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
Vvi19g284 . Blo03g01523 . . . . . . . . . . . . . Cpe06g00715 . Bhi09g01998 Tan01g4450 . . Hepe01g1356 Mch11g1110 . Cla11g01800 Cam11g1866 Cec11g1890 Cco11g1896 Clacu11g2029 Cmu11g1835 Cre11g2242 . . . . Lsi04g01284 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g285 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g286 . . . . . . . . Cmo16g00859 . . . . . . . . . . . . . . . Cla10g00613 Cam10g0607 Cec10g0636 Cco10g0611 Clacu10g0638 Cmu10g1457 Cre10g0849 . . . Cone15ag1088 . Csa03g00602 . . . . . . . . . . . . . Cma04g00914 . . Car16g00814 Cpe14g00696 . . . . . . . . . . . . . . . Lsi05g00693 . Chy06g01721 .
Vvi19g287 . . . . . . . . . . . . . . . . . . . . . . . . Cla10g00612 Cam10g0606 Cec10g0635 Cco10g0610 Clacu10g0637 Cmu10g1456 Cre10g0848 . . . . . Csa03g00601 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy06g01722 .
Vvi19g288 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g289 . . . . . . . . . . . . . . . Cpe06g00716 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g290 . . . . . . . . . . . . Car01g01000 . . Cpe06g00717 Cpe02g00724 . . . . . . . Cla11g01802 Cam11g1868 Cec11g1892 Cco11g1898 Clacu11g2031 Cmu11g1836 Cre11g2243 Cone6ag0115 Cone9ag0133 . . Lsi04g01282 . . . . . . . Bpe11g00502 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g291 . . Bda07g00275 . . Bpe02g01919 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g292 . . . . . . . . . . . . . . . . . . . . . . . . Cla10g00609 Cam10g0602 Cec10g0629 Cco10g0605 Clacu10g0631 . Cre10g0843 . . Cone14ag1086 . . Csa03g00597 . . . . . . . . . . . . . . . . Car16g00818 Cpe14g00700 . . . . . . . . . . . . . . . Lsi05g00688 . Chy06g01726 .
Vvi19g293 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 3915731 3916904 - Bda025356.1 Bda07g00275 275
9 55846469 55852255 - XM_039041140.1 Bhi09g01998 1998
3 42157754 42161527 - BLOR12704 Blo03g01523 1523
2 21148652 21149698 + Bpe009745.1 Bpe02g01919 1919
11 3873137 3877589 + Bpe003873.2 Bpe11g00502 502
10 9211158 9216530 + CaPI482276_10g006020.1 Cam10g0602 602
10 9259389 9265291 + CaPI482276_10g006060.1 Cam10g0606 606
10 9265758 9267796 - CaPI482276_10g006070.1 Cam10g0607 607
11 31211623 31221913 + CaPI482276_11g018660.1 Cam11g1866 1866
11 31232043 31237836 + CaPI482276_11g018680.1 Cam11g1868 1868
1 9474578 9480690 - Carg27980-RA Car01g01000 1000
16 5368019 5370132 + Carg24070-RA Car16g00814 814
16 5382774 5387516 - Carg24074-RA Car16g00818 818
10 8066385 8071702 + CcPI632755_10g006050.1 Cco10g0605 605
10 8115655 8119560 + CcPI632755_10g006100.1 Cco10g0610 610
10 8120024 8122498 - CcPI632755_10g006110.1 Cco10g0611 611
11 31654145 31664702 + CcPI632755_11g018960.1 Cco11g1896 1896
11 31674866 31680291 + CcPI632755_11g018980.1 Cco11g1898 1898
10 8415221 8420440 + CePI673135_10g006290.1 Cec10g0629 629
10 8457180 8461081 + CePI673135_10g006350.1 Cec10g0635 635
10 8461545 8463623 - CePI673135_10g006360.1 Cec10g0636 636
11 33114668 33125171 + CePI673135_11g018900.1 Cec11g1890 1890
