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
Vvi3g166 . . . Bda08g00990 . . Bma05g00371 . . . Cma02g00261 Cma20g00748 . Car20g00649 . . . . . . . . . . . . . . . . . . . . . Lsi10g00498 . Chy11g00252 . . . . . . Bpe05g00291 . . . Cmo02g00258 Cmo20g00744 . . . . Cpe16g00320 Cpe05g01370 Bhi10g01842 Tan05g1126 . . . . . Cla02g01171 Cam02g1250 Cec02g1260 Cco02g1298 Clacu02g1232 Cmu02g1198 Cre02g1514 . Csa02g01396 . Cme11g00377
Vvi3g167 . . . Bda08g00988 . Bpe12g00124 Bma05g00372 . Cmo19g00751 Cmo11g01743 Cma02g00262 . . . Sed04g3849 Cpe04g00595 Cpe15g00596 Bhi05g01709 Tan02g0679 Cmetu01g0520 . Hepe02g0422 . . Cla02g00424 Cam02g0433 Cec02g0431 Cco02g0449 Clacu02g0434 Cmu02g0429 Cre02g0763 . Cone8ag1288 . Cone10ag1176 Lsi10g00499 Csa07g00105 Chy11g00251 Cme01g01258 . Blo13g00502 Bda15g01031 . . Bpe05g00292 . . Sed05g3503 Cmo02g00259 . Cma11g01378 Cma19g00742 . Car19g00571 . Cpe05g01369 Bhi10g01840 Tan05g1124 Cmetu11g0635 . Hepe08g0298 . . Cla02g01172 Cam02g1251 Cec02g1261 Cco02g1299 Clacu02g1233 Cmu02g1199 Cre02g1515 Lsi11g01203 Csa02g01397 Chy01g00678 Cme11g00376
Vvi3g168 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1235 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g169 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo13g00501 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g170 . . . . . . . . . Cmo11g01745 . . . . . Cpe04g00597 . . . . . . . . Cla02g00422 Cam02g0431 Cec02g0429 Cco02g0447 Clacu02g0432 Cmu02g0427 Cre02g0761 . . . . . . . Cme01g01256 Blo04g00571 . . Bda14g00619 Bpe15g00809 . Bma03g00612 . . . . . . . . . . . . . . . . . . . . . . . . Lsi11g01205 . Chy01g00676 .
Vvi3g171 . . . . . . . . Cmo19g00752 . . . . . . . Cpe15g00597 . . . . . . . . . . . . . . . Cone8ag1289 . . . Csa07g00106 . . . . . . . . . . . . . Cma11g01377 Cma19g00743 . Car19g00572 . . . . . . . . . . . . . . . . . . . .
Vvi3g172 . . . Bda08g00987 . Bpe12g00125 Bma05g00373 . Cmo19g00753 Cmo11g01746 . . . . . Cpe04g00598 Cpe15g00598 Bhi05g01707 Tan02g2063 . . Hepe02g0419 . . Cla02g00420 Cam02g0429 Cec02g0427 Cco02g0445 Clacu02g0430 Cmu02g0425 Cre02g0759 . . . . . Csa07g00108 . Cme01g01253 Blo04g00573 Blo13g00500 Bda15g01030 Bda14g00620 Bpe15g00808 . Bma03g00613 Bma08g00749 . . . Cma11g01375 Cma19g00744 . . . . . . . . . . . Cla02g01174 Cam02g1253 Cec02g1263 Cco02g1301 Clacu02g1235 Cmu02g1201 Cre02g1517 Lsi11g01207 . Chy01g00675 .
