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
Vvi5g439 . . . . . Bpe14g01319 . . Cmo08g01138 Cmo17g00253 Cma06g01430 Cma14g01680 Car06g01232 Car14g01514 Sed02g1266 Cpe08g00245 Cpe03g01418 Bhi01g00853 Tan10g0882 Cmetu06g2649 Lac12g2323 Hepe05g1526 . Lcy11g1512 Cla06g00549 Cam06g0592 Cec06g0589 Cco06g0597 Clacu06g0578 Cmu06g0573 Cre06g1339 . . Cone7ag0219 Cone4ag0211 Lsi05g01451 . . Cme06g00637 Blo02g00590 Blo07g00208 Bda11g00563 . . Bpe13g00620 Bma02g00692 Bma06g01542 . Cmo06g01433 Cmo14g01725 . Cma17g00267 Car08g01043 Car17g00241 Cpe12g00222 Cpe17g00129 Bhi12g01809 . . . . . . Cla05g00574 Cam05g0629 Cec05g0640 Cco05g0634 Clacu05g0625 Cmu05g0593 Cre05g0661 Lsi09g01353 Csa03g01363 Chy06g00607 Cme11g01931
Vvi5g440 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g441 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag0756 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g442 . . . . . Bpe14g01317 . . . . . Cma14g01681 . Car14g01515 . . Cpe03g01419 Bhi01g00850 . . . . . . . . . . . . . . . Cone7ag0220 Cone4ag0212 Lsi05g01449 . . Cme06g00636 . . . . . . Bma02g00691 . . . Cmo14g01726 . . . . . . . . . . . . . Cla05g00573 Cam05g0628 Cec05g0639 Cco05g0633 Clacu05g0624 Cmu05g0592 Cre05g0660 . Csa03g01361 Chy06g00606 .
Vvi5g443 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g444 . . . . . . . . Cmo08g01137 Cmo17g00252 . . . . . . . . . . . . . . Cla06g00550 Cam06g0593 Cec06g0590 Cco06g0598 Clacu06g0579 Cmu06g0574 Cre06g1340 Cone14ag0827 . . . . . . . . . . . . . . . . . . Cma08g01165 Cma17g00266 Car08g01042 Car17g00240 Cpe12g00221 Cpe17g00130 Bhi12g01811 . . . . . . . . . . . . . Lsi09g01350 . . Cme11g01930
Vvi5g445 . . . . . Bpe14g01316 . . . . . Cma14g01683 . Car14g01517 Sed02g1264 . Cpe03g01420 Bhi01g00848 Tan10g0877 Cmetu06g2420 . Hepe05g1528 . Lcy11g1514 . . . . . . . Cone14ag0828 . . . Lsi05g01447 . . Cme06g00634 . . . . . . Bma02g00690 . . Cmo06g01432 Cmo14g01729 . . . . . . . . . . . . . Cla05g00570 Cam05g0626 Cec05g0637 Cco05g0632 Clacu05g0622 Cmu05g0590 Cre05g0659 . Csa03g01360 Chy06g00604 .
Vvi5g446 . . . . . . . . . . Cma06g01428 . Car06g01231 . . Cpe08g00246 . . . . . . . . . . . . . . . . . . . Lsi05g01446 . . . . . Bda11g00564 . . Bpe13g00619 . Bma06g01543 . Cmo06g01431 . . . . . . . . . . . . . . Cla05g00569 Cam05g0625 Cec05g0636 Cco05g0631 Clacu05g0621 Cmu05g0589 Cre05g0658 . Csa03g01359 Chy06g00603 .
Vvi5g447 . . . . . Bpe14g01315 . . . . Cma06g01427 . . . Sed02g1262 Cpe08g00247 . Bhi01g00846 Tan10g0875 Cmetu06g2026 . . . . . . . . . . . . . . . Lsi05g01445 . . Cme06g00632 . . . . . . . . . . . . . . . . . . . . . . . . Cla05g00568 Cam05g0624 Cec05g0634 Cco05g0629 Clacu05g0620 Cmu05g0588 Cre05g0656 . Csa03g01358 Chy06g00602 .
