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
Vvi3g176 . . . Bda08g00986 . . Bma05g00376 . . . Cma02g00266 Cma20g00743 . Car20g00646 . . . . . . . . . . . . . . . . . . . . . Lsi10g00503 . Chy11g00246 . . . . . . Bpe05g00294 . . Sed01g0183 Cmo02g00262 Cmo20g00741 . . . . Cpe16g00323 Cpe05g01366 Bhi10g01831 Tan05g1116 Cmetu11g0944 . Hepe08g0304 . . Cla02g01177 Cam02g1256 Cec02g1265 Cco02g1304 Clacu02g1238 Cmu02g1205 Cre02g1520 . Csa02g01402 . Cme11g00371
Vvi3g177 . . . . . . . . . . Cma02g00267 Cma20g00742 . Car20g00644 . . . . . . . . . . . . . . . . . Cone12ag1239 Cone8ag1294 . . Lsi10g00504 . . . . . . . . . . . . Cmo02g00263 Cmo20g00740 . . . . . Cpe05g01365 Bhi10g01829 . . . Hepe08g0305 . . Cla02g01178 Cam02g1257 Cec02g1266 Cco02g1305 Clacu02g1239 Cmu02g1206 Cre02g1521 . Csa02g01403 . Cme11g00370
Vvi3g178 . . . . . . . . . Cmo11g01749 . . . . Sed05g3908 Cpe04g00601 . Bhi05g01696 Tan02g0668 Cmetu01g1432 . Hepe02g0416 . . Cla02g00416 Cam02g0426 Cec02g0424 Cco02g0442 Clacu02g0427 Cmu02g0422 Cre02g0756 . . Cone3ag0958 Cone10ag1231 . Csa07g00111 . Cme01g01251 . . . . . . . . . . . Cma11g01369 . . . . . . . . . . . . . . . . . . . Lsi11g01211 . Chy01g00672 .
Vvi3g179 . . . . . Bpe12g00127 . . Cmo19g00757 Cmo11g01750 . . . . . Cpe04g00602 Cpe15g00601 Bhi05g01695 Tan02g0667 . . Hepe02g0415 . . Cla02g00415 Cam02g0425 Cec02g0423 Cco02g0441 Clacu02g0426 Cmu02g0421 Cre02g0755 . . . . . Csa07g00112 . Cme01g01250 . Blo13g00498 Bda15g01028 . . . . Bma08g00613 . . . Cma11g01368 . . Car19g00576 . . . . . . . . . . . . . . . . . . Chy01g00671 .
Vvi3g180 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo04g00603 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g181 . . . . . . . . Cmo19g00759 . . . . . Sed04g3841 . Cpe15g00602 Bhi05g01693 Tan02g0663 Cmetu01g2493 . Hepe02g0414 . . Cla02g00414 Cam02g0424 Cec02g0422 Cco02g0440 Clacu02g0425 Cmu02g0420 Cre02g0754 Cone12ag1241 Cone8ag1296 . . . Csa07g00113 . Cme01g01246 Blo04g00580 . . Bda14g00623 Bpe15g00804 . . . . . . . Cma19g00748 . Car19g00578 . . . . . . . . . . . . . . . . Lsi11g01212 . Chy01g00670 .
Vvi3g182 . . . . . . . . Cmo19g00760 . . . . . Sed05g2244 . Cpe15g00603 Bhi05g01692 Tan02g0662 Cmetu01g1510 . . . . Cla02g00413 Cam02g0423 Cec02g0421 Cco02g0439 Clacu02g0424 Cmu02g0419 Cre02g0753 . Cone8ag1297 . . . Csa07g00114 . Cme01g01245 Blo04g00581 . . . . . . . . . . . . . Car19g00580 . . . . . . . . . . . . . . . . . . Chy01g00669 .
Vvi3g183 . . . Bda08g00985 . . Bma05g00377 . . . . . . . Sed05g2245 . . Bhi05g01691 Tan02g0661 Cmetu01g1207 . Hepe02g0413 . . Cla02g00412 Cam02g0421 Cec02g0420 Cco02g0438 Clacu02g0423 Cmu02g0418 Cre02g0752 Cone12ag1242 Cone8ag1298 . . . Csa07g00115 . Cme01g01244 . . . . . . . . . . . . . . Car19g00582 . . . . . . . . . . . . . . . . . . Chy01g00667 .
