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
Vvi3g816 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g817 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g818 Blo02g00908 . . . . . Bma05g00629 . Cmo19g00529 . . . . . Sed11g0910 . Cpe15g00412 Bhi05g00994 Tan02g1686 Cmetu03g2238 Lac12g0130 Hepe02g0672 . . Cla02g00722 Cam02g0770 Cec02g0766 Cco02g0797 Clacu02g0764 Cmu02g0757 Cre02g1071 . . Cone3ag1057 Cone10ag1073 Lsi03g00639 Csa07g00653 . Cme01g00150 . . . . . Bpe05g00453 . . . . . . Cma19g00516 . Car19g00391 . . . . . . . . . . . . . . . . . . Chy01g00159 .
Vvi3g819 Blo02g00907 . . . . . Bma05g00628 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe05g00452 . . . . . . . . . . . . . . . . . . . . . . . . . Lsi03g00993 . . .
Vvi3g820 . . . . . Bpe12g00727 . . Cmo19g00528 Cmo11g01438 . . . . Sed10g1931 Cpe04g00342 Cpe15g00411 Bhi05g00992 Tan02g1082 Cmetu01g1396 . Hepe02g0673 . . Cla02g00723 Cam02g0771 Cec02g0767 Cco02g0798 Clacu02g0765 Cmu02g0758 Cre02g1073 . . . Cone10ag1074 Lsi03g00640 Csa07g00652 . Cme01g00151 . . Bda15g00474 . . . . Bma08g00023 . . . Cma11g01685 Cma19g00515 Car11g01155 Car19g00390 . . . . . . . . . . . . . . . . . . Chy01g00160 .
Vvi3g821 . Blo03g00047 Bda06g01143 . Bpe07g00301 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1060 Cone10ag1075 . . . . . . . . . . . . . . Cmo16g00310 . . . . Cpe14g00242 . Bhi11g01083 . . . . . . . . . . . . . Lsi03g00992 . . Cme07g02225
Vvi3g822 . . . . . . . . Cmo19g00527 . . . . . . . Cpe15g00410 Bhi05g00991 . . . . . . Cla02g00724 . . . . . . Cone4ag1267 Cone7ag0877 Cone17ag1152 . Lsi03g00641 Csa07g00651 . Cme01g00152 . . . . . . . . . . . . Cma19g00514 . Car19g00389 . . . . . . . . . . . . . . . . . . . .
Vvi3g823 . . . . . Bpe12g00725 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1061 Cone10ag1076 . . . . . . Bda15g00476 . . . . Bma08g00024 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g824 . . . . . Bpe12g00724 . . . Cmo11g01440 . . . . Sed06g0823 . . Bhi05g00989 Tan02g1085 Cmetu01g0416 Lac12g0127 Hepe02g0675 . . Cla02g00727 Cam02g0774 Cec02g0771 Cco02g0801 Clacu02g0769 Cmu02g0761 Cre02g1076 . . Cone3ag1062 Cone10ag1077 . Csa07g00648 . Cme01g00154 . . . . . . . . . . . . . Car11g01156 . . . . . . . . . . . . . . . . . . . Chy01g00163 .