Vvi3g173 . . . . . . . . . . Cma02g00265 Cma20g00746 . Car20g00648 . . . . . . . . . . . . . . . . . . . . . Lsi10g00501 . Chy11g00249 . . . . . . . . . Sed01g0188 Cmo02g00261 Cmo20g00743 . . . . Cpe16g00321 Cpe05g01367 Bhi10g01837 Tan05g1122 Cmetu11g0186 . Hepe08g0301 . . Cla02g01175 Cam02g1254 . Cco02g1302 Clacu02g1236 Cmu02g1203 Cre02g1518 . Csa02g01399 . Cme11g00374
Vvi3g174 . . . . . . . . Cmo19g00756 Cmo11g01748 . . . . Sed05g2587 Cpe04g00600 Cpe15g00600 Bhi05g01697 Tan02g0669 Cmetu01g2019 . Hepe02g0417 . . Cla02g00417 Cam02g0427 Cec02g0425 Cco02g0443 Clacu02g0428 Cmu02g0423 Cre02g0757 . . . . . . . . Blo04g00576 . . Bda14g00621 Bpe15g00806 . Bma03g00615 . . . . Cma11g01372 Cma19g00746 . Car19g00575 . . . . . . . . . . . . . . . . Lsi11g01209 . . .
Vvi3g175 . . . . . . . . . . . Cma20g00745 . Car20g00647 . . . . . . . . . . . . . . . . . . Cone8ag1293 . . Lsi10g00502 . Chy11g00247 . . . . Bda14g00622 Bpe15g00805 . . . Sed01g0184 . Cmo20g00742 . . . . Cpe16g00322 . Bhi10g01832 Tan05g1117 Cmetu11g1432 . Hepe08g0303 . . Cla02g01176 Cam02g1255 Cec02g1264 Cco02g1303 Clacu02g1237 Cmu02g1204 Cre02g1519 . Csa02g01401 . Cme11g00372
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 19958937 19959983 - Bda029663.1 Bda08g00987 987
8 20122396 20124624 + Bda029664.2 Bda08g00988 988
8 20200665 20203083 - Bda029665.2 Bda08g00990 990
14 4656836 4658172 + Bda027374.1 Bda14g00619 619
14 4659157 4665478 + Bda027375.1 Bda14g00620 620
14 4668395 4673818 + Bda027376.1 Bda14g00621 621
14 4674083 4674678 - Bda027377.1 Bda14g00622 622
15 19294203 19295190 - Bda013015.1 Bda15g01030 1030
15 19299394 19301071 + Bda013016.1 Bda15g01031 1031
5 55300130 55303873 - XM_039032728.1 Bhi05g01697 1697
5 55341197 55343475 - XM_039033114.1 Bhi05g01707 1707
5 55383271 55384699 + XM_039031288.1 Bhi05g01709 1709
10 45805506 45808194 + XM_039046699.1 Bhi10g01832 1832
10 45905198 45908629 + XM_039044940.1 Bhi10g01837 1837
10 45936719 45941221 + XM_039045451.1 Bhi10g01840 1840
10 45941747 45945667 - XM_039045456.1 Bhi10g01842 1842
4 4921476 4922825 + BLOR13483 Blo04g00571 571
4 4927713 4928799 + BLOR13485 Blo04g00573 573
4 4936815 4938746 + BLOR13488 Blo04g00576 576
13 26328730 26329713 - BLOR05781 Blo13g00500 500
13 26333179 26334279 - BLOR05782 Blo13g00501 501
13 26343840 26345684 + BLOR05783 Blo13g00502 502
3 5028677 5030025 + Bma016902.1 Bma03g00612 612
3 5030967 5037266 + Bma016903.1 Bma03g00613 613
3 5045522 5047994 + Bma016905.1 Bma03g00615 615
5 11693258 11695766 + Bma021190.1 Bma05g00371 371
5 11696815 11700008 - Bma021191.1 Bma05g00372 372
