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
Vvi3g526 . Blo15g00719 . . Bpe07g00403 . . Bma12g00482 . . Cma02g00427 Cma20g00879 Car02g00284 Car20g00758 . . . . . . . . . . . . . . . . . Cone12ag1124 Cone8ag1168 . . Lsi10g00329 . Chy11g00419 . . . . . . . . . Sed05g3643 Cmo02g00428 Cmo20g00886 . . . . . Cpe05g01234 Bhi10g02061 Tan05g1365 Cmetu11g1444 . Hepe08g1048 . . Cla09g01736 Cam09g1830 Cec09g1890 Cco09g1983 . . Cre01g0680 . Csa02g01217 . Cme11g00480
Vvi3g527 . Blo15g00718 Bda06g01024 Bda08g01318 Bpe07g00404 Bpe12g00071 . Bma12g00483 Cmo19g00652 Cmo11g01329 . . . . Sed11g0992 . . Bhi05g01171 Tan02g1913 Cmetu03g1602 . Hepe02g0551 . . Cla02g00560 Cam02g0588 Cec02g0589 Cco02g0600 Clacu02g0586 Cmu02g0584 Cre02g0914 . . . . . Csa07g00816 . . . Blo13g00559 Bda15g00021 Bda14g00532 . . . . . . . Cma11g01780 Cma19g00639 . . . . . . . . . . . . . . . . . . . . Chy01g00013 .
Vvi3g528 . . . . . . . . Cmo19g00653 . . . . . Sed10g2069 . Cpe15g00515 Bhi05g01172 Tan02g0856 Cmetu01g1581 . . . . Cla02g00559 Cam02g0587 Cec02g0588 Cco02g0599 Clacu02g0585 Cmu02g0583 Cre02g0913 Cone12ag1125 Cone8ag1169 . . . Csa07g00817 . . Blo04g00499 . . . Bpe15g00881 . Bma03g00533 . . . . . Cma19g00640 . Car19g00486 . . . . . . . . . . . . . . . . Lsi11g01048 . Chy01g00012 .
Vvi3g529 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g530 . . . Bda08g01314 . . . . . . . . . . Sed11g0996 . . Bhi05g01173 Tan02g1916 Cmetu03g1973 . Hepe02g0550 . . Cla02g00558 Cam02g0586 Cec02g0587 Cco02g0598 Clacu02g0584 Cmu02g0582 Cre02g0912 . . . . . . . Cme01g00010 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy01g00011 .
Vvi3g531 . . . . . . . . Cmo19g00654 Cmo11g01328 . . . . Sed10g2071 . Cpe15g00516 Bhi05g01174 Tan02g0854 Cmetu01g2737 . Hepe02g0549 . . . . . . . . . . . . . . Csa07g00818 . Cme01g00009 . . . . . . . . . . . Cma11g01781 Cma19g00641 . Car19g00487 . . . . . . . . . . . . . . . . Lsi11g01051 . Chy01g00010 .
Vvi3g532 . . . Bda08g01303 . . . . . . . . . . . Cpe04g00126 . . . . . . . . . . . . . . . Cone12ag1126 Cone8ag1170 . . . Csa07g00819 . . . . . . . . . . . . . . . Car11g01070 . . . . . . . . . . . . . . . . . Lsi11g01052 . . .
