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
Vvi5g609 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g610 Blo01g00098 . . Bda08g00267 . . . Bma05g01077 . Cmo17g00177 Cma06g01341 Cma14g01777 Car06g01163 Car14g01598 . Cpe08g00308 . . . . . . . . Cla06g00636 Cam06g0680 Cec06g0683 Cco06g0689 Clacu06g0666 Cmu06g0658 Cre06g1426 . . . Cone4ag0293 Lsi05g01668 Csa02g01091 Chy05g00352 Cme06g00544 . . . . Bpe05g00867 . . . . Cmo06g01353 Cmo14g01814 . Cma17g00180 . Car17g00162 Cpe12g00156 . Bhi12g01661 . . . Hepe03g0254 . . Cla05g00487 Cam05g0531 Cec05g0543 Cco05g0543 Clacu05g0529 Cmu05g0501 Cre05g0569 Lsi09g01264 Csa03g01262 Chy06g00517 Cme05g00531
Vvi5g611 . . . . . . . . . . . Cma14g01778 . Car14g01599 . . Cpe03g01487 . . . . . . . . . . . . . . . . . Cone4ag0294 Lsi05g01670 . . Cme06g00543 . . . . . . . . . . Cmo14g01815 . . . . . . . . . . . . . Cla05g00486 Cam05g0529 Cec05g0542 Cco05g0542 Clacu05g0528 Cmu05g0500 Cre05g0567 . Csa03g01261 Chy06g00516 .
Vvi5g612 . . . . . . . . Cmo08g01078 Cmo17g00176 . . . . . . . . . . . . . . Cla06g00637 Cam06g0681 Cec06g0684 Cco06g0690 Clacu06g0667 Cmu06g0659 Cre06g1427 . . . Cone4ag0295 . Csa02g01090 Chy05g00351 . . . . . . . . Bma06g01583 . . . Cma08g01106 Cma17g00179 Car08g00979 Car17g00161 Cpe12g00155 . . . . . . . . . . . . . . . Lsi09g01263 . . Cme05g00532
Vvi5g613 . . . . . Bpe14g01227 . . Cmo08g01077 Cmo17g00175 . . Car06g01162 Car14g01600 . Cpe08g00309 Cpe03g01488 . . . . . . . Cla06g00638 Cam06g0682 Cec06g0685 Cco06g0691 Clacu06g0668 Cmu06g0660 Cre06g1428 . . . . Lsi05g01671 Csa02g01089 Chy05g00350 Cme06g00542 Blo02g00606 Blo07g00244 Bda11g00612 Bda13g00090 . . Bma02g00810 Bma06g01584 . . Cmo14g01816 Cma08g01105 Cma17g00178 Car08g00978 Car17g00160 Cpe12g00154 Cpe17g00178 . . . . . . . Cla05g00485 Cam05g0528 Cec05g0541 Cco05g0541 Clacu05g0527 Cmu05g0499 Cre05g0566 . Csa03g01260 Chy06g00515 Cme05g00534
Vvi5g614 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag0297 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g615 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g616 . . . . . . . . . . . Cma14g01779 Car06g01161 Car14g01601 . . Cpe03g01489 . . . . . . . . . . . . . . . . . Cone4ag0298 . Csa02g01087 Chy05g00349 Cme06g00541 . Blo07g00245 . . . Bpe13g00575 . . . . . . Cma17g00177 . Car17g00159 Cpe12g00153 . . . . . . . . Cla05g00484 Cam05g0527 Cec05g0540 Cco05g0540 Clacu05g0526 Cmu05g0498 Cre05g0565 . Csa03g01259 Chy06g00514 Cme05g00535
Vvi5g617 . . . . . . . . . . Cma06g01340 . Car06g01160 . . Cpe08g00310 . . . . . . . . Cla06g00639 Cam06g0683 Cec06g0686 Cco06g0692 Clacu06g0669 Cmu06g0661 Cre06g1429 . . . . Lsi05g01673 . . . . Blo07g00246 . . . . . . Sed09g0707 . . . . . . . . Bhi12g01657 Tan06g2444 Cmetu05g1440 Lac12g2207 Hepe03g0257 . Lcy13g0343 . . . . . . . Lsi09g01262 . . .
