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
Vvi3g796 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g797 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g798 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi10g00272 . . . . . . . . . . . . . . . . . . . . Bhi10g01655 . . . . . . Cla09g01671 . . . . . . . . . .
Vvi3g799 Blo02g00914 . Bda06g01146 . Bpe07g00300 . . Bma12g00312 Cmo19g00541 . . . . . . . Cpe15g00420 . . . . . . . Cla02g00709 Cam02g0746 Cec02g0757 Cco02g0784 Clacu02g0752 Cmu02g0746 Cre02g1061 . Cone8ag1053 . . Lsi03g00626 Csa07g00658 . Cme01g00144 . . . . . Bpe05g00458 . . . . . Cma11g01690 Cma19g00532 . . . Cpe01g00380 . . . . . . . . . . . . . . . . Chy01g00153 .
Vvi3g800 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g801 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g802 . . Bda06g01145 . . . . . Cmo19g00540 . . . . . . Cpe04g00339 Cpe15g00419 . . . . . . . Cla02g00713 Cam02g0763 Cec02g0761 Cco02g0787 Clacu02g0754 Cmu02g0748 Cre02g1065 . . . . Lsi03g00627 Csa07g00657 . Cme01g00145 . . . . . . . . Sed07g1155 . . Cma11g01688 . . . . . Bhi11g01091 Tan01g0594 Cmetu07g1308 . . . . . . . . . . . Lsi03g00997 . Chy01g00154 .
Vvi3g803 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g804 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g805 Blo02g00912 Blo03g00050 . . . . Bma05g00634 Bma12g00314 Cmo19g00538 Cmo11g01434 . . . . Sed06g0830 . Cpe15g00418 Bhi05g00999 Tan02g1068 Cmetu01g1966 Lac12g0134 . . . Cla02g00718 Cam02g0764 Cec02g0762 Cco02g0790 Clacu02g0757 Cmu02g0752 Cre02g1067 . . . . Lsi03g00628 Csa07g00656 . Cme01g00146 . . . . . Bpe05g00457 . . . Cmo04g00453 . . Cma19g00527 . . . . . . . . . . . . . . . . . . . . Chy01g00155 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 40448609 40449076 + Bda022943.1 Bda06g01145 1145
6 40518334 40518801 + Bda022947.1 Bda06g01146 1146
5 35297752 35298461 + XM_039032672.1 Bhi05g00999 999
10 41755050 41757248 + XM_039046334.1 Bhi10g01655 1655
11 32066887 32067363 + XM_039048386.1 Bhi11g01091 1091
2 35216388 35216867 + BLOR10642 Blo02g00912 912
2 35321288 35321776 + BLOR10644 Blo02g00914 914
3 1854990 1855469 + BLOR11231 Blo03g00050 50
5 37289685 37290173 + Bma021664.1 Bma05g00634 634
12 4478672 4479151 - Bma007221.1 Bma12g00312 312
12 4541972 4618436 - Bma030496 Bma12g00314 314
5 18925547 18926035 + Bpe017876.1 Bpe05g00457 457
5 18927884 18928369 + Bpe017877.1 Bpe05g00458 458
7 2171208 2171687 - Bpe021110.1 Bpe07g00300 300
2 9022328 9022828 + CaPI482276_02g007460.1 Cam02g0746 746
2 9161043 9161534 + CaPI482276_02g007630.1 Cam02g0763 763
2 9221564 9222046 - CaPI482276_02g007640.1 Cam02g0764 764
2 8470323 8470805 - CcPI632755_02g007840.1 Cco02g0784 784
2 8515476 8515739 - CcPI632755_02g007870.1 Cco02g0787 787
2 8567795 8568277 - CcPI632755_02g007900.1 Cco02g0790 790
2 8361455 8361952 - CePI673135_02g007570.1 Cec02g0757 757
2 8419992 8420447 + CePI673135_02g007610.1 Cec02g0761 761
2 8460816 8461298 - CePI673135_02g007620.1 Cec02g0762 762
1 1050234 1051377 - Chy1G001530.1 Chy01g00153 153