Vvi3g533 . Blo15g00717 Bda06g01022 Bda08g00910 Bpe07g00407 . . Bma12g00487 . . Cma02g00426 Cma20g00878 Car02g00283 Car20g00757 . . . . . . . . . . . . . . . . . . . Cone3ag1128 Cone10ag1137 Lsi10g00330 . Chy11g00418 . . . . . . . . . Sed01g0322 Cmo02g00427 Cmo20g00885 . . . . . Cpe05g01235 Bhi10g02059 Tan05g1361 Cmetu11g1465 . Hepe08g1047 . . Cla09g01737 Cam09g1831 Cec09g1891 Cco09g1984 . . Cre01g0679 . Csa02g01218 . Cme11g00479
Vvi3g534 . Blo15g00716 Bda06g01017 . Bpe07g00408 . . Bma12g00488 . . . Cma20g00877 . Car20g00756 . . . . . . . . . . . . . . . . . . . . Cone10ag1138 Lsi10g00331 . Chy11g00417 . . . . . . . . . Sed05g3642 . Cmo20g00884 . . . . . . Bhi10g02058 Tan05g1360 Cmetu11g2170 . Hepe08g1046 . . Cla09g01738 Cam09g1832 Cec09g1892 Cco09g1985 . . Cre01g0678 . Csa02g01219 . Cme11g00478
Vvi3g535 Blo02g00787 Blo15g00714 Bda06g01015 Bda08g00907 Bpe07g00411 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1131 Cone10ag1141 . . . . . . . . . . . . . . . . . . . . . Bhi10g02042 . . . Hepe08g1032 . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 35466075 35467079 - Bda022751.1 Bda06g01015 1015
6 35633324 35638780 - Bda022754.1 Bda06g01017 1017
6 35879405 35890306 - Bda022764.1 Bda06g01022 1022
6 35935121 35936521 - Bda022767.1 Bda06g01024 1024
8 16510651 16511687 - Bda029527.1 Bda08g00907 907
8 16528126 16529721 - Bda029530.1 Bda08g00910 910
8 52765024 52766613 + Bda030338.1 Bda08g01303 1303
8 52945448 52947037 + Bda030351.1 Bda08g01314 1314
8 53022834 53024180 - Bda030356.1 Bda08g01318 1318
14 3851052 3852467 - Bda027278.1 Bda14g00532 532
15 1547337 1548749 + Bda011773.1 Bda15g00021 21
5 41880529 41882606 - XM_039033013.1 Bhi05g01171 1171
5 41907662 41913525 + XM_039033076.1 Bhi05g01172 1172
5 41991690 41993333 + XM_039030967.1 Bhi05g01173 1173
5 42078572 42080308 + XM_039032898.1 Bhi05g01174 1174
10 51066131 51068751 - XM_039045694.1 Bhi10g02042 2042
10 51441479 51456470 + XM_039045531.1 Bhi10g02058 2058
10 51469272 51472290 - XM_039046855.1 Bhi10g02059 2059
10 51489223 51496338 + XM_039045608.1 Bhi10g02061 2061
2 26724461 26725503 + BLOR10517 Blo02g00787 787
4 4146710 4150252 + BLOR13411 Blo04g00499 499
13 27589234 27593444 + BLOR19611 Blo13g00559 559
15 23208351 23209383 - BLOR07108 Blo15g00714 714
15 23365620 23379577 + BLOR07110 Blo15g00716 716
15 23540235 23541605 - BLOR07111 Blo15g00717 717
15 23646177 23654633 + BLOR07112 Blo15g00718 718
15 23812085 23817160 + BLOR07113 Blo15g00719 719
3 4139569 4145102 + Bma016816.1 Bma03g00533 533
12 13972938 13979164 - Bma007516.1 Bma12g00482 482
12 14084881 14086275 - Bma007519.1 Bma12g00483 483
12 14362340 14376868 + Bma007526.1 Bma12g00487 487
12 14439292 14444702 - Bma007528.1 Bma12g00488 488