Vvi5g618 . . . . . Bpe14g01228 . . . . . Cma14g01781 . Car14g01602 . . Cpe03g01490 . . . . . . . . . . . . . . Cone14ag0137 Cone15ag0142 Cone7ag0299 Cone4ag0300 Lsi05g01674 . . Cme06g00540 . . Bda11g00614 Bda13g00089 . Bpe13g00571 Bma02g00807 . . . Cmo14g01817 . . . . . . . . . . . . . Cla05g00483 Cam05g0526 Cec05g0539 Cco05g0539 Clacu05g0525 Cmu05g0497 Cre05g0564 . Csa03g01258 Chy06g00513 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 2749683 2750210 - Bda024696.1 Bda08g00267 267
11 6190706 6191903 - Bda005355.1 Bda11g00612 612
11 6208958 6217696 - Bda005359.3 Bda11g00614 614
13 1197428 1201943 - Bda000941.1 Bda13g00089 89
13 1232496 1233919 + Bda032836 Bda13g00090 90
12 53469206 53488414 + XM_039018794.1 Bhi12g01657 1657
12 53614183 53616885 - XM_039019728.1 Bhi12g01661 1661
1 1400427 1400951 + BLOR00098 Blo01g00098 98
2 11841889 11844835 - BLOR10336 Blo02g00606 606
7 3023128 3024474 - BLOR18176 Blo07g00244 244
7 3028935 3029756 - BLOR18177 Blo07g00245 245
7 3029800 3035173 - BLOR18178 Blo07g00246 246
2 43786340 43790914 + Bma015543.1 Bma02g00807 807
2 44118573 44120069 + Bma015550.1 Bma02g00810 810
5 49504890 49505456 + Bma022244.2 Bma05g01077 1077
6 52076229 52076925 + Bma024701.1 Bma06g01583 1583
6 52077418 52078688 - Bma031335 Bma06g01584 1584
5 21868154 21868678 + Bpe025832 Bpe05g00867 867
13 12893030 12896081 + Bpe010274.1 Bpe13g00571 571
13 12913980 12919149 + Bpe010277.2 Bpe13g00575 575
14 9189913 9191372 - Bpe014588.1 Bpe14g01227 1227
14 9200173 9204683 - Bpe014589.1 Bpe14g01228 1228
5 4645258 4650369 + CaPI482276_05g005260.1 Cam05g0526 526
5 4668440 4670879 + CaPI482276_05g005270.1 Cam05g0527 527
5 4673151 4674521 + CaPI482276_05g005280.1 Cam05g0528 528
5 4675723 4680305 - CaPI482276_05g005290.1 Cam05g0529 529
5 4683781 4685527 + CaPI482276_05g005310.1 Cam05g0531 531
6 9138952 9139921 - CaPI482276_06g006800.1 Cam06g0680 680
6 9152890 9154053 + CaPI482276_06g006810.1 Cam06g0681 681
6 9158415 9160164 - CaPI482276_06g006820.1 Cam06g0682 682
6 9162352 9174847 - CaPI482276_06g006830.1 Cam06g0683 683
6 8562422 8563693 + Carg06197-RA Car06g01160 1160
6 8563786 8565138 + Carg06196-RA Car06g01161 1161
6 8565684 8567618 + Carg06195-RA Car06g01162 1162
6 8569540 8571296 + Carg06194-RA Car06g01163 1163
8 6494976 6497786 + Carg10944-RA Car08g00978 978
8 6499066 6500204 - Carg10943-RA Car08g00979 979
14 12944122 12946884 - Carg16589-RA Car14g01598 1598
14 12948266 12952392 + Carg16588-RA Car14g01599 1599
14 12952633 12954564 - Carg16587-RA Car14g01600 1600
14 12955222 12957789 - Carg16586-RA Car14g01601 1601
14 12962044 12968669 - Carg16585-RA Car14g01602 1602
17 979971 983992 + Carg10072-RA Car17g00159 159
17 984531 986192 + Carg10071-RA Car17g00160 160
17 986871 987785 - Carg10070-RA Car17g00161 161
