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
Vvi3g306 . . . . . . . . . Cmo11g01798 . . . . Sed05g2142 Cpe04g00640 . Bhi05g01552 Tan02g0549 Cmetu01g0266 Lac12g0456 Hepe02g0352 . . Cla02g00332 Cam02g0341 Cec02g0342 Cco02g0346 Clacu02g0332 Cmu02g0330 Cre02g0662 Cone12ag1288 Cone8ag1342 . Cone10ag1012 . Csa07g00207 . . Blo04g00610 Blo13g00466 . Bda14g00652 Bpe15g00777 . . . . . . Cma11g01323 . Car11g01424 . . . . . . . . . . . . . . . . . Lsi11g01302 . Chy01g00573 .
Vvi3g307 . . . . . Bpe12g00157 . . Cmo19g00830 . . . . . . . Cpe15g00651 Bhi05g01551 Tan02g0548 . . Hepe02g0351 . . . . . . . . . . . Cone3ag1254 Cone10ag1207 . Csa07g00208 . . Blo04g00611 Blo13g00465 . . Bpe15g00776 . Bma03g00643 Bma08g00710 . . . . . . Car19g00627 . . . . . . . . . . . . . . . . Lsi11g01303 . Chy01g00572 .
Vvi3g308 . . . . . . . . Cmo19g00831 . . . . . . . Cpe15g00652 Bhi05g01549 . . . Hepe02g0350 . . Cla02g00331 . . Cco02g0345 . . . . . . . . Csa07g00209 . . Blo04g00548 . . . . . . . . . . . Cma19g00809 . Car19g00628 . . . . . . . . . . . . . . . . Lsi11g01304 . Chy01g00571 .
Vvi3g309 . . . . . . . . . . . . . Car20g00609 . . . . . . . . . . . . . . . . . . . Cone3ag1256 . . . . . . . . . . . . . . . Cmo20g00704 . . . . Cpe16g00356 . . . . . . . . Cla02g01056 . . . . . . . . . Cme11g01030
Vvi3g310 . . . . . . . . . . Cma02g00306 . Car02g00185 . . . . . . . . . . . . . . . . . . . . Cone17ag1276 . . . . . . . . . . . . . . Cmo02g00300 . . . . . . Cpe05g01333 . . . . . . . Cla02g01055 Cam02g1127 Cec02g1131 Cco02g1169 Clacu02g1115 Cmu02g1078 Cre02g1382 . . . Cme11g01027
Vvi3g311 . . . . . . . . Cmo19g00832 Cmo11g01800 . . . . Sed04g3773 Cpe04g00642 Cpe15g00654 Bhi05g01546 Tan02g0544 Cmetu01g0725 Lac12g0453 Hepe02g0348 . . Cla02g00330 Cam02g0339 Cec02g0340 Cco02g0343 Clacu02g0330 Cmu02g0328 Cre02g0660 . . . . . Csa07g00210 . . . . . Bda14g00654 Bpe15g00774 . Bma03g00645 . . . . Cma11g01321 Cma19g00811 Car11g01426 Car19g00630 . . . . . . . . . . . . . . . . Lsi11g01305 . Chy01g00569 .
Vvi3g312 . Blo15g00413 Bda06g00450 . Bpe07g00683 . . . Cmo19g00834 Cmo11g01802 . . . . Sed04g3772 . Cpe15g00656 Bhi05g01545 Tan02g0543 Cmetu01g0113 Lac12g0452 . . . Cla02g00329 Cam02g0338 Cec02g0339 Cco02g0342 Clacu02g0329 Cmu02g0327 . . . . . . Csa07g00211 . . . . . . . . . . . . . . Cma19g00814 Car11g01427 Car19g00632 . . . . . . . . . . . . . . . . Lsi11g01308 . Chy01g00568 Cme11g01314
Vvi3g313 . . . . . . . . . . . . . . Sed12g0547 . . Bhi05g01544 Tan02g0542 Cmetu07g1477 Lac12g0451 Hepe02g0347 . . Cla02g00328 Cam02g0337 Cec02g0337 Cco02g0341 Clacu02g0328 Cmu02g0326 Cre02g0659 Cone12ag1287 Cone8ag1344 . . . Csa07g00214 . . Blo04g00612 . . Bda14g00655 Bpe15g00773 . Bma03g00646 . . . . . Cma19g00815 . Car19g00633 . . . . . . . . . . . . . . . . Lsi11g01309 . Chy01g00567 .