Vvi5g448 . . . . . . . . Cmo08g01135 . . . . . . . . . . . . . . . Cla06g00551 Cam06g0594 Cec06g0592 . Clacu06g0580 Cmu06g0575 Cre06g1341 . . Cone7ag0223 Cone4ag0214 . . . . . . . . . . . . . . . Cma08g01163 Cma17g00264 Car08g01041 Car17g00238 Cpe12g00220 Cpe17g00132 Bhi12g01813 . . . . . . . . . . . . . Lsi09g01348 . . Cme11g01928
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 5843246 5844540 + Bda005301.1 Bda11g00563 563
11 5849120 5849630 + Bda005302.1 Bda11g00564 564
1 16020472 16022694 - XM_039036579.1 Bhi01g00846 846
1 16034897 16039006 - XM_039041853.1 Bhi01g00848 848
1 16042364 16047794 + XM_039022309.1 Bhi01g00850 850
1 16047891 16050960 - XM_039022312.1 Bhi01g00853 853
12 57903248 57910156 + XM_039018821.1 Bhi12g01809 1809
12 57956316 57959912 + XM_039019389.1 Bhi12g01811 1811
12 57984927 57988187 + XM_039050816.1 Bhi12g01813 1813
2 11165995 11167823 + BLOR10320 Blo02g00590 590
7 2651634 2653347 + BLOR18140 Blo07g00208 208
2 25352615 25356443 - Bma015329.2 Bma02g00690 690
2 25362094 25363779 + Bma015330.1 Bma02g00691 691
2 25548046 25550022 - Bma015331.1 Bma02g00692 692
6 51767456 51768771 + Bma024659.1 Bma06g01542 1542
6 51774024 51776509 + Bma024660.1 Bma06g01543 1543
13 13170688 13171199 - Bpe010319.1 Bpe13g00619 619
13 13176807 13178166 - Bpe010320.1 Bpe13g00620 620
14 10149369 10151190 - Bpe025555 Bpe14g01315 1315
14 10153527 10157260 - Bpe014670.1 Bpe14g01316 1316
14 10159622 10162271 + Bpe014671.3 Bpe14g01317 1317
14 10182890 10184909 - Bpe014673.1 Bpe14g01319 1319
5 5435074 5436973 - CaPI482276_05g006240.1 Cam05g0624 624
5 5442964 5443546 - CaPI482276_05g006250.1 Cam05g0625 625
5 5445704 5448906 - CaPI482276_05g006260.1 Cam05g0626 626
5 5453899 5458680 + CaPI482276_05g006280.1 Cam05g0628 628
5 5459305 5462220 - CaPI482276_05g006290.1 Cam05g0629 629
6 8050622 8055377 + CaPI482276_06g005920.1 Cam06g0592 592
6 8067311 8069894 + CaPI482276_06g005930.1 Cam06g0593 593
6 8088625 8094855 + CaPI482276_06g005940.1 Cam06g0594 594
6 8912342 8914251 - Carg17404-RA Car06g01231 1231
6 8918106 8920261 - Carg17403-RA Car06g01232 1232
8 7116466 7120159 - Carg15920-RA Car08g01041 1041
8 7121111 7124253 - Carg15921-RA Car08g01042 1042
8 7127318 7130360 - Carg15922-RA Car08g01043 1043
14 12483521 12485324 + Carg23818-RA Car14g01514 1514
14 12485484 12490408 - Carg23817-RA Car14g01515 1515
14 12493069 12496234 + Carg23815-RA Car14g01517 1517
17 1464180 1466197 - Carg05444-RA Car17g00238 238
17 1468093 1471582 - Carg05446-RA Car17g00240 240
17 1475245 1478797 - Carg05447-RA Car17g00241 241