17 990610 991137 + Carg10069-RA Car17g00162 162
5 4299341 4304452 + CcPI632755_05g005390.1 Cco05g0539 539
5 4322380 4324815 + CcPI632755_05g005400.1 Cco05g0540 540
5 4327137 4328515 + CcPI632755_05g005410.1 Cco05g0541 541
5 4329885 4333977 - CcPI632755_05g005420.1 Cco05g0542 542
5 4343296 4345641 + CcPI632755_05g005430.1 Cco05g0543 543
6 7714277 7714957 - CcPI632755_06g006890.1 Cco06g0689 689
6 7729511 7730667 + CcPI632755_06g006900.1 Cco06g0690 690
6 7734625 7738265 - CcPI632755_06g006910.1 Cco06g0691 691
6 7738747 7749921 - CcPI632755_06g006920.1 Cco06g0692 692
5 4300045 4305153 + CePI673135_05g005390.1 Cec05g0539 539
5 4324958 4327415 + CePI673135_05g005400.1 Cec05g0540 540
5 4329753 4331128 + CePI673135_05g005410.1 Cec05g0541 541
5 4332931 4337028 - CePI673135_05g005420.1 Cec05g0542 542
5 4341747 4342398 + CePI673135_05g005430.1 Cec05g0543 543
6 7732008 7732535 - CePI673135_06g006830.1 Cec06g0683 683
6 7746864 7748015 + CePI673135_06g006840.1 Cec06g0684 684
6 7752035 7753784 - CePI673135_06g006850.1 Cec06g0685 685
6 7755961 7762047 - CePI673135_06g006860.1 Cec06g0686 686
5 3629297 3638234 + Chy5G093950.1 Chy05g00349 349
5 3660635 3662291 + Chy5G093960.1 Chy05g00350 350
5 3664111 3665241 - Chy5G093970.1 Chy05g00351 351
5 3675152 3675813 + Chy5G093980.1 Chy05g00352 352
6 3461902 3466903 + Chy6G110410.1 Chy06g00513 513
6 3476027 3478456 + Chy6G110420.1 Chy06g00514 514
6 3481588 3482957 + Chy6G110430.1 Chy06g00515 515
6 3484638 3488698 - Chy6G110440.1 Chy06g00516 516
6 3490862 3493235 + Chy6G110450.1 Chy06g00517 517
5 4352924 4357981 + ClG42_05g0052500.10 Clacu05g0525 525
5 4376070 4378572 + ClG42_05g0052600.10 Clacu05g0526 526
5 4380231 4381603 + ClG42_05g0052700.10 Clacu05g0527 527
5 4382684 4387355 - ClG42_05g0052800.10 Clacu05g0528 528
5 4387424 4391554 + ClG42_05g0052900.10 Clacu05g0529 529
6 7690572 7691099 - ClG42_06g0066600.10 Clacu06g0666 666
6 7706086 7707240 + ClG42_06g0066700.10 Clacu06g0667 667
6 7711711 7713458 - ClG42_06g0066800.10 Clacu06g0668 668
6 7715611 7727865 - ClG42_06g0066900.10 Clacu06g0669 669
5 4366780 4374188 + ClCG05G004600.1 Cla05g00483 483
5 4396301 4401621 + ClCG05G004610.1 Cla05g00484 484
5 4402984 4404958 + ClCG05G004620.2 Cla05g00485 485
5 4406058 4410657 - ClCG05G004630.1 Cla05g00486 486
5 4412980 4415093 + ClCG05G004640.2 Cla05g00487 487
6 7849247 7851782 - ClCG06G006715.1 Cla06g00636 636
6 7864577 7865859 + ClCG06G006720.2 Cla06g00637 637
6 7870035 7872159 - ClCG06G006730.1 Cla06g00638 638
6 7873824 7886468 - ClCG06G006740.2 Cla06g00639 639
6 8802239 8806546 + CmaCh06G013400.1 Cma06g01340 1340
6 8807669 8809434 + CmaCh06G013410.1 Cma06g01341 1341
8 6860161 6864833 + CmaCh08G011050.1 Cma08g01105 1105