Vvi3g314 . Blo15g00412 Bda06g00451 . Bpe07g00684 . . Bma12g00888 Cmo19g00835 . . . . . Sed05g2139 . Cpe15g00657 Bhi05g01543 Tan02g0541 Cmetu11g0170 . Hepe02g0346 . . Cla02g00327 Cam02g0336 Cec02g0336 Cco02g0340 Clacu02g0327 Cmu02g0325 Cre02g0658 . . . Cone10ag1201 . Csa07g00215 . . . . . . . . . . . . . . Cma19g00816 . Car19g00634 . . . . . . . . . . . . . . . . Lsi11g01310 . Chy01g00566 .
Vvi3g315 . . . . . Bpe12g00159 . . . Cmo11g01803 . . . . Sed05g2136 Cpe04g00646 Cpe15g00658 Bhi05g01542 Tan02g0540 Cmetu01g0851 Lac12g0438 Hepe02g0345 . . . . . . . . . . . . . . Csa07g00216 . . . Blo13g00462 . . . . . . . . . Cma11g01317 Cma19g00818 Car11g01430 Car19g00635 . . . . . . . . . . . . . . . . Lsi11g01311 . Chy01g00565 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 6546181 6547339 + Bda023694.1 Bda06g00450 450
6 6548377 6552601 + Bda023695.1 Bda06g00451 451
14 4885202 4886573 + Bda027409.1 Bda14g00652 652
14 4899255 4900660 + Bda027411.1 Bda14g00654 654
14 4900804 4902144 - Bda033940 Bda14g00655 655
5 52073663 52083418 - XM_039032821.1 Bhi05g01542 1542
5 52136544 52142139 - XM_039032474.1 Bhi05g01543 1543
5 52211797 52213526 + XM_039032261.1 Bhi05g01544 1544
5 52213478 52215198 - XM_039032260.1 Bhi05g01545 1545
5 52219255 52224307 - XM_039031668.1 Bhi05g01546 1546
5 52338254 52342016 + XM_039031048.1 Bhi05g01549 1549
5 52345807 52351544 + XM_039032346.1 Bhi05g01551 1551
5 52351710 52353572 - XM_039032348.1 Bhi05g01552 1552
4 4739744 4741162 + BLOR13460 Blo04g00548 548
4 5283778 5285150 + BLOR13522 Blo04g00610 610
4 5285510 5291975 - BLOR13523 Blo04g00611 611
4 5295864 5297349 - BLOR13524 Blo04g00612 612
13 25220617 25232863 - BLOR05743 Blo13g00462 462
13 25368800 25374787 + BLOR05746 Blo13g00465 465
13 25375146 25376514 - BLOR05747 Blo13g00466 466
15 5880483 5884780 - BLOR06806 Blo15g00412 412
15 5885000 5888079 - BLOR06807 Blo15g00413 413
3 5309088 5312957 - Bma016936.2 Bma03g00643 643
3 5316653 5320021 + Bma016938.1 Bma03g00645 645
3 5320818 5321643 - Bma016939.1 Bma03g00646 646
8 42903359 42906803 + Bma031459 Bma08g00710 710
12 40168425 40172961 + Bma008215.1 Bma12g00888 888
7 13496850 13498009 + Bpe021531.1 Bpe07g00683 683
7 13498714 13502910 + Bpe021532.1 Bpe07g00684 684
12 1145136 1151852 - Bpe005394.1 Bpe12g00157 157
12 1174528 1188907 + Bpe005396.1 Bpe12g00159 159
15 18055252 18056074 + Bpe001700.1 Bpe15g00773 773
15 18056849 18058283 - Bpe001701.1 Bpe15g00774 774
15 18062315 18066045 + Bpe001703.1 Bpe15g00776 776
15 18066406 18067773 - Bpe001704.1 Bpe15g00777 777
2 4128285 4134851 - CaPI482276_02g003360.1 Cam02g0336 336
2 4136286 4137218 + CaPI482276_02g003370.1 Cam02g0337 337
2 4137936 4142455 - CaPI482276_02g003380.1 Cam02g0338 338
2 4144311 4149176 - CaPI482276_02g003390.1 Cam02g0339 339
2 4169642 4170982 - CaPI482276_02g003410.1 Cam02g0341 341
2 21153645 21156505 + CaPI482276_02g011270.1 Cam02g1127 1127
