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
Vvi1g511 . . . . . . Bma14g01919 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g512 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g513 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g514 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g515 Blo01g00773 Blo16g00758 Bda01g01794 Bda11g00189 Bpe13g01005 . . . . . . . . . . . Cpe01g01853 . . . . . . . . . . . . . . . . Cone6ag0353 . . Csa05g01977 . . . . . Bda11g00189 . Bpe02g01969 Bma01g00490 Bma06g01133 . Cmo04g02227 . Cma04g02134 . Car04g02071 . . . Bhi12g00955 . . . Hepe02g2611 . Lcy10g1378 Cla01g00646 Cam01g0674 Cec01g0665 Cco01g0693 Clacu01g0662 Cmu01g0635 Cre09g1870 Lsi09g00697 . Chy09g00812 .
Vvi1g516 . . . . . . . Bma15g00272 Cmo04g01112 . Cma04g01042 Cma04g00086 . . . . . . . . . . . . . . . . . . . Cone8ag0594 . . . . . . . . Blo11g00904 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g517 . . . . . Bpe10g01006 . Bma15g00023 Cmo04g01113 . Cma04g01043 Cma04g00087 Car04g00973 . . . . Bhi07g00418 . . Lac13g1296 Hepe01g0614 . . Cla07g00520 Cam07g0555 Cec07g0608 Cco07g0580 Clacu07g0559 Cmu07g0596 Cre07g0928 . . Cone6ag0351 Cone9ag0384 Lsi04g00994 . Chy10g00217 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01128 . .
Vvi1g518 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g519 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g520 Blo01g00774 . Bda01g01790 . Bpe13g01003 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0350 Cone9ag0383 . Csa05g01975 . . Blo06g01034 . . . . Bpe02g01968 Bma01g00491 . . Cmo04g02228 Cmo15g00933 Cma04g02135 . Car04g02072 Car15g00839 Cpe13g00422 . Bhi12g00956 . . . Hepe02g2610 . Lcy10g1377 Cla01g00647 Cam01g0676 Cec01g0667 Cco01g0695 Clacu01g0664 Cmu01g0637 Cre09g1869 Lsi09g00699 . Chy09g00811 Cme09g01326
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 54085324 54086928 + Bda004078.1 Bda01g01790 1790
1 54154843 54159171 + Bda004085.1 Bda01g01794 1794
11 2418361 2421232 - Bda004906.1 Bda11g00189 189
7 18686629 18689938 + XM_039036353.1 Bhi07g00418 418
12 28917952 28927128 - XM_039018830.1 Bhi12g00955 955
12 28989155 28992308 - XM_039018608.1 Bhi12g00956 956
1 11106570 11111058 - BLOR00773 Blo01g00773 773
1 11154752 11156825 - BLOR00774 Blo01g00774 774
6 33657480 33664617 - BLOR17617 Blo06g01034 1034
11 18486430 18495684 - BLOR03780 Blo11g00904 904
16 31258442 31277428 - BLOR21545 Blo16g00758 758
1 4016697 4020840 - Bma000666.1 Bma01g00490 490
1 4025154 4026809 - Bma000667.1 Bma01g00491 491
6 48229842 48232950 - Bma024229.2 Bma06g01133 1133
14 40970258 40971397 - Bma012709.1 Bma14g01919 1919
15 271501 273186 - Bma012992.1 Bma15g00023 23
15 2657284 2658138 - Bma013251.1 Bma15g00272 272
2 21535475 21537107 + Bpe009791.1 Bpe02g01968 1968
2 21541826 21546019 + Bpe009792.1 Bpe02g01969 1969
10 15497542 15499201 + Bpe003311.1 Bpe10g01006 1006
13 15785846 15787312 + Bpe010686.1 Bpe13g01003 1003
13 15790513 15793324 + Bpe025261 Bpe13g01005 1005
1 7415202 7423782 - CaPI482276_01g006740.1 Cam01g0674 674
1 7446540 7449377 - CaPI482276_01g006760.1 Cam01g0676 676
7 8362608 8365698 - CaPI482276_07g005550.1 Cam07g0555 555
4 5615581 5618201 + Carg00149-RA Car04g00973 973
4 16849292 16853608 - Carg25245-RA Car04g02071 2071
4 16857531 16859330 - Carg25246-RA Car04g02072 2072
15 4831510 4832862 + Carg01316-RA Car15g00839 839
1 7192424 7201724 - CcPI632755_01g006930.1 Cco01g0693 693
