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
Vvi1g561 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g562 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g563 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g564 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g565 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g566 . . Bda01g01768 . . . . Bma15g00269 . Cmo18g00664 . . . . . Cpe09g00607 Cpe01g01630 . . . . . . . . . . . . . . Cone13ag0715 Cone19ag0714 . . . . . . Blo06g00801 Blo11g00988 Bda07g01670 . . Bpe02g01947 Bma01g00510 . . . Cmo15g00911 . Cma15g00876 Car04g01856 Car15g00824 Cpe13g00438 . Bhi12g00983 . . . Hepe02g2584 . Lcy10g1581 Cla01g00666 Cam01g0697 Cec01g0689 Cco01g0717 Clacu01g0685 Cmu01g0660 Cre09g1846 Lsi09g00721 Csa05g01296 . Cme09g01284
Vvi1g567 . . . . . . . . . . . . . . . . Cpe01g01867 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo04g02250 . Cma04g02154 . Car04g02089 . . . Bhi12g00994 . . . . . Lcy10g1576 Cla01g00669 Cam01g0701 Cec01g0693 Cco01g0721 Clacu01g0689 Cmu01g0664 Cre09g1843 Lsi09g00727 Csa05g01302 Chy09g00462 Cme09g01275
Vvi1g568 . . . . . . . . . . . . Car04g00999 . . . . Bhi07g00467 . . . . . . Cla07g00469 Cam07g0504 Cec07g0559 Cco07g0523 Clacu07g0513 Cmu07g0551 Cre07g0885 . . . . Lsi04g01031 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g569 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0742 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g570 Blo01g00797 . . . . . . . . . . . . . . . Cpe01g01868 . . . . . . . . . . . . . . . . Cone6ag0329 . . . . . . . . . . Bpe02g01946 Bma01g00511 . . Cmo04g02252 Cmo15g00910 Cma04g02155 Cma15g00875 Car04g02090 Car15g00823 Cpe13g00439 . Bhi12g00995 . . . Hepe02g2581 . Lcy10g1575 Cla01g00671 Cam01g0703 Cec01g0697 Cco01g0724 Clacu01g0691 Cmu01g0666 Cre09g1841 Lsi09g00729 Csa05g01304 Chy09g00461 Cme09g01269
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 53931472 53935141 + Bda004057.1 Bda01g01768 1768
7 30992736 30997677 - Bda028554.1 Bda07g01670 1670
7 20490161 20496755 + XM_039035386.1 Bhi07g00467 467
12 29917941 29922155 - XM_039019864.1 Bhi12g00983 983
12 30286291 30304813 + XM_039019462.1 Bhi12g00994 994
12 30353515 30355617 - XM_039019036.1 Bhi12g00995 995
1 11876529 11877673 - BLOR00797 Blo01g00797 797
6 31273041 31277276 - BLOR17384 Blo06g00801 801
11 24231887 24261250 - BLOR03864 Blo11g00988 988
1 4193783 4196740 - Bma000689.1 Bma01g00510 510
1 4203824 4204967 - Bma000690.1 Bma01g00511 511
15 2641034 2645361 + Bma013248.1 Bma15g00269 269
2 21405322 21406469 + Bpe009772.1 Bpe02g01946 1946
2 21409682 21414517 + Bpe009773.1 Bpe02g01947 1947
1 7824176 7827272 - CaPI482276_01g006970.1 Cam01g0697 697
1 7866509 7887443 + CaPI482276_01g007010.1 Cam01g0701 701
1 7913001 7914838 - CaPI482276_01g007030.1 Cam01g0703 703
7 7227337 7234677 - CaPI482276_07g005040.1 Cam07g0504 504
4 5743448 5747947 + Carg00175-RA Car04g00999 999
4 10740716 10748107 + Carg24408-RA Car04g01856 1856
4 17028428 17052358 + Carg25263-RA Car04g02089 2089
4 17076200 17077292 - Carg17697-RA Car04g02090 2090
15 4684148 4685124 + Carg01332-RA Car15g00823 823
15 4690566 4693890 + Carg01331-RA Car15g00824 824
1 7618846 7621947 - CcPI632755_01g007170.1 Cco01g0717 717
1 7667656 7688369 + CcPI632755_01g007210.1 Cco01g0721 721
1 7710610 7712465 - CcPI632755_01g007240.1 Cco01g0724 724
7 6586106 6592186 - CcPI632755_07g005230.1 Cco07g0523 523
1 7685157 7688253 - CePI673135_01g006890.1 Cec01g0689 689
1 7740216 7759093 + CePI673135_01g006930.1 Cec01g0693 693