8 6865949 6867038 - CmaCh08G011060.1 Cma08g01106 1106
14 12870885 12872905 - CmaCh14G017770.1 Cma14g01777 1777
14 12873572 12877909 + CmaCh14G017780.1 Cma14g01778 1778
14 12878532 12883175 - CmaCh14G017790.1 Cma14g01779 1779
14 12891396 12893779 - CmaCh14G017810.1 Cma14g01781 1781
17 919304 928278 + CmaCh17G001770.1 Cma17g00177 177
17 928774 930841 + CmaCh17G001780.1 Cma17g00178 178
17 931252 932143 - CmaCh17G001790.1 Cma17g00179 179
17 934982 935631 + CmaCh17G001800.1 Cma17g00180 180
5 5119483 5122765 - MELO3C026776.2.1 Cme05g00531 531
5 5126162 5127554 + MELO3C026778.2.1 Cme05g00532 532
5 5137968 5140075 - MELO3C026780.2.1 Cme05g00534 534
5 5152801 5160243 - MELO3C026781.2.1 Cme05g00535 535
6 3394036 3400828 + MELO3C006469.2.1 Cme06g00540 540
6 3416100 3418865 + MELO3C006470.2.1 Cme06g00541 541
6 3421588 3423295 + MELO3C006471.2.1 Cme06g00542 542
6 3424151 3428781 - MELO3C006472.2.1 Cme06g00543 543
6 3429533 3431715 + MELO3C006473.2.1 Cme06g00544 544
5 18692347 18700367 + PI0021269.1 Cmetu05g1440 1440
6 10026390 10026968 + CmoCh06G013530.1 Cmo06g01353 1353
8 6938877 6941530 + CmoCh08G010770.1 Cmo08g01077 1077
8 6942893 6944076 - CmoCh08G010780.1 Cmo08g01078 1078
14 13852296 13854113 - CmoCh14G018140.1 Cmo14g01814 1814
14 13855366 13859527 + CmoCh14G018150.1 Cmo14g01815 1815
14 13859755 13865060 - CmoCh14G018160.1 Cmo14g01816 1816
14 13869348 13875962 - CmoCh14G018170.1 Cmo14g01817 1817
17 1030807 1032977 + CmoCh17G001750.1 Cmo17g00175 175
17 1033327 1034281 - CmoCh17G001760.1 Cmo17g00176 176
17 1037064 1037591 + CmoCh17G001770.1 Cmo17g00177 177
5 4196422 4201479 + CmPI595203_05g004970.1 Cmu05g0497 497
5 4219542 4222044 + CmPI595203_05g004980.1 Cmu05g0498 498
5 4223702 4225074 + CmPI595203_05g004990.1 Cmu05g0499 499
5 4226156 4230827 - CmPI595203_05g005000.1 Cmu05g0500 500
5 4230896 4235034 + CmPI595203_05g005010.1 Cmu05g0501 501
6 7496337 7496864 - CmPI595203_06g006580.1 Cmu06g0658 658
6 7511819 7512973 + CmPI595203_06g006590.1 Cmu06g0659 659
6 7517375 7519122 - CmPI595203_06g006600.1 Cmu06g0660 660
6 7521274 7533564 - CmPI595203_06g006610.1 Cmu06g0661 661
4 1345920 1347382 - Conep04aG0030400.1 Cone4ag0293 293
4 1347614 1351033 + Conep04aG0030500.1 Cone4ag0294 294
4 1351279 1352192 + Conep04aG0030600.1 Cone4ag0295 295
4 1354880 1356101 + Conep04aG0030800.1 Cone4ag0297 297
4 1355841 1358159 - Conep04aG0030900.1 Cone4ag0298 298
4 1365752 1373404 - Conep04aG0031100.1 Cone4ag0300 300
7 1292555 1295525 - Conep07aG0030600.1 Cone7ag0299 299
14 642690 644504 - Conep14aG0014000.1 Cone14ag0137 137
15 669778 672521 - Conep15aG0014400.1 Cone15ag0142 142
3 11754853 11759133 + Cp4.1LG03g10290.1 Cpe03g01487 1487
3 11759616 11761420 - Cp4.1LG03g10240.1 Cpe03g01488 1488
3 11761861 11764525 - Cp4.1LG03g10230.1 Cpe03g01489 1489