2 1104571 1108624 - Carg19774-RA Car02g00185 185
11 11628123 11630234 + Carg18106-RA Car11g01424 1424
11 11636641 11638998 + Carg18104-RA Car11g01426 1426
11 11641504 11643468 + Carg18103-RA Car11g01427 1427
11 11652983 11656446 + Carg18100-RA Car11g01430 1430
19 7681715 7686335 - Carg04108-RA Car19g00627 627
19 7688944 7692529 - Carg04109-RA Car19g00628 628
19 7698786 7701892 + Carg04111-RA Car19g00630 630
19 7703571 7704842 + Carg04113-RA Car19g00632 632
19 7705513 7706509 - Carg04114-RA Car19g00633 633
19 7707363 7714015 + Carg04115-RA Car19g00634 634
19 7715321 7724596 + Carg04116-RA Car19g00635 635
20 3425910 3427796 - Carg16129-RA Car20g00609 609
2 3125411 3131973 - CcPI632755_02g003400.1 Cco02g0340 340
2 3133422 3134354 + CcPI632755_02g003410.1 Cco02g0341 341
2 3135073 3139587 - CcPI632755_02g003420.1 Cco02g0342 342
2 3141468 3146223 - CcPI632755_02g003430.1 Cco02g0343 343
2 3162634 3167241 + CcPI632755_02g003450.1 Cco02g0345 345
2 3167797 3169138 - CcPI632755_02g003460.1 Cco02g0346 346
2 20429898 20433672 + CcPI632755_02g011690.1 Cco02g1169 1169
2 3135729 3142257 - CePI673135_02g003360.1 Cec02g0336 336
2 3143690 3144606 + CePI673135_02g003370.1 Cec02g0337 337
2 3145323 3146861 - CePI673135_02g003390.1 Cec02g0339 339
2 3151768 3156674 - CePI673135_02g003400.1 Cec02g0340 340
2 3177248 3178589 - CePI673135_02g003420.1 Cec02g0342 342
2 25206580 25209458 + CePI673135_02g011310.1 Cec02g1131 1131
1 4061447 4071131 - Chy1G005650.1 Chy01g00565 565
1 4073599 4079887 - Chy1G005660.1 Chy01g00566 566
1 4081865 4082815 + Chy1G005670.1 Chy01g00567 567
1 4083549 4084866 - Chy1G005680.1 Chy01g00568 568
1 4088446 4092589 - Chy1G005690.1 Chy01g00569 569
1 4098188 4101266 + Chy1G005710.1 Chy01g00571 571
1 4103705 4107870 + Chy1G005720.1 Chy01g00572 572
1 4108440 4109796 - Chy1G005730.1 Chy01g00573 573
2 3005013 3010885 - ClG42_02g0032700.10 Clacu02g0327 327
2 3012317 3013249 + ClG42_02g0032800.10 Clacu02g0328 328
2 3013966 3015508 - ClG42_02g0032900.10 Clacu02g0329 329
2 3020366 3025283 - ClG42_02g0033000.10 Clacu02g0330 330
2 3046577 3047918 - ClG42_02g0033200.10 Clacu02g0332 332
2 21111062 21113942 + ClG42_02g0111500.10 Clacu02g1115 1115
2 3195499 3216742 - ClCG02G003230.2 Cla02g00327 327
2 3217996 3219327 + ClCG02G003250.1 Cla02g00328 328
2 3219680 3221222 - ClCG02G003260.1 Cla02g00329 329
2 3226067 3230981 - ClCG02G003270.2 Cla02g00330 330
2 3235293 3252014 + ClCG02G003280.2 Cla02g00331 331
2 3252199 3253659 - ClCG02G003300.1 Cla02g00332 332
2 21891120 21894570 + ClCG02G010790.1 Cla02g01055 1055
2 22029630 22031504 - ClCG02G010810.1 Cla02g01056 1056
2 1433405 1436951 - CmaCh02G003060.1 Cma02g00306 306
11 8749582 8766691 - CmaCh11G013170.1 Cma11g01317 1317
11 8773577 8775977 - CmaCh11G013210.1 Cma11g01321 1321
11 8782232 8784427 - CmaCh11G013230.1 Cma11g01323 1323
19 7791495 7801220 - CmaCh19G008090.1 Cma19g00809 809