1 7224147 7227001 - CcPI632755_01g006950.1 Cco01g0695 695
7 7818865 7821983 - CcPI632755_07g005800.1 Cco07g0580 580
1 7249624 7258243 - CePI673135_01g006650.1 Cec01g0665 665
1 7282857 7285767 - CePI673135_01g006670.1 Cec01g0667 667
7 8151557 8154648 - CePI673135_07g006080.1 Cec07g0608 608
9 10821353 10823326 + Chy9G165270.1 Chy09g00811 811
9 10841988 10848179 + Chy9G165280.1 Chy09g00812 812
10 5495462 5498661 + Chy10G174110.1 Chy10g00217 217
1 7064043 7072601 - ClG42_01g0066200.10 Clacu01g0662 662
1 7094977 7097779 - ClG42_01g0066400.10 Clacu01g0664 664
7 7574491 7577579 - ClG42_07g0055900.10 Clacu07g0559 559
1 7445644 7454203 - ClCG01G006630.2 Cla01g00646 646
1 7479543 7489872 - ClCG01G006640.1 Cla01g00647 647
7 7703432 7706520 - ClCG07G005430.2 Cla07g00520 520
4 429400 433173 + CmaCh04G000860.1 Cma04g00086 86
4 434488 440081 + CmaCh04G000870.1 Cma04g00087 87
4 5399688 5401688 + CmaCh04G010420.1 Cma04g01042 1042
4 5404408 5407866 + CmaCh04G010430.1 Cma04g01043 1043
4 14912910 14917293 - CmaCh04G021340.1 Cma04g02134 2134
4 14921759 14922922 - CmaCh04G021350.1 Cma04g02135 2135
9 18309688 18313304 - MELO3C005260.2.1 Cme09g01326 1326
4 5669684 5673607 + CmoCh04G011120.1 Cmo04g01112 1112
4 5675420 5678524 + CmoCh04G011130.1 Cmo04g01113 1113
4 16639377 16646382 - CmoCh04G022270.1 Cmo04g02227 2227
4 16650696 16652523 - CmoCh04G022280.1 Cmo04g02228 2228
15 4774560 4776689 + CmoCh15G009330.1 Cmo15g00933 933
1 7033898 7042466 - CmPI595203_01g006350.1 Cmu01g0635 635
1 7064993 7067793 - CmPI595203_01g006370.1 Cmu01g0637 637
7 7733089 7736178 - CmPI595203_07g005960.1 Cmu07g0596 596
6 1705707 1707644 + Conep06aG0035800.1 Cone6ag0350 350
6 1708509 1711439 - Conep06aG0035900.1 Cone6ag0351 351
6 1726123 1729255 + Conep06aG0036100.1 Cone6ag0353 353
8 5022593 5026824 + Conep08aG0061500.1 Cone8ag0594 594
9 1741600 1743423 + Conep09aG0039300.1 Cone9ag0383 383
9 1744371 1746895 - Conep09aG0039400.1 Cone9ag0384 384
1 15776703 15781262 - Cp4.1LG01g18530.1 Cpe01g01853 1853
13 4557364 4558733 - Cp4.1LG13g06680.1 Cpe13g00422 422
7 8966675 8969750 - CrPI670011_07g009280.1 Cre07g0928 928
9 37251888 37255827 + CrPI670011_09g018690.1 Cre09g1869 1869
9 37271624 37280947 + CrPI670011_09g018700.1 Cre09g1870 1870
5 11518997 11524654 + CsaV3_5G014520.1 Csa05g01128 1128
5 23124197 23126078 + CsaV3_5G027940.1 Csa05g01975 1975
5 23141653 23150181 + CsaV3_5G027960.1 Csa05g01977 1977
1 67503291 67508467 + Hsped.01g06140.1 Hepe01g0614 614
2 73385146 73388652 + Hsped.02g26100.1 Hepe02g2610 2610
2 73404628 73418941 + Hsped.02g26110.1 Hepe02g2611 2611
13 11899759 11903216 - Lag0041092.1 Lac13g1296 1296
10 37062778 37066245 + Maker00008792 Lcy10g1377 1377
10 37082960 37093898 + Maker00008663 Lcy10g1378 1378
4 10876336 10881038 + Lsi04G009940.1 Lsi04g00994 994
9 7897142 7906690 - Lsi09G006970.1 Lsi09g00697 697
9 7923414 7924541 - Lsi09G006990.1 Lsi09g00699 699
1 5672819 5681127 - Vvi1g511 Vvi1g511 511
1 5681624 5683551 - Vvi1g512 Vvi1g512 512
1 5687001 5688994 + Vvi1g513 Vvi1g513 513
1 5694700 5696103 - Vvi1g514 Vvi1g514 514
1 5701246 5706199 - Vvi1g515 Vvi1g515 515
1 5722390 5726992 - Vvi1g516 Vvi1g516 516
1 5753718 5757294 + Vvi1g517 Vvi1g517 517
1 5757320 5757961 + Vvi1g518 Vvi1g518 518
1 5758616 5758826 - Vvi1g519 Vvi1g519 519
1 5758852 5764898 - Vvi1g520 Vvi1g520 520
       

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