7 3848109 3856722 - Bpe021223.3 Bpe07g00403 403
7 3892838 3894238 - Bpe021225.1 Bpe07g00404 404
7 4002929 4004584 + Bpe021230.1 Bpe07g00407 407
7 4081526 4086943 - Bpe021231.1 Bpe07g00408 408
7 4157473 4158482 + Bpe021234.1 Bpe07g00411 411
12 500549 501949 - Bpe005309.1 Bpe12g00071 71
15 18771701 18775069 - Bpe024587 Bpe15g00881 881
2 6674203 6677745 - CaPI482276_02g005860.1 Cam02g0586 586
2 6698194 6703671 - CaPI482276_02g005870.1 Cam02g0587 587
2 6738454 6739878 + CaPI482276_02g005880.1 Cam02g0588 588
9 32792560 32797675 - CaPI482276_09g018300.1 Cam09g1830 1830
9 32808667 32811206 + CaPI482276_09g018310.1 Cam09g1831 1831
9 32815125 32827384 - CaPI482276_09g018320.1 Cam09g1832 1832
2 1909782 1911679 - Carg22968-RA Car02g00283 283
2 1914389 1919314 + Carg22969-RA Car02g00284 284
11 8272837 8274276 - Carg26482-RA Car11g01070 1070
19 6473577 6477839 + Carg22038-RA Car19g00486 486
19 6480823 6482264 + Carg22037-RA Car19g00487 487
20 4428893 4439324 + Carg23627-RA Car20g00756 756
20 4441041 4442483 - Carg23626-RA Car20g00757 757
20 4444692 4448977 + Carg23625-RA Car20g00758 758
2 5822504 5826041 - CcPI632755_02g005980.1 Cco02g0598 598
2 5848875 5854356 - CcPI632755_02g005990.1 Cco02g0599 599
2 5889563 5890990 + CcPI632755_02g006000.1 Cco02g0600 600
9 34027241 34032346 - CcPI632755_09g019830.1 Cco09g1983 1983
9 34042646 34049166 + CcPI632755_09g019840.1 Cco09g1984 1984
9 34053106 34065500 - CcPI632755_09g019850.1 Cco09g1985 1985
2 5706820 5710171 - CePI673135_02g005870.1 Cec02g0587 587
2 5735122 5740604 - CePI673135_02g005880.1 Cec02g0588 588
2 5780978 5782375 + CePI673135_02g005890.1 Cec02g0589 589
9 35729208 35734328 - CePI673135_09g018900.1 Cec09g1890 1890
9 35748438 35750984 + CePI673135_09g018910.1 Cec09g1891 1891
9 35754871 35767069 - CePI673135_09g018920.1 Cec09g1892 1892
1 81273 82801 - Chy1G000100.1 Chy01g00010 10
1 88100 89619 - Chy1G000110.1 Chy01g00011 11
1 93621 99715 - Chy1G000120.1 Chy01g00012 12
1 117818 119221 + Chy1G000130.1 Chy01g00013 13
11 3993460 4013859 + Chy11G189970.1 Chy11g00417 417
11 4016102 4018370 - Chy11G189980.1 Chy11g00418 418
11 4026944 4031912 + Chy11G189990.1 Chy11g00419 419
2 5642251 5645755 - ClG42_02g0058400.10 Clacu02g0584 584
2 5668117 5673600 - ClG42_02g0058500.10 Clacu02g0585 585
2 5710490 5711914 + ClG42_02g0058600.10 Clacu02g0586 586
2 5902632 5914930 - ClCG02G005440.1 Cla02g00558 558
2 5937123 5942606 - ClCG02G005470.2 Cla02g00559 559
2 5979571 5980995 + ClCG02G005475.1 Cla02g00560 560
9 34700504 34706016 - ClCG09G017730.2 Cla09g01736 1736
9 34717920 34720537 + ClCG09G017740.1 Cla09g01737 1737
9 34724287 34737290 - ClCG09G017750.1 Cla09g01738 1738
2 2153987 2157688 - CmaCh02G004260.1 Cma02g00426 426