19 7807270 7810496 + CmaCh19G008110.1 Cma19g00811 811
19 7812356 7814113 + CmaCh19G008140.1 Cma19g00814 814
19 7814302 7815290 - CmaCh19G008150.1 Cma19g00815 815
19 7816251 7823798 + CmaCh19G008160.1 Cma19g00816 816
19 7831288 7833984 + CmaCh19G008180.1 Cma19g00818 818
11 14848958 14851875 + MELO3C013482.2.1 Cme11g01027 1027
11 14888760 14890634 - MELO3C035015.2.1 Cme11g01030 1030
11 19942997 19944663 - MELO3C025907.2.1 Cme11g01314 1314
1 4382653 4384031 - PI0020729.1 Cmetu01g0113 113
1 4406888 4408414 - PI0004721.1 Cmetu01g0266 266
1 4386765 4391542 - PI0018251.1 Cmetu01g0725 725
1 4360529 4370816 - PI0028457.1 Cmetu01g0851 851
7 2206158 2207545 - PI0018368.1 Cmetu07g1477 1477
11 27463611 27471791 - PI0014801.1 Cmetu11g0170 170
2 1495844 1500034 - CmoCh02G003000.1 Cmo02g00300 300
11 12624730 12626838 + CmoCh11G017980.1 Cmo11g01798 1798
11 12633687 12636029 + CmoCh11G018000.1 Cmo11g01800 1800
11 12638289 12640424 + CmoCh11G018020.1 Cmo11g01802 1802
11 12643485 12653259 + CmoCh11G018030.1 Cmo11g01803 1803
19 8145648 8150575 - CmoCh19G008300.1 Cmo19g00830 830
19 8151873 8160459 - CmoCh19G008310.1 Cmo19g00831 831
19 8161474 8162158 + CmoCh19G008320.1 Cmo19g00832 832
19 8165813 8167779 + CmoCh19G008340.1 Cmo19g00834 834
19 8169906 8176759 + CmoCh19G008350.1 Cmo19g00835 835
20 3481994 3483880 - CmoCh20G007040.1 Cmo20g00704 704
2 2998874 3004746 - CmPI595203_02g003250.1 Cmu02g0325 325
2 3006179 3007111 + CmPI595203_02g003260.1 Cmu02g0326 326
2 3007828 3012350 - CmPI595203_02g003270.1 Cmu02g0327 327
2 3014216 3019129 - CmPI595203_02g003280.1 Cmu02g0328 328
2 3040417 3041758 - CmPI595203_02g003300.1 Cmu02g0330 330
2 20983487 20986367 + CmPI595203_02g010780.1 Cmu02g1078 1078
3 31377721 31381726 - Conep03aG0176100.1 Cone3ag1254 1254
3 31386880 31388844 - Conep03aG0176300.1 Cone3ag1256 1256
8 10793398 10794757 + Conep08aG0138100.1 Cone8ag1342 1342
8 10799859 10803194 - Conep08aG0138300.1 Cone8ag1344 1344
10 7009428 7012678 + Conep10aG0103900.1 Cone10ag1012 1012
10 8870751 8876046 - Conep10aG0123600.1 Cone10ag1201 1201
10 8954340 8958568 + Conep10aG0124200.1 Cone10ag1207 1207
12 9828122 9828535 + Conep12aG0132800.1 Cone12ag1287 1287
12 9833913 9835428 - Conep12aG0132900.1 Cone12ag1288 1288
17 9183973 9189626 - Conep17aG0130700.1 Cone17ag1276 1276
4 6594983 6597134 + Cp4.1LG04g04430.1 Cpe04g00640 640
4 6604069 6606781 + Cp4.1LG04g04410.1 Cpe04g00642 642
4 6614974 6624560 + Cp4.1LG04g04440.1 Cpe04g00646 646
5 9379832 9387113 + Cp4.1LG05g13340.1 Cpe05g01333 1333
15 7208912 7213636 - Cp4.1LG15g06570.1 Cpe15g00651 651
15 7214923 7217789 - Cp4.1LG15g06600.1 Cpe15g00652 652
15 7224576 7228018 + Cp4.1LG15g06470.1 Cpe15g00654 654
15 7229662 7232654 + Cp4.1LG15g06480.1 Cpe15g00656 656
15 7234007 7241510 + Cp4.1LG15g06490.1 Cpe15g00657 657
15 7243059 7252399 + Cp4.1LG15g06520.1 Cpe15g00658 658
16 5284327 5288008 + Cp4.1LG16g03510.1 Cpe16g00356 356