5 5129364 5131048 - CcPI632755_05g006290.1 Cco05g0629 629
5 5137356 5138358 - CcPI632755_05g006310.1 Cco05g0631 631
5 5139520 5148724 - CcPI632755_05g006320.1 Cco05g0632 632
5 5149171 5153854 + CcPI632755_05g006330.1 Cco05g0633 633
5 5154491 5157134 - CcPI632755_05g006340.1 Cco05g0634 634
6 6497020 6501813 + CcPI632755_06g005970.1 Cco06g0597 597
6 6515513 6518140 + CcPI632755_06g005980.1 Cco06g0598 598
5 5146491 5148186 - CePI673135_05g006340.1 Cec05g0634 634
5 5154965 5155970 - CePI673135_05g006360.1 Cec05g0636 636
5 5158129 5161328 - CePI673135_05g006370.1 Cec05g0637 637
5 5165819 5170900 + CePI673135_05g006390.1 Cec05g0639 639
5 5171170 5173825 - CePI673135_05g006400.1 Cec05g0640 640
6 6580279 6587904 + CePI673135_06g005890.1 Cec06g0589 589
6 6601359 6603986 + CePI673135_06g005900.1 Cec06g0590 590
6 6619217 6621590 + CePI673135_06g005920.1 Cec06g0592 592
6 4115287 4118485 - Chy6G111300.1 Chy06g00602 602
6 4120550 4121680 - Chy6G111310.1 Chy06g00603 603
6 4123908 4127526 - Chy6G111320.1 Chy06g00604 604
6 4130988 4135181 + Chy6G111340.1 Chy06g00606 606
6 4135781 4138290 - Chy6G111350.1 Chy06g00607 607
5 5151365 5152911 - ClG42_05g0062000.10 Clacu05g0620 620
5 5158999 5159581 - ClG42_05g0062100.10 Clacu05g0621 621
5 5161740 5164944 - ClG42_05g0062200.10 Clacu05g0622 622
5 5171277 5176057 + ClG42_05g0062400.10 Clacu05g0624 624
5 5176672 5179099 - ClG42_05g0062500.10 Clacu05g0625 625
6 6598536 6603285 + ClG42_06g0057800.10 Clacu06g0578 578
6 6616445 6619025 + ClG42_06g0057900.10 Clacu06g0579 579
6 6634361 6640547 + ClG42_06g0058000.10 Clacu06g0580 580
5 5210362 5212036 - ClCG05G005330.2 Cla05g00568 568
5 5218091 5218673 - ClCG05G005340.2 Cla05g00569 569
5 5219060 5224036 - ClCG05G005350.2 Cla05g00570 570
5 5230564 5235344 + ClCG05G005360.2 Cla05g00573 573
5 5235843 5238710 - ClCG05G005380.1 Cla05g00574 574
6 6687157 6694200 + ClCG06G005850.1 Cla06g00549 549
6 6706667 6710082 + ClCG06G005860.1 Cla06g00550 550
6 6726649 6733667 + ClCG06G005870.2 Cla06g00551 551
6 9179333 9181838 - CmaCh06G014270.1 Cma06g01427 1427
6 9183978 9184445 - CmaCh06G014280.1 Cma06g01428 1428
6 9189279 9191191 - CmaCh06G014300.1 Cma06g01430 1430
8 7162156 7168229 - CmaCh08G011630.1 Cma08g01163 1163
8 7170051 7173471 - CmaCh08G011650.1 Cma08g01165 1165
14 12525384 12527820 + CmaCh14G016800.1 Cma14g01680 1680
14 12527817 12532216 - CmaCh14G016810.1 Cma14g01681 1681
14 12533541 12538094 + CmaCh14G016830.1 Cma14g01683 1683
17 1362733 1365008 - CmaCh17G002640.1 Cma17g00264 264
17 1367114 1370533 - CmaCh17G002660.1 Cma17g00266 266