2 2160407 2165457 + CmaCh02G004270.1 Cma02g00427 427
11 11907978 11909375 - CmaCh11G017800.1 Cma11g01780 1780
11 11918812 11920254 + CmaCh11G017810.1 Cma11g01781 1781
19 6798534 6799952 - CmaCh19G006390.1 Cma19g00639 639
19 6811352 6816114 + CmaCh19G006400.1 Cma19g00640 640
19 6819021 6820910 + CmaCh19G006410.1 Cma19g00641 641
20 4192277 4200746 + CmaCh20G008770.1 Cma20g00877 877
20 4202286 4204015 - CmaCh20G008780.1 Cma20g00878 878
20 4206037 4210522 + CmaCh20G008790.1 Cma20g00879 879
1 78963 80856 - MELO3C018412.2.1 Cme01g00009 9
1 82985 85696 - MELO3C018413.2.1 Cme01g00010 10
11 4648462 4657114 + MELO3C021941.2.1 Cme11g00478 478
11 4658916 4661749 - MELO3C021940.2.1 Cme11g00479 479
11 4668830 4675009 + MELO3C021939.2.1 Cme11g00480 480
1 113588 119277 - PI0003768.1 Cmetu01g1581 1581
1 99932 101828 - PI0021823.1 Cmetu01g2737 2737
3 1624684 1626783 - PI0009511.1 Cmetu03g1602 1602
3 1644644 1646623 - PI0019666.1 Cmetu03g1973 1973
11 26985088 26989433 - PI0023638.1 Cmetu11g1444 1444
11 26997680 27000425 + PI0025884.1 Cmetu11g1465 1465
11 27003934 27010854 - PI0028595.1 Cmetu11g2170 2170
2 2232936 2235360 - CmoCh02G004270.1 Cmo02g00427 427
2 2238080 2243251 + CmoCh02G004280.1 Cmo02g00428 428
11 9170165 9171607 - CmoCh11G013280.1 Cmo11g01328 1328
11 9182026 9183423 + CmoCh11G013290.1 Cmo11g01329 1329
19 7014601 7016019 - CmoCh19G006520.1 Cmo19g00652 652
19 7028056 7032523 + CmoCh19G006530.1 Cmo19g00653 653
19 7035716 7037368 + CmoCh19G006540.1 Cmo19g00654 654
20 4461074 4470210 + CmoCh20G008840.1 Cmo20g00884 884
20 4471787 4473595 - CmoCh20G008850.1 Cmo20g00885 885
20 4475151 4480186 + CmoCh20G008860.1 Cmo20g00886 886
2 5557585 5561097 - CmPI595203_02g005820.1 Cmu02g0582 582
2 5583454 5588937 - CmPI595203_02g005830.1 Cmu02g0583 583
2 5625897 5627321 + CmPI595203_02g005840.1 Cmu02g0584 584
3 29879320 29881509 + Conep03aG0163200.1 Cone3ag1128 1128
3 29907927 29909571 + Conep03aG0163500.1 Cone3ag1131 1131
8 10093889 10098135 - Conep08aG0120000.1 Cone8ag1168 1168
8 10098490 10107282 + Conep08aG0120100.1 Cone8ag1169 1169
8 10108017 10109468 + Conep08aG0120200.1 Cone8ag1170 1170
10 8201848 8203791 + Conep10aG0116900.1 Cone10ag1137 1137
10 8211596 8217063 - Conep10aG0117000.1 Cone10ag1138 1138
10 8257850 8259552 + Conep10aG0117300.1 Cone10ag1141 1141
12 9058873 9062519 - Conep12aG0116000.1 Cone12ag1124 1124
12 9069336 9072039 + Conep12aG0116100.1 Cone12ag1125 1125
12 9073403 9074869 + Conep12aG0116200.1 Cone12ag1126 1126
4 1136910 1141597 + Cp4.1LG04g00860.1 Cpe04g00126 126
5 8646536 8651675 - Cp4.1LG05g12280.1 Cpe05g01234 1234
5 8653607 8656035 + Cp4.1LG05g12210.1 Cpe05g01235 1235
15 6075588 6080307 + Cp4.1LG15g05180.1 Cpe15g00515 515