Vvi3g184 . . . . . . . . Cmo19g00761 . . . . . . . Cpe15g00604 Bhi05g01690 . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe05g00295 . . . . . . . . . . . . . . . . . . . . . . . . . Lsi11g01213 . . .
Vvi3g185 . . . . . . . . . . Cma02g00268 Cma20g00741 . Car20g00643 . . . . . . . . . . . . . . . . . . Cone8ag1299 . . Lsi10g00505 . Chy11g00245 . . . . . . . . . Sed01g0181 Cmo02g00265 Cmo20g00739 . . . . Cpe16g00324 Cpe05g01364 Bhi10g01827 Tan05g1113 Cmetu11g1096 . Hepe08g0306 . . Cla02g01179 Cam02g1258 Cec02g1267 Cco02g1307 Clacu02g1240 Cmu02g1207 Cre02g1522 . Csa02g01404 . Cme11g01081
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 19897025 19915539 + Bda029659.2 Bda08g00985 985
8 19917832 19918290 - Bda029660.1 Bda08g00986 986
14 4675049 4676840 - Bda027378.1 Bda14g00623 623
15 19241049 19244081 + Bda013010.1 Bda15g01028 1028
5 55167755 55189220 + XM_039031586.1 Bhi05g01690 1690
5 55167759 55189220 + XM_039031587.1 Bhi05g01691 1691
5 55197935 55200991 + XM_039032987.1 Bhi05g01692 1692
5 55211317 55217340 + XM_039031801.1 Bhi05g01693 1693
5 55256342 55259680 + XM_039033023.1 Bhi05g01695 1695
5 55260449 55263103 - XM_039031515.1 Bhi05g01696 1696
10 45742872 45756032 + XM_039046110.1 Bhi10g01827 1827
10 45792101 45801595 + XM_039046695.1 Bhi10g01829 1829
10 45804356 45805206 - XM_039046700.1 Bhi10g01831 1831
4 4999138 4999629 - BLOR13492 Blo04g00580 580
4 5000199 5001632 + BLOR13493 Blo04g00581 581
4 5206603 5211800 + BLOR13515 Blo04g00603 603
13 26263782 26280599 + BLOR05779 Blo13g00498 498
5 11977697 11978155 + Bma021196.1 Bma05g00376 376
5 11980763 11992559 - Bma021197.1 Bma05g00377 377
8 38581482 38584504 + Bma027919.1 Bma08g00613 613
5 16213376 16213834 + Bpe017708.1 Bpe05g00294 294
5 16216596 16240483 - Bpe017709.1 Bpe05g00295 295
12 907090 910140 - Bpe005367.1 Bpe12g00127 127
15 18245289 18247097 + Bpe001730.1 Bpe15g00804 804
2 4939064 4951124 + CaPI482276_02g004210.1 Cam02g0421 421
2 4962229 4968592 + CaPI482276_02g004230.1 Cam02g0423 423
2 4971315 4976591 + CaPI482276_02g004240.1 Cam02g0424 424
2 4978902 4981640 + CaPI482276_02g004250.1 Cam02g0425 425
2 4983831 4986204 - CaPI482276_02g004260.1 Cam02g0426 426
2 24774483 24774923 + CaPI482276_02g012560.1 Cam02g1256 1256
2 24779581 24788312 - CaPI482276_02g012570.1 Cam02g1257 1257
2 24793678 24804653 - CaPI482276_02g012580.1 Cam02g1258 1258
19 7210384 7213428 - Carg19343-RA Car19g00576 576
19 7235101 7235929 - Carg25767-RA Car19g00578 578
19 7239626 7242534 - Carg25765-RA Car19g00580 580
19 7250317 7254344 - Carg25763-RA Car19g00582 582
20 3628387 3634036 + Carg16163-RA Car20g00643 643
20 3635454 3642814 + Carg16164-RA Car20g00644 644
20 3644362 3644799 - Carg16166-RA Car20g00646 646
2 3943050 3955092 + CcPI632755_02g004380.1 Cco02g0438 438