17 1374088 1377784 - CmaCh17G002670.1 Cma17g00267 267
6 4062150 4064967 - MELO3C006553.2.1 Cme06g00632 632
6 4070736 4074984 - MELO3C006555.2.1 Cme06g00634 634
6 4082322 4087277 + MELO3C006557.2.1 Cme06g00636 636
6 4087369 4090371 - MELO3C006558.2.1 Cme06g00637 637
11 27339803 27342530 - MELO3C021410.2.1 Cme11g01928 1928
11 27345890 27348852 - MELO3C021408.2.1 Cme11g01930 1930
11 27358921 27362202 - MELO3C021407.2.1 Cme11g01931 1931
6 4321537 4324951 - PI0017566.1 Cmetu06g2026 2026
6 4330573 4335538 - PI0013501.1 Cmetu06g2420 2420
6 4343707 4346106 - PI0013036.1 Cmetu06g2649 2649
6 10382539 10384139 - CmoCh06G014310.1 Cmo06g01431 1431
6 10386789 10387136 - CmoCh06G014320.1 Cmo06g01432 1432
6 10387909 10391108 - CmoCh06G014330.1 Cmo06g01433 1433
8 7253945 7259718 - CmoCh08G011350.1 Cmo08g01135 1135
8 7261238 7265123 - CmoCh08G011370.1 Cmo08g01137 1137
8 7267398 7270578 - CmoCh08G011380.1 Cmo08g01138 1138
14 13490374 13492748 + CmoCh14G017250.1 Cmo14g01725 1725
14 13492607 13494500 - CmoCh14G017260.1 Cmo14g01726 1726
14 13499673 13505188 + CmoCh14G017290.1 Cmo14g01729 1729
17 1479434 1487397 - CmoCh17G002520.1 Cmo17g00252 252
17 1491047 1494662 - CmoCh17G002530.1 Cmo17g00253 253
5 4995114 4996660 - CmPI595203_05g005880.1 Cmu05g0588 588
5 5002305 5003302 - CmPI595203_05g005890.1 Cmu05g0589 589
5 5005461 5008664 - CmPI595203_05g005900.1 Cmu05g0590 590
5 5014989 5019771 + CmPI595203_05g005920.1 Cmu05g0592 592
5 5020386 5022840 - CmPI595203_05g005930.1 Cmu05g0593 593
6 6405105 6409830 + CmPI595203_06g005730.1 Cmu06g0573 573
6 6423067 6425646 + CmPI595203_06g005740.1 Cmu06g0574 574
6 6440968 6447151 + CmPI595203_06g005750.1 Cmu06g0575 575
3 3923223 3925606 + Conep03aG0077900.1 Cone3ag0756 756
4 968910 970730 + Conep04aG0022000.1 Cone4ag0211 211
4 970718 973072 - Conep04aG0022100.1 Cone4ag0212 212
4 986554 987963 + Conep04aG0022300.1 Cone4ag0214 214
7 943303 945328 + Conep07aG0022400.1 Cone7ag0219 219
7 945480 947831 - Conep07aG0022500.1 Cone7ag0220 220
7 953148 953986 + Conep07aG0022800.1 Cone7ag0223 223
14 5036078 5039113 + Conep14aG0084400.1 Cone14ag0827 827
14 5039415 5051683 + Conep14aG0084500.1 Cone14ag0828 828
3 11402238 11405160 + Cp4.1LG03g10900.1 Cpe03g01418 1418
3 11403248 11411208 - Cp4.1LG03g10820.1 Cpe03g01419 1419
3 11411747 11417598 + Cp4.1LG03g10940.1 Cpe03g01420 1420
8 1609094 1611521 + Cp4.1LG08g04310.1 Cpe08g00245 245
8 1615373 1616992 + Cp4.1LG08g04300.1 Cpe08g00246 246
8 1618064 1626793 + Cp4.1LG08g04340.1 Cpe08g00247 247