Vvi3g825 . . . . . . . . . . . . . . . Cpe04g00343 . . . . . . . . . . . . . . . . . . . Lsi03g00643 . . . . . Bda15g00477 . . . . Bma08g00025 . . . Cma11g01684 . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 40376988 40380638 + Bda022940.1 Bda06g01143 1143
15 7917251 7920283 + Bda012303.1 Bda15g00474 474
15 7932042 7935204 + Bda012305.1 Bda15g00476 476
15 7935758 7936771 - Bda012306.1 Bda15g00477 477
5 34841944 34844981 + XM_039032149.1 Bhi05g00989 989
5 34971786 34975365 + XM_039031964.1 Bhi05g00991 991
5 34975692 34979867 - XM_039031966.1 Bhi05g00992 992
5 35039348 35046847 + XM_039031769.1 Bhi05g00994 994
11 31884268 31892374 + XM_039049919.1 Bhi11g01083 1083
2 35053551 35055916 - BLOR10637 Blo02g00907 907
2 35072767 35074999 - BLOR10638 Blo02g00908 908
3 1786419 1790200 + BLOR11228 Blo03g00047 47
5 37235480 37237392 - Bma021658.1 Bma05g00628 628
5 37239456 37241604 - Bma021659.1 Bma05g00629 629
8 413066 414928 + Bma027015.1 Bma08g00023 23
8 418817 421663 + Bma027016.1 Bma08g00024 24
8 422355 423625 - Bma027017.1 Bma08g00025 25
5 18889679 18891542 - Bpe017871.1 Bpe05g00452 452
5 18892841 18894983 - Bpe017872.1 Bpe05g00453 453
7 2188409 2191554 - Bpe026050 Bpe07g00301 301
12 12775836 12777107 + Bpe005985.1 Bpe12g00724 724
12 12777626 12780823 - Bpe005986.1 Bpe12g00725 725
12 12786163 12788000 - Bpe005988.1 Bpe12g00727 727
2 9387415 9394582 - CaPI482276_02g007700.1 Cam02g0770 770
2 9430527 9434102 + CaPI482276_02g007710.1 Cam02g0771 771
2 9512486 9515176 - CaPI482276_02g007740.1 Cam02g0774 774
11 9278281 9281631 + Carg23049-RA Car11g01155 1155
11 9282060 9284916 - Carg23050-RA Car11g01156 1156
19 5706454 5709727 + Carg16310-RA Car19g00389 389
19 5710501 5714459 - Carg16311-RA Car19g00390 390
19 5722026 5728171 + Carg16312-RA Car19g00391 391
2 8740028 8747385 - CcPI632755_02g007970.1 Cco02g0797 797
2 8789642 8793183 + CcPI632755_02g007980.1 Cco02g0798 798
2 8832618 8835313 - CcPI632755_02g008010.1 Cco02g0801 801
2 8618539 8625783 - CePI673135_02g007660.1 Cec02g0766 766
2 8663644 8667216 + CePI673135_02g007670.1 Cec02g0767 767
2 8723912 8726611 - CePI673135_02g007710.1 Cec02g0771 771
1 1087145 1091654 - Chy1G001590.1 Chy01g00159 159
1 1100468 1104051 + Chy1G001600.1 Chy01g00160 160
1 1129685 1132470 - Chy1G001630.1 Chy01g00163 163
2 8309705 8317034 - ClG42_02g0076400.10 Clacu02g0764 764
2 8355499 8359313 + ClG42_02g0076500.10 Clacu02g0765 765
2 8434573 8437251 - ClG42_02g0076900.10 Clacu02g0769 769
2 8695624 8702989 - ClCG02G007380.2 Cla02g00722 722
2 8741743 8745728 + ClCG02G007390.1 Cla02g00723 723
2 8746058 8749433 - ClCG02G007400.1 Cla02g00724 724
2 8822551 8825713 - ClCG02G007430.1 Cla02g00727 727
11 11101687 11115128 + CmaCh11G016840.1 Cma11g01684 1684
11 11115466 11119346 - CmaCh11G016850.1 Cma11g01685 1685
19 6033034 6036672 + CmaCh19G005140.1 Cma19g00514 514
19 6035838 6041041 - CmaCh19G005150.1 Cma19g00515 515
19 6047297 6053659 + CmaCh19G005160.1 Cma19g00516 516
1 1078271 1081094 - MELO3C018550.2.1 Cme01g00150 150
1 1092194 1095845 + MELO3C018551.2.1 Cme01g00151 151
1 1095995 1099881 - MELO3C018552.2.1 Cme01g00152 152
1 1107378 1110305 - MELO3C018554.2.1 Cme01g00154 154
7 26413985 26421707 - MELO3C018038.2.1 Cme07g02225 2225
1 1263836 1266738 - PI0005746.1 Cmetu01g0416 416
1 1246429 1250419 + PI0014288.2 Cmetu01g1396 1396