1 1053223 1056983 - Chy1G001540.1 Chy01g00154 154
1 1057372 1059628 - Chy1G001550.1 Chy01g00155 155
2 8021657 8022145 - ClG42_02g0075200.10 Clacu02g0752 752
2 8048171 8048617 - ClG42_02g0075400.10 Clacu02g0754 754
2 8075451 8076189 - ClG42_02g0075700.10 Clacu02g0757 757
2 8405309 8405791 - ClCG02G007250.1 Cla02g00709 709
2 8470277 8470768 + ClCG02G007290.1 Cla02g00713 713
2 8518115 8518597 - ClCG02G007340.1 Cla02g00718 718
9 33475743 33483002 + ClCG09G017030.1 Cla09g01671 1671
11 11143161 11143604 + CmaCh11G016880.1 Cma11g01688 1688
11 11158319 11158756 + CmaCh11G016900.1 Cma11g01690 1690
19 6126791 6127270 + CmaCh19G005270.1 Cma19g00527 527
19 6148546 6149016 - CmaCh19G005320.1 Cma19g00532 532
1 1042545 1043212 - MELO3C018544.2.1 Cme01g00144 144
1 1046949 1047446 - MELO3C018545.2.1 Cme01g00145 145
1 1049107 1049883 - MELO3C018546.2.1 Cme01g00146 146
1 1205901 1206383 - PI0025352.1 Cmetu01g1966 1966
7 202149 202904 + PI0010663.1 Cmetu07g1308 1308
4 2255787 2256287 + CmoCh04G004530.1 Cmo04g00453 453
11 10092788 10097388 - CmoCh11G014340.1 Cmo11g01434 1434
19 6261258 6261737 + CmoCh19G005380.1 Cmo19g00538 538
19 6272186 6272668 - CmoCh19G005400.1 Cmo19g00540 540
19 6275721 6276194 - CmoCh19G005410.1 Cmo19g00541 541
2 7929906 7930394 - CmPI595203_02g007460.1 Cmu02g0746 746
2 7956448 7956894 - CmPI595203_02g007480.1 Cmu02g0748 748
2 8000213 8000704 + CmPI595203_02g007520.1 Cmu02g0752 752
8 9634890 9635480 + Conep08aG0108200.1 Cone8ag1053 1053
1 2196405 2198904 + Cp4.1LG01g02850.1 Cpe01g00380 380
4 4114922 4115404 - Cp4.1LG04g07460.1 Cpe04g00339 339
15 5338985 5339467 - Cp4.1LG15g04200.1 Cpe15g00418 418
15 5341479 5341961 - Cp4.1LG15g04210.1 Cpe15g00419 419
15 5346921 5347412 + Cp4.1LG15g04120.1 Cpe15g00420 420
2 8572159 8572641 - CrPI670011_02g010610.1 Cre02g1061 1061
2 8642611 8643108 - CrPI670011_02g010650.1 Cre02g1065 1065
2 8699809 8700291 - CrPI670011_02g010670.1 Cre02g1067 1067
7 4714813 4715562 + CsaV3_7G007550.1 Csa07g00656 656
7 4717004 4717945 + CsaV3_7G007560.1 Csa07g00657 657
7 4719160 4720042 + CsaV3_7G007570.1 Csa07g00658 658
12 1510068 1510550 + Lag0014506.1 Lac12g0134 134
3 7785978 7786475 - Lsi03G006260.1 Lsi03g00626 626
3 7796401 7796898 - Lsi03G006270.1 Lsi03g00627 627
3 7805463 7805954 - Lsi03G006280.1 Lsi03g00628 628
3 19231417 19231917 + Lsi03G009970.1 Lsi03g00997 997
10 4344517 4346490 - Lsi10G002720.1 Lsi10g00272 272
6 8986276 8987104 + Sed0003091.1 Sed06g0830 830
7 8657220 8657717 - Sed0021858.1 Sed07g1155 1155
1 5463869 5464369 + Tan0022256.1 Tan01g0594 594
2 17670273 17671044 - Tan0003695.1 Tan02g1068 1068
3 9050244 9061593 + Vvi3g796 Vvi3g796 796
3 9072902 9073766 - Vvi3g797 Vvi3g797 797
3 9080158 9083772 + Vvi3g798 Vvi3g798 798
3 9101006 9101492 - Vvi3g799 Vvi3g799 799
3 9109631 9110250 - Vvi3g800 Vvi3g800 800
3 9111918 9120041 + Vvi3g801 Vvi3g801 801
3 9120044 9130663 - Vvi3g802 Vvi3g802 802
3 9139936 9145805 - Vvi3g803 Vvi3g803 803
3 9146221 9147403 - Vvi3g804 Vvi3g804 804
3 9150088 9150574 - Vvi3g805 Vvi3g805 805
       

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