11 33134821 33140610 + CePI673135_11g018920.1 Cec11g1892 1892
6 20101097 20104271 + Chy6G122490.1 Chy06g01721 1721
6 20106114 20107416 - Chy6G122500.1 Chy06g01722 1722
6 20124453 20130689 - Chy6G122540.1 Chy06g01726 1726
10 8549171 8554511 + ClG42_10g0063100.10 Clacu10g0631 631
10 8605444 8609372 + ClG42_10g0063700.10 Clacu10g0637 637
10 8609832 8611871 - ClG42_10g0063800.10 Clacu10g0638 638
11 31253741 31264290 + ClG42_11g0202900.10 Clacu11g2029 2029
11 31274313 31280026 + ClG42_11g0203100.10 Clacu11g2031 2031
10 9043046 9048565 + ClCG10G006520.1 Cla10g00609 609
10 9103228 9109351 + ClCG10G006550.2 Cla10g00612 612
10 9109187 9111807 - ClCG10G006570.1 Cla10g00613 613
11 31654095 31664718 + ClCG11G018420.2 Cla11g01800 1800
11 31674527 31680609 + ClCG11G018450.2 Cla11g01802 1802
4 4739002 4743237 + CmaCh04G009140.1 Cma04g00914 914
16 4575698 4578268 + CmoCh16G008590.1 Cmo16g00859 859
10 9179414 9183331 + CmPI595203_10g014560.1 Cmu10g1456 1456
10 9183795 9185834 - CmPI595203_10g014570.1 Cmu10g1457 1457
11 30503272 30513823 + CmPI595203_11g018350.1 Cmu11g1835 1835
11 30523876 30529659 + CmPI595203_11g018360.1 Cmu11g1836 1836
6 553259 557448 - Conep06aG0011500.1 Cone6ag0115 115
9 582894 587137 - Conep09aG0013400.1 Cone9ag0133 133
14 9086462 9089451 - Conep14aG0110800.1 Cone14ag1086 1086
15 8960535 8962518 + Conep15aG0111400.1 Cone15ag1088 1088
2 4585522 4591503 + Cp4.1LG02g01520.1 Cpe02g00724 724
6 4443195 4452551 + Cp4.1LG06g07100.1 Cpe06g00715 715
6 4453347 4455896 - Cp4.1LG06g07120.1 Cpe06g00716 716
6 4457683 4462449 + Cp4.1LG06g07070.1 Cpe06g00717 717
14 4588962 4592635 + Cp4.1LG14g00200.1 Cpe14g00696 696
14 4602691 4607340 - Cp4.1LG14g00180.1 Cpe14g00700 700
10 9186178 9191540 + CrPI670011_10g008430.1 Cre10g0843 843
10 9233353 9237216 + CrPI670011_10g008480.1 Cre10g0848 848
10 9237680 9239737 - CrPI670011_10g008490.1 Cre10g0849 849
11 34181529 34184115 + CrPI670011_11g022420.1 Cre11g2242 2242
11 34193952 34199727 + CrPI670011_11g022430.1 Cre11g2243 2243
3 5135428 5141637 + CsaV3_3G005970.1 Csa03g00597 597
3 5158671 5160001 + CsaV3_3G006010.1 Csa03g00601 601
3 5161101 5164917 - CsaV3_3G006020.1 Csa03g00602 602
1 78746421 78751330 - Hsped.01g13560.1 Hepe01g1356 1356
4 20241871 20247773 - Lsi04G012820.1 Lsi04g01282 1282
4 20264860 20277753 - Lsi04G012840.1 Lsi04g01284 1284
5 9155968 9161346 + Lsi05G006880.1 Lsi05g00688 688
5 9191341 9194389 - Lsi05G006930.1 Lsi05g00693 693
11 7748321 7753033 + MC11g0913 Mch11g1110 1110
1 109832010 109839778 + Tan0004681.3 Tan01g4450 4450
19 3606188 3608810 + Vvi19g284 Vvi19g284 284
19 3610667 3614137 + Vvi19g285 Vvi19g285 285
19 3614863 3619201 + Vvi19g286 Vvi19g286 286
19 3619993 3623415 - Vvi19g287 Vvi19g287 287
19 3624908 3626699 - Vvi19g288 Vvi19g288 288
19 3626940 3634812 - Vvi19g289 Vvi19g289 289
19 3639942 3650257 + Vvi19g290 Vvi19g290 290
19 3653740 3655574 + Vvi19g291 Vvi19g291 291
19 3658551 3664452 - Vvi19g292 Vvi19g292 292
19 3665666 3667741 - Vvi19g293 Vvi19g293 293
       

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