5 11918162 11919290 + Bma021192.1 Bma05g00373 373
8 43945857 43948464 - Bma028124.1 Bma08g00749 749
5 16124865 16127291 + Bpe025804 Bpe05g00291 291
5 16128411 16130593 - Bpe017705.1 Bpe05g00292 292
12 877445 879119 - Bpe005364.1 Bpe12g00124 124
12 883734 884721 + Bpe005365.2 Bpe12g00125 125
15 18247473 18248134 + Bpe001731.1 Bpe15g00805 805
15 18248485 18254072 - Bpe001732.1 Bpe15g00806 806
15 18257018 18263307 - Bpe001734.1 Bpe15g00808 808
15 18264316 18265599 - Bpe001735.1 Bpe15g00809 809
2 4987763 4991245 - CaPI482276_02g004270.1 Cam02g0427 427
2 5011142 5012847 - CaPI482276_02g004290.1 Cam02g0429 429
2 5029254 5030575 - CaPI482276_02g004310.1 Cam02g0431 431
2 5046231 5048416 + CaPI482276_02g004330.1 Cam02g0433 433
2 24713809 24717672 + CaPI482276_02g012500.1 Cam02g1250 1250
2 24718609 24722136 - CaPI482276_02g012510.1 Cam02g1251 1251
2 24750848 24754280 + CaPI482276_02g012530.1 Cam02g1253 1253
2 24755744 24764424 - CaPI482276_02g012540.1 Cam02g1254 1254
2 24770748 24772177 - CaPI482276_02g012550.1 Cam02g1255 1255
19 7184691 7187021 - Carg19348-RA Car19g00571 571
19 7188124 7191110 + Carg19347-RA Car19g00572 572
19 7205032 7208788 + Carg19345-RA Car19g00575 575
20 3645807 3647535 + Carg16167-RA Car20g00647 647
20 3650730 3658910 + Carg16168-RA Car20g00648 648
20 3658905 3663966 - Carg16169-RA Car20g00649 649
2 3993208 3996690 - CcPI632755_02g004430.1 Cco02g0443 443
2 4016780 4018543 - CcPI632755_02g004450.1 Cco02g0445 445
2 4034818 4036060 - CcPI632755_02g004470.1 Cco02g0447 447
2 4051696 4053881 + CcPI632755_02g004490.1 Cco02g0449 449
2 24690484 24702205 + CcPI632755_02g012980.1 Cco02g1298 1298
2 24703100 24706625 - CcPI632755_02g012990.1 Cco02g1299 1299
2 24748590 24752094 + CcPI632755_02g013010.1 Cco02g1301 1301
2 24752939 24761606 - CcPI632755_02g013020.1 Cco02g1302 1302
2 24768592 24770757 - CcPI632755_02g013030.1 Cco02g1303 1303
2 4003926 4007408 - CePI673135_02g004250.1 Cec02g0425 425
2 4029701 4031434 - CePI673135_02g004270.1 Cec02g0427 427
2 4047859 4049105 - CePI673135_02g004290.1 Cec02g0429 429
2 4064803 4066959 + CePI673135_02g004310.1 Cec02g0431 431
2 29210088 29213988 + CePI673135_02g012600.1 Cec02g1260 1260
2 29214900 29218418 - CePI673135_02g012610.1 Cec02g1261 1261
2 29263697 29267152 + CePI673135_02g012630.1 Cec02g1263 1263
2 29268625 29286075 - CePI673135_02g012640.1 Cec02g1264 1264
1 4879412 4880603 - Chy1G006750.1 Chy01g00675 675
1 4887697 4900835 - Chy1G006760.1 Chy01g00676 676
1 4911980 4914380 + Chy1G006780.1 Chy01g00678 678
11 2336000 2342743 + Chy11G188270.1 Chy11g00247 247