2 3966550 3969594 + CcPI632755_02g004390.1 Cco02g0439 439
2 3969776 3981813 + CcPI632755_02g004400.1 Cco02g0440 440
2 3984225 3986964 + CcPI632755_02g004410.1 Cco02g0441 441
2 3989151 3991635 - CcPI632755_02g004420.1 Cco02g0442 442
2 24772348 24772788 + CcPI632755_02g013040.1 Cco02g1304 1304
2 24777359 24782874 - CcPI632755_02g013050.1 Cco02g1305 1305
2 24791656 24801444 - CcPI632755_02g013070.1 Cco02g1307 1307
2 3962821 3974913 + CePI673135_02g004200.1 Cec02g0420 420
2 3982369 3985705 + CePI673135_02g004210.1 Cec02g0421 421
2 3986321 3992605 + CePI673135_02g004220.1 Cec02g0422 422
2 3995059 3997799 + CePI673135_02g004230.1 Cec02g0423 423
2 4000149 4002360 - CePI673135_02g004240.1 Cec02g0424 424
2 29287905 29288345 + CePI673135_02g012650.1 Cec02g1265 1265
2 29292801 29301615 - CePI673135_02g012660.1 Cec02g1266 1266
2 29307980 29317781 - CePI673135_02g012670.1 Cec02g1267 1267
1 4814422 4826061 + Chy1G006670.1 Chy01g00667 667
1 4839478 4842029 + Chy1G006690.1 Chy01g00669 669
1 4844770 4849346 + Chy1G006700.1 Chy01g00670 670
1 4851340 4854383 + Chy1G006710.1 Chy01g00671 671
1 4855573 4857581 - Chy1G006720.1 Chy01g00672 672
11 2316394 2332099 + Chy11G188250.1 Chy11g00245 245
11 2335416 2335853 - Chy11G188260.1 Chy11g00246 246
2 3811410 3823467 + ClG42_02g0042300.10 Clacu02g0423 423
2 3833759 3837102 + ClG42_02g0042400.10 Clacu02g0424 424
2 3837706 3843941 + ClG42_02g0042500.10 Clacu02g0425 425
2 3846266 3849178 + ClG42_02g0042600.10 Clacu02g0426 426
2 3851467 3853712 - ClG42_02g0042700.10 Clacu02g0427 427
2 24941993 24942433 + ClG42_02g0123800.10 Clacu02g1238 1238
2 24946971 24955698 - ClG42_02g0123900.10 Clacu02g1239 1239
2 24961079 24970855 - ClG42_02g0124000.10 Clacu02g1240 1240
2 4050062 4064065 + ClCG02G003960.2 Cla02g00412 412
2 4073728 4077313 + ClCG02G003965.1 Cla02g00413 413
2 4073771 4084044 + ClCG02G003970.1 Cla02g00414 414
2 4086049 4089685 + ClCG02G003980.1 Cla02g00415 415
2 4091334 4094025 - ClCG02G003990.2 Cla02g00416 416
2 25245661 25246101 + ClCG02G012010.1 Cla02g01177 1177
2 25250381 25259205 - ClCG02G012020.1 Cla02g01178 1178
2 25264763 25274966 - ClCG02G012030.1 Cla02g01179 1179
2 1201977 1202435 + CmaCh02G002660.1 Cma02g00266 266
2 1204022 1213151 - CmaCh02G002670.1 Cma02g00267 267
2 1213157 1218819 - CmaCh02G002680.1 Cma02g00268 268
11 9059967 9063497 + CmaCh11G013680.1 Cma11g01368 1368
11 9063823 9067264 - CmaCh11G013690.1 Cma11g01369 1369
19 7441197 7463032 - CmaCh19G007480.1 Cma19g00748 748
20 3480104 3484847 + CmaCh20G007410.1 Cma20g00741 741
20 3484983 3493694 + CmaCh20G007420.1 Cma20g00742 742
20 3494152 3495457 - CmaCh20G007430.1 Cma20g00743 743
1 15820630 15832090 + MELO3C013338.2.1 Cme01g01244 1244
1 15836031 15837945 + MELO3C013339.2.1 Cme01g01245 1245
1 15838317 15838802 + MELO3C001148.2.1 Cme01g01246 1246
1 15884078 15887829 + MELO3C013344.2.1 Cme01g01250 1250