12 1435457 1437981 - Cp4.1LG12g02180.1 Cpe12g00220 220
12 1439966 1443360 - Cp4.1LG12g02210.1 Cpe12g00221 221
12 1447675 1451062 - Cp4.1LG12g02230.1 Cpe12g00222 222
17 814253 817537 + Cp4.1LG17g01160.1 Cpe17g00129 129
17 819492 823244 + Cp4.1LG17g01310.1 Cpe17g00130 130
17 824923 827775 + Cp4.1LG17g01370.1 Cpe17g00132 132
5 5787159 5788693 - CrPI670011_05g006560.1 Cre05g0656 656
5 5795748 5796328 - CrPI670011_05g006580.1 Cre05g0658 658
5 5798490 5801691 - CrPI670011_05g006590.1 Cre05g0659 659
5 5806390 5811673 + CrPI670011_05g006600.1 Cre05g0660 660
5 5812190 5815176 - CrPI670011_05g006610.1 Cre05g0661 661
6 7463804 7468559 + CrPI670011_06g013390.1 Cre06g1339 1339
6 7482249 7484876 + CrPI670011_06g013400.1 Cre06g1340 1340
6 7497394 7505669 + CrPI670011_06g013410.1 Cre06g1341 1341
3 10245268 10248845 - CsaV3_3G013580.1 Csa03g01358 1358
3 10250065 10253403 - CsaV3_3G013590.1 Csa03g01359 1359
3 10253748 10258012 - CsaV3_3G013600.1 Csa03g01360 1360
3 10260030 10265499 + CsaV3_3G013610.1 Csa03g01361 1361
3 10265908 10269265 - CsaV3_3G013630.1 Csa03g01363 1363
5 64817583 64820751 + Hsped.05g15260.1 Hepe05g1526 1526
5 64838219 64842445 + Hsped.05g15280.1 Hepe05g1528 1528
12 40356214 40362796 - Lag0016695.1 Lac12g2323 2323
11 39018492 39021603 + Maker00032006 Lcy11g1512 1512
11 39034450 39037920 + Maker00031483 Lcy11g1514 1514
5 22337774 22340658 - Lsi05G014450.1 Lsi05g01445 1445
5 22343787 22346002 - Lsi05G014460.1 Lsi05g01446 1446
5 22346974 22351151 - Lsi05G014470.1 Lsi05g01447 1447
5 22355405 22360127 + Lsi05G014490.1 Lsi05g01449 1449
5 22363601 22364244 - Lsi05G014510.1 Lsi05g01451 1451
9 21434203 21436903 - Lsi09G013480.1 Lsi09g01348 1348
9 21444234 21447513 - Lsi09G013500.1 Lsi09g01350 1350
9 21464738 21470955 - Lsi09G013530.1 Lsi09g01353 1353
2 49344170 49348440 - Sed0017985.3 Sed02g1262 1262
2 49354715 49358277 - Sed0011286.1 Sed02g1264 1264
2 49363907 49368746 - Sed0008049.1 Sed02g1266 1266
10 7317733 7320835 - Tan0019677.2 Tan10g0875 875
10 7342231 7346787 - Tan0018724.1 Tan10g0877 877
10 7362248 7364657 - Tan0015850.1 Tan10g0882 882
5 4484043 4487627 + Vvi5g439 Vvi5g439 439
5 4488818 4490843 + Vvi5g440 Vvi5g440 440
5 4491106 4495464 + Vvi5g441 Vvi5g441 441
5 4495885 4502434 - Vvi5g442 Vvi5g442 442
5 4502462 4509891 - Vvi5g443 Vvi5g443 443
5 4510251 4514346 + Vvi5g444 Vvi5g444 444
5 4515439 4529233 + Vvi5g445 Vvi5g445 445
5 4531078 4532024 + Vvi5g446 Vvi5g446 446
5 4535667 4538945 + Vvi5g447 Vvi5g447 447
5 4540076 4546658 + Vvi5g448 Vvi5g448 448
       

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