11 2349420 2351291 + Chy11G188290.1 Chy11g00249 249
11 2365235 2368869 + Chy11G188310.1 Chy11g00251 251
11 2369648 2372082 - Chy11G188320.1 Chy11g00252 252
2 3855260 3858742 - ClG42_02g0042800.10 Clacu02g0428 428
2 3878375 3880096 - ClG42_02g0043000.10 Clacu02g0430 430
2 3896447 3897692 - ClG42_02g0043200.10 Clacu02g0432 432
2 3912467 3914650 + ClG42_02g0043400.10 Clacu02g0434 434
2 24880711 24883540 + ClG42_02g0123200.10 Clacu02g1232 1232
2 24884857 24888358 - ClG42_02g0123300.10 Clacu02g1233 1233
2 24916977 24920442 + ClG42_02g0123500.10 Clacu02g1235 1235
2 24921275 24931933 - ClG42_02g0123600.10 Clacu02g1236 1236
2 24938227 24940403 - ClG42_02g0123700.10 Clacu02g1237 1237
2 4095436 4098541 - ClCG02G004010.2 Cla02g00417 417
2 4119110 4121077 - ClCG02G004030.1 Cla02g00420 420
2 4137253 4138777 - ClCG02G004050.1 Cla02g00422 422
2 4146819 4155630 + ClCG02G004070.2 Cla02g00424 424
2 25181949 25185527 + ClCG02G011950.2 Cla02g01171 1171
2 25186790 25190514 - ClCG02G011960.1 Cla02g01172 1172
2 25220123 25223588 + ClCG02G011980.1 Cla02g01174 1174
2 25225354 25235036 - ClCG02G011990.2 Cla02g01175 1175
2 25241872 25243479 - ClCG02G012000.2 Cla02g01176 1176
2 1180526 1184391 + CmaCh02G002610.1 Cma02g00261 261
2 1184456 1188107 - CmaCh02G002620.1 Cma02g00262 262
2 1198444 1200245 - CmaCh02G002650.1 Cma02g00265 265
11 9069112 9071853 - CmaCh11G013720.1 Cma11g01372 1372
11 9078606 9080113 - CmaCh11G013750.1 Cma11g01375 1375
11 9091077 9093936 - CmaCh11G013770.1 Cma11g01377 1377
11 9096447 9099677 + CmaCh11G013780.1 Cma11g01378 1378
19 7415131 7417979 - CmaCh19G007420.1 Cma19g00742 742
19 7418862 7422158 + CmaCh19G007430.1 Cma19g00743 743
19 7425701 7427079 + CmaCh19G007440.1 Cma19g00744 744
19 7435816 7439472 + CmaCh19G007460.1 Cma19g00746 746
20 3496253 3498326 + CmaCh20G007450.1 Cma20g00745 745
20 3501067 3507432 + CmaCh20G007460.1 Cma20g00746 746
20 3508988 3513284 - CmaCh20G007480.1 Cma20g00748 748
1 15927926 15929948 - MELO3C013347.2.1 Cme01g01253 1253
1 15949377 15951310 - MELO3C013349.2.1 Cme01g01256 1256
1 15959452 15962256 + MELO3C013351.2.1 Cme01g01258 1258
11 3770170 3774396 + MELO3C034703.2.1 Cme11g00372 372
11 3784250 3787515 + MELO3C020824.2.1 Cme11g00374 374
11 3799943 3803941 + MELO3C020822.2.1 Cme11g00376 376
11 3804384 3807865 - MELO3C020821.2.1 Cme11g00377 377
1 5218365 5221423 + PI0021497.1 Cmetu01g0520 520
1 5172505 5173861 - PI0029034.1 Cmetu01g2019 2019
11 28652570 28655986 - PI0003172.1 Cmetu11g0186 186
11 28635962 28640050 - PI0020561.1 Cmetu11g0635 635
11 28666594 28667931 - PI0022251.1 Cmetu11g1432 1432