3 11768741 11776336 - Cp4.1LG03g10210.1 Cpe03g01490 1490
8 1970926 1972747 - Cp4.1LG08g03740.1 Cpe08g00308 308
8 1973799 1975478 - Cp4.1LG08g03690.1 Cpe08g00309 309
8 1975965 1978716 - Cp4.1LG08g03710.1 Cpe08g00310 310
12 982963 987068 + Cp4.1LG12g01450.1 Cpe12g00153 153
12 987461 989710 + Cp4.1LG12g01460.1 Cpe12g00154 154
12 989986 990909 - Cp4.1LG12g01640.1 Cpe12g00155 155
12 991069 995385 + Cp4.1LG12g01550.1 Cpe12g00156 156
17 1149729 1152646 - Cp4.1LG17g01900.1 Cpe17g00178 178
5 4989668 4994784 + CrPI670011_05g005640.1 Cre05g0564 564
5 5012808 5015277 + CrPI670011_05g005650.1 Cre05g0565 565
5 5017152 5018533 + CrPI670011_05g005660.1 Cre05g0566 566
5 5019794 5024376 - CrPI670011_05g005670.1 Cre05g0567 567
5 5029163 5029858 + CrPI670011_05g005690.1 Cre05g0569 569
6 8594506 8595036 - CrPI670011_06g014260.1 Cre06g1426 1426
6 8609935 8611083 + CrPI670011_06g014270.1 Cre06g1427 1427
6 8615481 8617230 - CrPI670011_06g014280.1 Cre06g1428 1428
6 8619419 8631764 - CrPI670011_06g014290.1 Cre06g1429 1429
2 10600921 10610422 + CsaV3_2G013030.1 Csa02g01087 1087
2 10622707 10624936 + CsaV3_2G013050.1 Csa02g01089 1089
2 10626443 10627763 - CsaV3_2G013060.1 Csa02g01090 1090
2 10631192 10633642 + CsaV3_2G013070.1 Csa02g01091 1091
3 9622192 9629433 + CsaV3_3G012580.1 Csa03g01258 1258
3 9638128 9641016 + CsaV3_3G012590.1 Csa03g01259 1259
3 9643519 9645574 + CsaV3_3G012600.1 Csa03g01260 1260
3 9646176 9651152 - CsaV3_3G012610.1 Csa03g01261 1261
3 9651697 9654222 + CsaV3_3G012620.1 Csa03g01262 1262
3 3317315 3319394 - Hsped.03g02540.1 Hepe03g0254 254
3 3347279 3360618 - Hsped.03g02570.1 Hepe03g0257 257
12 39201788 39209735 + Lag0016579.1 Lac12g2207 2207
13 3822476 3829883 - Maker00024006 Lcy13g0343 343
5 24315404 24320472 - Lsi05G016680.1 Lsi05g01668 1668
5 24320545 24324980 + Lsi05G016700.1 Lsi05g01670 1670
5 24325771 24327693 - Lsi05G016710.1 Lsi05g01671 1671
5 24329694 24334774 - Lsi05G016730.1 Lsi05g01673 1673
5 24347495 24352927 - Lsi05G016740.1 Lsi05g01674 1674
9 20280009 20292461 + Lsi09G012620.1 Lsi09g01262 1262
9 20303550 20304929 - Lsi09G012630.1 Lsi09g01263 1263
9 20311143 20312879 + Lsi09G012640.1 Lsi09g01264 1264
9 10802824 10821647 + Sed0026279.1 Sed09g0707 707
6 76920750 76932716 + Tan0016496.2 Tan06g2444 2444
5 6611321 6615958 + Vvi5g609 Vvi5g609 609
5 6616101 6623426 - Vvi5g610 Vvi5g610 610
5 6624064 6632689 + Vvi5g611 Vvi5g611 611
5 6635386 6637839 + Vvi5g612 Vvi5g612 612
5 6644453 6647555 - Vvi5g613 Vvi5g613 613
5 6654004 6654965 + Vvi5g614 Vvi5g614 614
5 6654967 6660852 - Vvi5g615 Vvi5g615 615
5 6661341 6682869 - Vvi5g616 Vvi5g616 616
5 6694356 6698226 - Vvi5g617 Vvi5g617 617
5 6700722 6711313 - Vvi5g618 Vvi5g618 618
       

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