1 15888446 15890884 - MELO3C013345.2.1 Cme01g01251 1251
11 3758927 3767786 + MELO3C020827.2.1 Cme11g00370 370
11 3770154 3770895 - MELO3C020826.2.1 Cme11g00371 371
11 15933818 15936406 - MELO3C013532.2.1 Cme11g01081 1081
1 5139605 5148850 + PI0022518.1 Cmetu01g1207 1207
1 5167552 5170123 - PI0024024.1 Cmetu01g1432 1432
1 5152404 5155507 + PI0012546.1 Cmetu01g1510 1510
1 5158094 5161723 + PI0007331.1 Cmetu01g2493 2493
11 28668019 28669288 + PI0013137.1 Cmetu11g0944 944
11 28683009 28688986 - PI0002501.1 Cmetu11g1096 1096
2 1257197 1257655 + CmoCh02G002620.1 Cmo02g00262 262
2 1258735 1268632 - CmoCh02G002630.1 Cmo02g00263 263
2 1269690 1274952 - CmoCh02G002650.1 Cmo02g00265 265
11 12333376 12336630 + CmoCh11G017490.1 Cmo11g01749 1749
11 12337468 12340976 - CmoCh11G017500.1 Cmo11g01750 1750
19 7699578 7702890 - CmoCh19G007570.1 Cmo19g00757 757
19 7707020 7707971 - CmoCh19G007590.1 Cmo19g00759 759
19 7708639 7714547 - CmoCh19G007600.1 Cmo19g00760 760
19 7715719 7726215 - CmoCh19G007610.1 Cmo19g00761 761
20 3691206 3696860 + CmoCh20G007390.1 Cmo20g00739 739
20 3698271 3705276 + CmoCh20G007400.1 Cmo20g00740 740
20 3707078 3707515 - CmoCh20G007410.1 Cmo20g00741 741
2 3807378 3819437 + CmPI595203_02g004180.1 Cmu02g0418 418
2 3829724 3833067 + CmPI595203_02g004190.1 Cmu02g0419 419
2 3833671 3839925 + CmPI595203_02g004200.1 Cmu02g0420 420
2 3842256 3845168 + CmPI595203_02g004210.1 Cmu02g0421 421
2 3847464 3849709 - CmPI595203_02g004220.1 Cmu02g0422 422
2 24809541 24809981 + CmPI595203_02g012050.1 Cmu02g1205 1205
2 24814516 24823239 - CmPI595203_02g012060.1 Cmu02g1206 1206
2 24828625 24838391 - CmPI595203_02g012070.1 Cmu02g1207 1207
3 5318299 5320856 + Conep03aG0098900.1 Cone3ag0958 958
8 10596994 10602155 - Conep08aG0133200.1 Cone8ag1294 1294
8 10607174 10609560 - Conep08aG0133400.1 Cone8ag1296 1296
8 10610013 10612433 - Conep08aG0133500.1 Cone8ag1297 1297
8 10614734 10619801 - Conep08aG0133600.1 Cone8ag1298 1298
8 10620488 10623717 - Conep08aG0133700.1 Cone8ag1299 1299
10 9291492 9294429 - Conep10aG0126600.1 Cone10ag1231 1231
12 9584266 9590283 - Conep12aG0127900.1 Cone12ag1239 1239
12 9596016 9597693 - Conep12aG0128100.1 Cone12ag1241 1241
12 9598321 9602326 - Conep12aG0128200.1 Cone12ag1242 1242
4 6304382 6307480 + Cp4.1LG04g04830.1 Cpe04g00601 601
4 6308036 6311663 - Cp4.1LG04g04770.1 Cpe04g00602 602
5 9596779 9602763 + Cp4.1LG05g13610.1 Cpe05g01364 1364
5 9604139 9612009 + Cp4.1LG05g13630.1 Cpe05g01365 1365
5 9613853 9614311 - Cp4.1LG05g13650.1 Cpe05g01366 1366
15 6740248 6744126 - Cp4.1LG15g05990.1 Cpe15g00601 601
15 6745023 6748886 - Cp4.1LG15g06030.1 Cpe15g00602 602
15 6749761 6752681 - Cp4.1LG15g06040.1 Cpe15g00603 603
15 6753948 6765218 - Cp4.1LG15g06020.1 Cpe15g00604 604
16 5072915 5073352 + Cp4.1LG16g03150.1 Cpe16g00323 323