2 1237476 1240550 + CmoCh02G002580.1 Cmo02g00258 258
2 1240617 1244338 - CmoCh02G002590.1 Cmo02g00259 259
2 1253118 1255988 - CmoCh02G002610.1 Cmo02g00261 261
11 12304062 12307140 - CmoCh11G017430.1 Cmo11g01743 1743
11 12313607 12315052 + CmoCh11G017450.1 Cmo11g01745 1745
11 12320740 12322234 + CmoCh11G017460.1 Cmo11g01746 1746
11 12328919 12331641 + CmoCh11G017480.1 Cmo11g01748 1748
19 7672674 7675287 - CmoCh19G007510.1 Cmo19g00751 751
19 7676439 7679668 + CmoCh19G007520.1 Cmo19g00752 752
19 7683024 7684429 + CmoCh19G007530.1 Cmo19g00753 753
19 7694317 7697983 + CmoCh19G007560.1 Cmo19g00756 756
20 3708718 3710604 + CmoCh20G007420.1 Cmo20g00742 742
20 3713610 3721063 + CmoCh20G007430.1 Cmo20g00743 743
20 3721807 3731566 - CmoCh20G007440.1 Cmo20g00744 744
2 3851255 3854289 - CmPI595203_02g004230.1 Cmu02g0423 423
2 3874388 3876109 - CmPI595203_02g004250.1 Cmu02g0425 425
2 3892478 3893723 - CmPI595203_02g004270.1 Cmu02g0427 427
2 3908498 3910681 + CmPI595203_02g004290.1 Cmu02g0429 429
2 24748213 24751454 + CmPI595203_02g011980.1 Cmu02g1198 1198
2 24752356 24755859 - CmPI595203_02g011990.1 Cmu02g1199 1199
2 24784472 24787928 + CmPI595203_02g012010.1 Cmu02g1201 1201
2 24796001 24799436 - CmPI595203_02g012030.1 Cmu02g1203 1203
2 24805781 24807959 - CmPI595203_02g012040.1 Cmu02g1204 1204
8 10576234 10577946 - Conep08aG0132600.1 Cone8ag1288 1288
8 10578260 10579915 + Conep08aG0132700.1 Cone8ag1289 1289
8 10595574 10596435 - Conep08aG0133100.1 Cone8ag1293 1293
10 8574811 8579919 + Conep10aG0121100.1 Cone10ag1176 1176
12 9565752 9568831 + Conep12aG0127500.1 Cone12ag1235 1235
4 6275219 6278251 - Cp4.1LG04g04740.1 Cpe04g00595 595
4 6284553 6285965 + Cp4.1LG04g04850.1 Cpe04g00597 597
4 6291765 6293313 + Cp4.1LG04g04870.1 Cpe04g00598 598
4 6299847 6302922 + Cp4.1LG04g04890.1 Cpe04g00600 600
5 9615257 9622201 + Cp4.1LG05g13620.1 Cpe05g01367 1367
5 9631073 9635450 + Cp4.1LG05g13590.1 Cpe05g01369 1369
5 9634048 9639038 - Cp4.1LG05g13640.1 Cpe05g01370 1370
15 6712407 6716817 - Cp4.1LG15g05940.1 Cpe15g00596 596
15 6717855 6720118 + Cp4.1LG15g05930.1 Cpe15g00597 597
15 6724194 6725663 + Cp4.1LG15g05890.1 Cpe15g00598 598
15 6735586 6739470 + Cp4.1LG15g05920.1 Cpe15g00600 600
16 5053452 5058412 + Cp4.1LG16g03200.1 Cpe16g00320 320
16 5059605 5067287 - Cp4.1LG16g03260.1 Cpe16g00321 321
16 5070195 5082100 - Cp4.1LG16g03270.1 Cpe16g00322 322
2 4419432 4422913 - CrPI670011_02g007570.1 Cre02g0757 757
2 4443352 4445128 - CrPI670011_02g007590.1 Cre02g0759 759
2 4460609 4461854 - CrPI670011_02g007610.1 Cre02g0761 761
