
2 5107023 5110975 + CmPI595203_02g005410.1 Cmu02g0541 541
2 5116485 5122493 - CmPI595203_02g005420.1 Cmu02g0542 542
2 5127616 5130282 + CmPI595203_02g005430.1 Cmu02g0543 543
2 5131427 5140975 - CmPI595203_02g005440.1 Cmu02g0544 544
3 30225966 30229284 - Conep03aG0166200.1 Cone3ag1157 1157
3 30230318 30242574 + Conep03aG0166300.1 Cone3ag1158 1158
3 30244692 30247295 - Conep03aG0166400.1 Cone3ag1159 1159
8 10187211 10192330 + Conep08aG0122700.1 Cone8ag1193 1193
8 10192481 10194954 - Conep08aG0122800.1 Cone8ag1194 1194
8 10195259 10201389 + Conep08aG0122900.1 Cone8ag1195 1195
8 10201400 10204319 - Conep08aG0123000.1 Cone8ag1196 1196
10 8483646 8484819 - Conep10aG0120000.1 Cone10ag1166 1166
10 8487116 8494020 - Conep10aG0120100.1 Cone10ag1167 1167
12 9156142 9160920 + Conep12aG0118100.1 Cone12ag1145 1145
12 9161592 9163898 - Conep12aG0118200.1 Cone12ag1146 1146
12 9164162 9170105 + Conep12aG0118300.1 Cone12ag1147 1147
12 9170193 9172008 - Conep12aG0118400.1 Cone12ag1148 1148
1 2476975 2479388 + Cp4.1LG01g02450.1 Cpe01g00429 429
4 1121801 1125155 + Cp4.1LG04g00850.1 Cpe04g00124 124
4 1125460 1133239 - Cp4.1LG04g00810.1 Cpe04g00125 125
4 3129477 3130313 - Cp4.1LG04g08290.1 Cpe04g00251 251
5 8763463 8766590 + Cp4.1LG05g12540.1 Cpe05g01252 1252
5 8767626 8776132 + Cp4.1LG05g12520.1 Cpe05g01253 1253
15 6214774 6223469 + Cp4.1LG15g05290.1 Cpe15g00532 532
15 6222067 6226394 - Cp4.1LG15g05350.1 Cpe15g00533 533
15 6228291 6234837 + Cp4.1LG15g05300.1 Cpe15g00534 534
15 6235703 6239911 - Cp4.1LG15g05390.1 Cpe15g00535 535
2 5679007 5682791 + CrPI670011_02g008720.1 Cre02g0872 872
2 5688420 5694731 - CrPI670011_02g008730.1 Cre02g0873 873
2 5699543 5702232 + CrPI670011_02g008740.1 Cre02g0874 874
2 5703374 5712971 - CrPI670011_02g008750.1 Cre02g0875 875
2 12215725 12221125 + CsaV3_2G014640.1 Csa02g01248 1248
2 12223389 12234260 + CsaV3_2G014650.1 Csa02g01249 1249
2 12240303 12247166 - CsaV3_2G014660.1 Csa02g01250 1250
7 5807578 5808426 - CsaV3_7G010220.1 Csa07g00824 824
2 5140658 5144637 + Hsped.02g05130.1 Hepe02g0513 513
2 5145487 5152294 - Hsped.02g05140.1 Hepe02g0514 514
2 5153421 5156472 + Hsped.02g05150.1 Hepe02g0515 515
8 9814608 9820066 + Hsped.08g10220.1 Hepe08g1022 1022
8 9821854 9830458 - Hsped.08g10230.1 Hepe08g1023 1023
10 5583232 5596364 + Lsi10G003580.1 Lsi10g00358 358
10 5605738 5609883 - Lsi10G003610.1 Lsi10g00361 361
10 9351279 9354057 + Lsi10G006730.1 Lsi10g00673 673
11 19075248 19086401 + Lsi11G010940.1 Lsi11g01094 1094
11 19086951 19090269 - Lsi11G010950.1 Lsi11g01095 1095
11 19098239 19104969 + Lsi11G010960.1 Lsi11g01096 1096
11 19110511 19114528 - Lsi11G010980.1 Lsi11g01098 1098
1 2362972 2372900 - Sed0011806.1 Sed01g0309 309
5 35678744 35683056 + Sed0013649.1 Sed05g2321 2321
5 35684395 35701112 - Sed0018667.1 Sed05g2322 2322
2 8204575 8208813 + Tan0003539.1 Tan02g0806 806
2 8223205 8229502 - Tan0018238.1 Tan02g0807 807
2 8267778 8270979 + Tan0012134.2 Tan02g0809 809
5 16385527 16394187 - Tan0001074.2 Tan05g1319 1319
3 5608888 5615417 + Vvi3g576 Vvi3g576 576
3 5622686 5623342 + Vvi3g577 Vvi3g577 577
3 5627127 5638418 + Vvi3g578 Vvi3g578 578
3 5641164 5655774 + Vvi3g579 Vvi3g579 579
3 5657468 5670765 - Vvi3g580 Vvi3g580 580
3 5671229 5673586 + Vvi3g581 Vvi3g581 581
3 5675382 5686006 + Vvi3g582 Vvi3g582 582
3 5686086 5687004 - Vvi3g583 Vvi3g583 583
3 5692420 5707098 - Vvi3g584 Vvi3g584 584
3 5719178 5724128 - Vvi3g585 Vvi3g585 585
       

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