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
Vvi3g1056 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi03g00768 Csa07g00545 . Cme01g00246 . . . . . . . . . . . . . . . . . . . . . . . . Cla09g01506 Cam09g1655 Cec09g1662 Cco09g1712 . . Cre09g1546 . . Chy01g00259 .
Vvi3g1057 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo04g00659 Cmo16g00534 . . . . . Cpe01g00553 . . . . . . . . . . . . . . . . . .
Vvi3g1058 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo04g00658 Cmo16g00535 . . . . Cpe14g00415 Cpe01g00552 . . . . . . . . . . . . . . . . . .
Vvi3g1059 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo04g00656 . . . . . Cpe14g00416 Cpe01g00551 . . . . . . . . . . . . . . . . . .
Vvi3g1060 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1061 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo04g00653 Cmo16g00537 . . . . Cpe14g00417 . . . . . . . . . . . . . . . . . . .
Vvi3g1062 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1063 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1064 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1065 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
9 28595886 28598572 - CaPI482276_09g016550.1 Cam09g1655 1655
9 28554848 28557802 + CcPI632755_09g017120.1 Cco09g1712 1712
9 30376310 30378959 + CePI673135_09g016620.1 Cec09g1662 1662
1 1812411 1818886 - Chy1G002590.1 Chy01g00259 259
9 29333846 29336950 + ClCG09G015350.2 Cla09g01506 1506
1 1790973 1793929 - MELO3C018648.2.1 Cme01g00246 246
4 3242262 3244657 - CmoCh04G006530.1 Cmo04g00653 653
4 3247498 3251941 - CmoCh04G006560.1 Cmo04g00656 656
4 3255391 3261940 + CmoCh04G006580.1 Cmo04g00658 658
4 3262872 3268538 + CmoCh04G006590.1 Cmo04g00659 659
16 2591694 2595372 - CmoCh16G005340.1 Cmo16g00534 534
16 2598924 2605912 - CmoCh16G005350.1 Cmo16g00535 535
16 2608907 2619221 + CmoCh16G005370.1 Cmo16g00537 537
1 3167494 3180030 - Cp4.1LG01g01180.1 Cpe01g00551 551
1 3181789 3188006 + Cp4.1LG01g01220.1 Cpe01g00552 552
1 3189085 3195393 + Cp4.1LG01g01240.1 Cpe01g00553 553
14 2600375 2606524 - Cp4.1LG14g02960.1 Cpe14g00415 415
14 2609955 2614048 + Cp4.1LG14g03040.1 Cpe14g00416 416
14 2618967 2620730 + Cp4.1LG14g03050.1 Cpe14g00417 417
9 31210510 31213195 + CrPI670011_09g015460.1 Cre09g1546 1546
7 3980777 3983803 + CsaV3_7G006440.1 Csa07g00545 545
3 10851086 10853968 - Lsi03G007680.1 Lsi03g00768 768
3 17907033 17917706 - Vvi3g1056 Vvi3g1056 1056
3 17918850 17928072 - Vvi3g1057 Vvi3g1057 1057
3 17935112 17947035 - Vvi3g1058 Vvi3g1058 1058
3 17953388 17966632 + Vvi3g1059 Vvi3g1059 1059
3 17971905 17975776 - Vvi3g1060 Vvi3g1060 1060
3 17992263 17995838 - Vvi3g1061 Vvi3g1061 1061
3 18008253 18010868 + Vvi3g1062 Vvi3g1062 1062
3 18171436 18173096 - Vvi3g1063 Vvi3g1063 1063
3 18194162 18194547 - Vvi3g1064 Vvi3g1064 1064
3 18284553 18284859 + Vvi3g1065 Vvi3g1065 1065
       

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