2 4478789 4480998 + CrPI670011_02g007630.1 Cre02g0763 763
2 27377422 27381336 + CrPI670011_02g015140.1 Cre02g1514 1514
2 27382296 27385819 - CrPI670011_02g015150.1 Cre02g1515 1515
2 27425297 27428759 + CrPI670011_02g015170.1 Cre02g1517 1517
2 27430606 27438967 - CrPI670011_02g015180.1 Cre02g1518 1518
2 27445282 27446780 - CrPI670011_02g015190.1 Cre02g1519 1519
2 13353720 13357327 + CsaV3_2G016120.1 Csa02g01396 1396
2 13357653 13361712 - CsaV3_2G016130.1 Csa02g01397 1397
2 13374853 13378106 - CsaV3_2G016150.1 Csa02g01399 1399
2 13388316 13390694 - CsaV3_2G016170.1 Csa02g01401 1401
7 940337 943499 - CsaV3_7G001050.1 Csa07g00105 105
7 947346 951152 + CsaV3_7G001060.1 Csa07g00106 106
7 967881 969569 + CsaV3_7G001080.1 Csa07g00108 108
2 3976085 3979850 - Hsped.02g04170.1 Hepe02g0417 417
2 3998850 4000247 - Hsped.02g04190.1 Hepe02g0419 419
2 4030597 4033610 + Hsped.02g04220.1 Hepe02g0422 422
8 2686379 2690593 - Hsped.08g02980.1 Hepe08g0298 298
8 2709026 2711797 - Hsped.08g03010.1 Hepe08g0301 301
8 2725588 2727036 - Hsped.08g03030.1 Hepe08g0303 303
10 7140498 7144389 + Lsi10G004980.1 Lsi10g00498 498
10 7144691 7148835 - Lsi10G004990.1 Lsi10g00499 499
10 7163006 7171668 - Lsi10G005010.1 Lsi10g00501 501
10 7177540 7181325 - Lsi10G005020.1 Lsi10g00502 502
11 20551814 20554576 - Lsi11G012030.1 Lsi11g01203 1203
11 20578346 20579998 + Lsi11G012050.1 Lsi11g01205 1205
11 20597963 20600278 + Lsi11G012070.1 Lsi11g01207 1207
11 20620419 20630270 + Lsi11G012090.1 Lsi11g01209 1209
1 1480847 1482190 + Sed0025670.1 Sed01g0184 184
1 1484803 1488267 + Sed0021554.4 Sed01g0188 188
4 46860191 46863439 + Sed0007413.1 Sed04g3849 3849
5 37614620 37617552 + Sed0005157.1 Sed05g2587 2587
5 43705946 43710553 - Sed0006688.1 Sed05g3503 3503
2 6211997 6214638 - Tan0017931.1 Tan02g0669 669
2 6348431 6350535 + Tan0001614.1 Tan02g0679 679
2 90094186 90098673 + Tan0015538.3 Tan02g2063 2063
5 10019508 10021231 + Tan0018273.1 Tan05g1117 1117
5 10077459 10079351 + Tan0007073.1 Tan05g1122 1122
5 10114782 10118931 + Tan0017929.1 Tan05g1124 1124
5 10118942 10123039 - Tan0004947.2 Tan05g1126 1126
3 1715842 1721233 + Vvi3g166 Vvi3g166 166
3 1722123 1725654 - Vvi3g167 Vvi3g167 167
3 1726992 1730564 - Vvi3g168 Vvi3g168 168
3 1740699 1746162 - Vvi3g169 Vvi3g169 169
3 1746494 1748076 - Vvi3g170 Vvi3g170 170
3 1749590 1753021 - Vvi3g171 Vvi3g171 171
3 1760910 1762467 + Vvi3g172 Vvi3g172 172
3 1764622 1768176 - Vvi3g173 Vvi3g173 173
3 1771004 1775813 + Vvi3g174 Vvi3g174 174
3 1776068 1776780 - Vvi3g175 Vvi3g175 175
       

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