3 801961 805554 - PI0019344.1 Cmetu03g2238 2238
11 10119978 10123345 + CmoCh11G014380.1 Cmo11g01438 1438
11 10124460 10126934 - CmoCh11G014400.1 Cmo11g01440 1440
16 1418025 1425834 + CmoCh16G003100.1 Cmo16g00310 310
19 6163173 6166566 + CmoCh19G005270.1 Cmo19g00527 527
19 6166296 6171216 - CmoCh19G005280.1 Cmo19g00528 528
19 6177350 6184559 + CmoCh19G005290.1 Cmo19g00529 529
2 8218229 8225555 - CmPI595203_02g007570.1 Cmu02g0757 757
2 8264057 8267871 + CmPI595203_02g007580.1 Cmu02g0758 758
2 8342062 8344740 - CmPI595203_02g007610.1 Cmu02g0761 761
3 29291508 29294520 - Conep03aG0155800.1 Cone3ag1057 1057
3 29319610 29322970 - Conep03aG0156100.1 Cone3ag1060 1060
3 29323152 29326314 - Conep03aG0156200.1 Cone3ag1061 1061
3 29326612 29328734 - Conep03aG0156300.1 Cone3ag1062 1062
4 10427416 10430698 - Conep04aG0131300.1 Cone4ag1267 1267
7 6792849 6796161 + Conep07aG0090600.1 Cone7ag0877 877
10 7445264 7449157 - Conep10aG0110000.1 Cone10ag1073 1073
10 7459922 7462936 + Conep10aG0110100.1 Cone10ag1074 1074
10 7465502 7468885 - Conep10aG0110200.1 Cone10ag1075 1075
10 7476562 7477833 - Conep10aG0110300.1 Cone10ag1076 1076
10 7479695 7481824 - Conep10aG0110400.1 Cone10ag1077 1077
17 8485685 8489003 - Conep17aG0118100.1 Cone17ag1152 1152
4 4134545 4138427 + Cp4.1LG04g07490.1 Cpe04g00342 342
4 4139003 4141790 - Cp4.1LG04g07390.1 Cpe04g00343 343
14 1402142 1409023 + Cp4.1LG14g04780.1 Cpe14g00242 242
15 5252990 5256298 + Cp4.1LG15g04090.1 Cpe15g00410 410
15 5257017 5261128 - Cp4.1LG15g04190.1 Cpe15g00411 411
15 5271594 5278504 + Cp4.1LG15g04060.1 Cpe15g00412 412
2 8856382 8863853 - CrPI670011_02g010710.1 Cre02g1071 1071
2 8904778 8908734 + CrPI670011_02g010730.1 Cre02g1073 1073
2 8957937 8960738 - CrPI670011_02g010760.1 Cre02g1076 1076
7 4652537 4656375 + CsaV3_7G007470.1 Csa07g00648 648
7 4672994 4676933 + CsaV3_7G007500.1 Csa07g00651 651
7 4677020 4681015 - CsaV3_7G007510.1 Csa07g00652 652
7 4688357 4693049 + CsaV3_7G007520.1 Csa07g00653 653
2 7384132 7389827 - Hsped.02g06720.1 Hepe02g0672 672
2 7410044 7413801 + Hsped.02g06730.1 Hepe02g0673 673
2 7436556 7440000 - Hsped.02g06750.1 Hepe02g0675 675
12 1397011 1401184 + Lag0014499.1 Lac12g0127 127
12 1444682 1450821 + Lag0014502.1 Lac12g0130 130
3 7952648 7966994 - Lsi03G006390.1 Lsi03g00639 639
3 7990043 7993973 + Lsi03G006400.1 Lsi03g00640 640
3 7993942 7997741 - Lsi03G006410.1 Lsi03g00641 641
3 8070225 8073620 - Lsi03G006430.1 Lsi03g00643 643
3 19134832 19143054 + Lsi03G009920.1 Lsi03g00992 992
3 19146955 19154820 + Lsi03G009930.1 Lsi03g00993 993
6 8901452 8904666 + Sed0011512.1 Sed06g0823 823
10 35974540 35979645 - Sed0010536.2 Sed10g1931 1931
11 22257359 22261509 - Sed0014007.2 Sed11g0910 910
2 18449585 18453306 + Tan0014774.1 Tan02g1082 1082
2 18550639 18553354 - Tan0008703.1 Tan02g1085 1085
2 79147581 79151650 - Tan0013573.1 Tan02g1686 1686
3 9349141 9352616 - Vvi3g816 Vvi3g816 816
3 9373662 9376239 + Vvi3g817 Vvi3g817 817
3 9385653 9388831 - Vvi3g818 Vvi3g818 818
3 9394206 9397960 - Vvi3g819 Vvi3g819 819
3 9408763 9412394 + Vvi3g820 Vvi3g820 820
3 9413164 9433562 - Vvi3g821 Vvi3g821 821
3 9439066 9442128 - Vvi3g822 Vvi3g822 822
3 9452228 9454982 + Vvi3g823 Vvi3g823 823
3 9454986 9459930 - Vvi3g824 Vvi3g824 824
3 9501863 9508762 - Vvi3g825 Vvi3g825 825
       

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