2 3543301 3549910 - CrPI670011_02g006580.1 Cre02g0658 658
2 3551348 3552280 + CrPI670011_02g006590.1 Cre02g0659 659
2 3552998 3564090 - CrPI670011_02g006600.1 Cre02g0660 660
2 3586468 3587808 - CrPI670011_02g006620.1 Cre02g0662 662
2 22507903 22510783 + CrPI670011_02g013820.1 Cre02g1382 1382
7 1660381 1662639 + CsaV3_7G002070.1 Csa07g00207 207
7 1662425 1666871 - CsaV3_7G002080.1 Csa07g00208 208
7 1669024 1676139 - CsaV3_7G002090.1 Csa07g00209 209
7 1677335 1681662 + CsaV3_7G002100.1 Csa07g00210 210
7 1682194 1686923 + CsaV3_7G002110.1 Csa07g00211 211
7 1687245 1688195 - CsaV3_7G002140.1 Csa07g00214 214
7 1689375 1696853 + CsaV3_7G002150.1 Csa07g00215 215
7 1698802 1709189 + CsaV3_7G002160.1 Csa07g00216 216
2 3270876 3283905 - Hsped.02g03450.1 Hepe02g0345 345
2 3286777 3292425 - Hsped.02g03460.1 Hepe02g0346 346
2 3297090 3300527 + Hsped.02g03470.1 Hepe02g0347 347
2 3302478 3307050 - Hsped.02g03480.1 Hepe02g0348 348
2 3312530 3315632 + Hsped.02g03500.1 Hepe02g0350 350
2 3318097 3322976 + Hsped.02g03510.1 Hepe02g0351 351
2 3323171 3324745 - Hsped.02g03520.1 Hepe02g0352 352
12 4878576 4888274 - Lag0014810.1 Lac12g0438 438
12 5013773 5014710 + Lag0014823.1 Lac12g0451 451
12 5015580 5016669 - Lag0014824.1 Lac12g0452 452
12 5018995 5023391 - Lag0014825.1 Lac12g0453 453
12 5042253 5043597 - Lag0014828.1 Lac12g0456 456
11 21647277 21648947 + Lsi11G013020.1 Lsi11g01302 1302
11 21648881 21653625 - Lsi11G013030.1 Lsi11g01303 1303
11 21657678 21665835 - Lsi11G013040.1 Lsi11g01304 1304
11 21667650 21667988 + Lsi11G013050.1 Lsi11g01305 1305
11 21684185 21686999 + Lsi11G013080.1 Lsi11g01308 1308
11 21687394 21688532 - Lsi11G013090.1 Lsi11g01309 1309
11 21689691 21696369 + Lsi11G013100.1 Lsi11g01310 1310
11 21702086 21713027 + Lsi11G013110.1 Lsi11g01311 1311
4 46358086 46360779 - Sed0015122.1 Sed04g3772 3772
4 46363902 46368639 - Sed0014792.1 Sed04g3773 3773
5 34402296 34414579 - Sed0020334.1 Sed05g2136 2136
5 34420127 34432050 - Sed0020521.3 Sed05g2139 2139
5 34444587 34448110 - Sed0009135.1 Sed05g2142 2142
12 3348088 3350055 - Sed0025758.1 Sed12g0547 547
2 4851995 4862406 - Tan0008577.1 Tan02g0540 540
2 4867994 4873918 - Tan0013684.1 Tan02g0541 541
2 4875484 4876426 + Tan0014242.1 Tan02g0542 542
2 4877190 4878289 - Tan0022246.1 Tan02g0543 543
2 4883112 4887527 - Tan0006924.1 Tan02g0544 544
2 4902763 4907773 + Tan0009656.2 Tan02g0548 548
2 4907841 4909507 - Tan0010505.1 Tan02g0549 549
3 2911376 2912923 + Vvi3g306 Vvi3g306 306
3 2913097 2918575 - Vvi3g307 Vvi3g307 307
3 2918805 2921293 - Vvi3g308 Vvi3g308 308
3 2921751 2923596 + Vvi3g309 Vvi3g309 309
3 2923761 2927199 - Vvi3g310 Vvi3g310 310
3 2930057 2932804 + Vvi3g311 Vvi3g311 311
3 2934473 2935485 + Vvi3g312 Vvi3g312 312
3 2936107 2937432 - Vvi3g313 Vvi3g313 313
3 2937534 2942467 + Vvi3g314 Vvi3g314 314
3 2942481 2962563 + Vvi3g315 Vvi3g315 315
       

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