15 6083290 6089475 + Cp4.1LG15g05200.1 Cpe15g00516 516
1 6247854 6261291 + CrPI670011_01g006780.1 Cre01g0678 678
1 6264962 6267497 - CrPI670011_01g006790.1 Cre01g0679 679
1 6279547 6285414 + CrPI670011_01g006800.1 Cre01g0680 680
2 6164564 6168442 - CrPI670011_02g009120.1 Cre02g0912 912
2 6191786 6197134 - CrPI670011_02g009130.1 Cre02g0913 913
2 6234719 6236143 + CrPI670011_02g009140.1 Cre02g0914 914
2 11964209 11970288 - CsaV3_2G014330.1 Csa02g01217 1217
2 11978795 11981760 + CsaV3_2G014340.1 Csa02g01218 1218
2 11982859 11990842 - CsaV3_2G014350.1 Csa02g01219 1219
7 5720257 5723441 - CsaV3_7G010140.1 Csa07g00816 816
7 5740458 5746851 + CsaV3_7G010150.1 Csa07g00817 817
7 5749198 5752040 + CsaV3_7G010160.1 Csa07g00818 818
7 5756113 5757988 + CsaV3_7G010170.1 Csa07g00819 819
2 5545568 5547314 - Hsped.02g05490.1 Hepe02g0549 549
2 5551713 5553232 - Hsped.02g05500.1 Hepe02g0550 550
2 5589071 5591184 + Hsped.02g05510.1 Hepe02g0551 551
8 9962474 9964969 + Hsped.08g10320.1 Hepe08g1032 1032
8 10067732 10076839 + Hsped.08g10460.1 Hepe08g1046 1046
8 10081377 10083484 - Hsped.08g10470.1 Hepe08g1047 1047
8 10094132 10098858 + Hsped.08g10480.1 Hepe08g1048 1048
10 5239161 5245092 - Lsi10G003290.1 Lsi10g00329 329
10 5257975 5261727 + Lsi10G003300.1 Lsi10g00330 330
10 5265349 5277768 - Lsi10G003310.1 Lsi10g00331 331
11 18007961 18013656 - Lsi11G010480.1 Lsi11g01048 1048
11 18200999 18204435 + Lsi11G010510.1 Lsi11g01051 1051
11 18217005 18218981 + Lsi11G010520.1 Lsi11g01052 1052
1 2433837 2437383 - Sed0019117.1 Sed01g0322 322
5 44665202 44675206 + Sed0000695.1 Sed05g3642 3642
5 44679112 44685279 + Sed0005225.1 Sed05g3643 3643
10 37187182 37193099 + Sed0018300.1 Sed10g2069 2069
10 37214708 37217231 + Sed0000461.1 Sed10g2071 2071
11 24942400 24945076 - Sed0006421.1 Sed11g0992 992
11 25044799 25046982 - Sed0019712.1 Sed11g0996 996
2 9374226 9377283 - Tan0000376.1 Tan02g0854 854
2 9464450 9475203 - Tan0012686.2 Tan02g0856 856
2 87571960 87574745 - Tan0011998.1 Tan02g1913 1913
2 87658440 87660464 - Tan0013036.1 Tan02g1916 1916
5 18268044 18278124 + Tan0000279.1 Tan05g1360 1360
5 18325794 18328328 - Tan0015521.1 Tan05g1361 1361
5 18481753 18487717 + Tan0015616.4 Tan05g1365 1365
3 5114313 5120632 - Vvi3g526 Vvi3g526 526
3 5125032 5126676 - Vvi3g527 Vvi3g527 527
3 5135428 5145069 + Vvi3g528 Vvi3g528 528
3 5149604 5150096 + Vvi3g529 Vvi3g529 529
3 5156560 5164408 - Vvi3g530 Vvi3g530 530
3 5183320 5191752 - Vvi3g531 Vvi3g531 531
3 5192901 5194353 - Vvi3g532 Vvi3g532 532
3 5200764 5204004 + Vvi3g533 Vvi3g533 533
3 5204560 5212695 - Vvi3g534 Vvi3g534 534
3 5229381 5231737 + Vvi3g535 Vvi3g535 535
       

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