16 5083364 5088958 - Cp4.1LG16g03250.1 Cpe16g00324 324
2 4378409 4390518 + CrPI670011_02g007520.1 Cre02g0752 752
2 4398256 4401355 + CrPI670011_02g007530.1 Cre02g0753 753
2 4401976 4408370 + CrPI670011_02g007540.1 Cre02g0754 754
2 4410798 4413521 + CrPI670011_02g007550.1 Cre02g0755 755
2 4415818 4418036 - CrPI670011_02g007560.1 Cre02g0756 756
2 27449100 27449540 + CrPI670011_02g015200.1 Cre02g1520 1520
2 27454097 27464453 - CrPI670011_02g015210.1 Cre02g1521 1521
2 27468335 27479457 - CrPI670011_02g015220.1 Cre02g1522 1522
2 13389865 13390302 + CsaV3_2G016180.1 Csa02g01402 1402
2 13391253 13401886 - CsaV3_2G016190.1 Csa02g01403 1403
2 13403130 13408765 - CsaV3_2G016200.1 Csa02g01404 1404
7 988938 991465 + CsaV3_7G001110.1 Csa07g00111 111
7 991763 995805 - CsaV3_7G001120.1 Csa07g00112 112
7 996281 999505 - CsaV3_7G001130.1 Csa07g00113 113
7 1001240 1004386 - CsaV3_7G001140.1 Csa07g00114 114
7 1012143 1023818 - CsaV3_7G001150.1 Csa07g00115 115
2 3944863 3958008 + Hsped.02g04130.1 Hepe02g0413 413
2 3960959 3964651 + Hsped.02g04140.1 Hepe02g0414 414
2 3966556 3970024 + Hsped.02g04150.1 Hepe02g0415 415
2 3970983 3973934 - Hsped.02g04160.1 Hepe02g0416 416
8 2727775 2729078 + Hsped.08g03040.1 Hepe08g0304 304
8 2730306 2738413 - Hsped.08g03050.1 Hepe08g0305 305
8 2740327 2746173 - Hsped.08g03060.1 Hepe08g0306 306
10 7183023 7183460 + Lsi10G005030.1 Lsi10g00503 503
10 7184770 7196277 - Lsi10G005040.1 Lsi10g00504 504
10 7199511 7205260 - Lsi10G005050.1 Lsi10g00505 505
11 20632189 20634495 + Lsi11G012110.1 Lsi11g01211 1211
11 20635913 20668146 - Lsi11G012120.1 Lsi11g01212 1212
11 20672030 20681053 - Lsi11G012130.1 Lsi11g01213 1213
1 1457244 1465062 + Sed0001500.1 Sed01g0181 181
1 1478885 1479859 - Sed0015003.1 Sed01g0183 183
4 46806206 46810706 + Sed0022161.1 Sed04g3841 3841
5 35107724 35111136 - Sed0001217.3 Sed05g2244 2244
5 35116793 35129581 - Sed0017736.1 Sed05g2245 2245
5 46465031 46475058 + Sed0018246.1 Sed05g3908 3908
2 6127847 6143137 + Tan0001503.1 Tan02g0661 661
2 6145167 6148405 + Tan0022822.1 Tan02g0662 662
2 6180872 6188246 + Tan0017272.1 Tan02g0663 663
2 6192451 6195734 + Tan0014240.4 Tan02g0667 667
2 6198142 6201119 - Tan0022050.1 Tan02g0668 668
5 9993413 10001468 + Tan0017979.1 Tan05g1113 1113
5 10014836 10015729 - Tan0001446.1 Tan05g1116 1116
3 1778144 1786685 + Vvi3g176 Vvi3g176 176
3 1786699 1794856 - Vvi3g177 Vvi3g177 177
3 1795805 1801225 + Vvi3g178 Vvi3g178 178
3 1801662 1806587 - Vvi3g179 Vvi3g179 179
3 1808725 1814064 - Vvi3g180 Vvi3g180 180
3 1816068 1818709 - Vvi3g181 Vvi3g181 181
3 1818709 1822094 - Vvi3g182 Vvi3g182 182
3 1824919 1835490 - Vvi3g183 Vvi3g183 183
3 1836019 1843230 - Vvi3g184 Vvi3g184 184
3 1843278 1854839 - Vvi3g185 Vvi3g185 185
       

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