1 7787638 7789511 - CePI673135_01g006970.1 Cec01g0697 697
7 6804319 6809858 - CePI673135_07g005590.1 Cec07g0559 559
9 4101650 4103425 + Chy9G161770.1 Chy09g00461 461
9 4118669 4137954 - Chy9G161780.1 Chy09g00462 462
1 7499189 7502284 - ClG42_01g0068500.10 Clacu01g0685 685
1 7541584 7562740 + ClG42_01g0068900.10 Clacu01g0689 689
1 7585784 7587615 - ClG42_01g0069100.10 Clacu01g0691 691
7 6458224 6465509 - ClG42_07g0051300.10 Clacu07g0513 513
1 7896847 7899942 - ClCG01G006830.2 Cla01g00666 666
1 7943042 7966222 + ClCG01G006860.2 Cla01g00669 669
1 7989357 7993515 - ClCG01G006870.1 Cla01g00671 671
7 6536596 6544027 - ClCG07G004960.1 Cla07g00469 469
4 15081201 15127514 + CmaCh04G021540.1 Cma04g02154 2154
4 15130237 15131768 - CmaCh04G021550.1 Cma04g02155 2155
15 4431177 4432319 + CmaCh15G008750.1 Cma15g00875 875
15 4437647 4441116 + CmaCh15G008760.1 Cma15g00876 876
9 17555890 17557780 + MELO3C005226.2.1 Cme09g01269 1269
9 17597423 17627963 - MELO3C005228.2.1 Cme09g01275 1275
9 17753753 17757209 + MELO3C005235.2.1 Cme09g01284 1284
4 16857606 16860865 + CmoCh04G022500.1 Cmo04g02250 2250
4 16866801 16868118 - CmoCh04G022520.1 Cmo04g02252 2252
15 4609679 4615712 + CmoCh15G009100.1 Cmo15g00910 910
15 4621166 4624839 + CmoCh15G009110.1 Cmo15g00911 911
18 8479056 8492863 + CmoCh18G006640.1 Cmo18g00664 664
1 7472573 7475668 - CmPI595203_01g006600.1 Cmu01g0660 660
1 7514966 7536171 + CmPI595203_01g006640.1 Cmu01g0664 664
1 7559127 7560973 - CmPI595203_01g006660.1 Cmu01g0666 666
7 6602402 6609680 - CmPI595203_07g005510.1 Cmu07g0551 551
6 1559199 1560586 - Conep06aG0033500.1 Cone6ag0329 329
12 6810352 6811599 + Conep12aG0076500.1 Cone12ag0742 742
13 6953765 6956924 + Conep13aG0073900.1 Cone13ag0715 715
19 5911087 5914274 + Conep19aG0073500.1 Cone19ag0714 714
1 9958863 9966069 + Cp4.1LG01g16360.1 Cpe01g01630 1630
1 15999896 16048823 + Cp4.1LG01g18670.1 Cpe01g01867 1867
1 16052121 16053639 - Cp4.1LG01g18730.1 Cpe01g01868 1868
9 4231206 4237781 + Cp4.1LG09g05800.1 Cpe09g00607 607
13 4710247 4714492 - Cp4.1LG13g06440.1 Cpe13g00438 438
13 4722926 4724136 - Cp4.1LG13g06420.1 Cpe13g00439 439
7 7660789 7666324 - CrPI670011_07g008850.1 Cre07g0885 885
9 36761521 36763407 + CrPI670011_09g018410.1 Cre09g1841 1841
9 36787937 36808663 - CrPI670011_09g018430.1 Cre09g1843 1843
9 36852465 36855562 + CrPI670011_09g018460.1 Cre09g1846 1846
5 13777780 13781371 - CsaV3_5G017190.1 Csa05g01296 1296
5 13822662 13845207 + CsaV3_5G017250.1 Csa05g01302 1302
5 13862919 13865325 - CsaV3_5G017270.1 Csa05g01304 1304
2 72793315 72794992 + Hsped.02g25810.1 Hepe02g2581 2581
2 72901507 72905449 + Hsped.02g25840.1 Hepe02g2584 2584
10 40097137 40098910 + Maker00006980 Lcy10g1575 1575
10 40116572 40128535 - Maker00006925 Lcy10g1576 1576
10 40167979 40171892 + Maker00039698 Lcy10g1581 1581
4 11824195 11831407 + Lsi04G010310.1 Lsi04g01031 1031
9 8297303 8300564 - Lsi09G007210.1 Lsi09g00721 721
9 8364274 8366469 + Lsi09G007270.1 Lsi09g00727 727
9 8399375 8401574 - Lsi09G007290.1 Lsi09g00729 729
1 6274422 6285766 - Vvi1g561 Vvi1g561 561
1 6286212 6286623 - Vvi1g562 Vvi1g562 562
1 6289242 6290820 + Vvi1g563 Vvi1g563 563
1 6298551 6305704 + Vvi1g564 Vvi1g564 564
1 6306238 6307845 + Vvi1g565 Vvi1g565 565
1 6319498 6325465 + Vvi1g566 Vvi1g566 566
1 6328678 6391646 + Vvi1g567 Vvi1g567 567
1 6391852 6397625 - Vvi1g568 Vvi1g568 568
1 6411340 6412579 + Vvi1g569 Vvi1g569 569
1 6416960 6418730 - Vvi1g570 Vvi1g570 570
       

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