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
Vvi3g1006 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1007 . . . . . . . . . Cmo11g01495 . . . . . . . Bhi05g00879 . . . . . . . . . . . . . . . . . Lsi03g00749 Csa07g00565 . Cme01g00227 . . . . . . . . . . . Cma11g01654 . Car11g01216 . . . . . . . . . . . . . . . . . . . Chy01g00240 .
Vvi3g1008 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla09g01553 Cam09g1607 Cec09g1709 Cco09g1763 . . Cre09g1600 . . . .
Vvi3g1009 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1010 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1011 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1012 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1013 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1014 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag0487 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1015 . . . . . . . . . . . . . . . . . Bhi05g00876 . . . . . . . . . . . . . . . . . Lsi03g00750 Csa07g00561 . Cme01g00228 . . . . . . . . . . . Cma11g01638 . . . . . . . . . . . . Cla09g01529 . . . . . . . . Chy01g00244 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 30020193 30023086 + XM_039032411.1 Bhi05g00876 876
5 30119359 30121149 - XM_039032390.1 Bhi05g00879 879
9 27366245 27371270 + CaPI482276_09g016070.1 Cam09g1607 1607
11 9885937 9888078 + Carg24001-RA Car11g01216 1216
9 29940084 29945874 - CcPI632755_09g017630.1 Cco09g1763 1763
9 31786149 31791128 - CePI673135_09g017090.1 Cec09g1709 1709
1 1647572 1649183 - Chy1G002400.1 Chy01g00240 240
1 1673014 1675342 - Chy1G002440.1 Chy01g00244 244
9 30282997 30284694 - ClCG09G015570.1 Cla09g01529 1529
9 30738782 30742897 - ClCG09G015820.1 Cla09g01553 1553
11 10761841 10763999 - CmaCh11G016380.1 Cma11g01638 1638
11 10890209 10892523 - CmaCh11G016540.1 Cma11g01654 1654
1 1614540 1622934 + MELO3C018627.2.1 Cme01g00227 227
1 1624399 1626393 - MELO3C018630.2.1 Cme01g00228 228
11 10608688 10611220 + CmoCh11G014950.1 Cmo11g01495 1495
1 4766701 4769467 - Conep01aG0050900.1 Cone1ag0487 487
9 32590160 32595197 - CrPI670011_09g016000.1 Cre09g1600 1600
7 4101484 4104321 + CsaV3_7G006600.1 Csa07g00561 561
7 4131191 4133023 + CsaV3_7G006640.1 Csa07g00565 565
3 10246741 10249023 + Lsi03G007490.1 Lsi03g00749 749
3 10257486 10259724 + Lsi03G007500.1 Lsi03g00750 750
3 16433626 16441033 - Vvi3g1006 Vvi3g1006 1006
3 16533645 16536550 - Vvi3g1007 Vvi3g1007 1007
3 16584415 16599132 + Vvi3g1008 Vvi3g1008 1008
3 16640516 16642082 - Vvi3g1009 Vvi3g1009 1009
3 16647756 16648117 + Vvi3g1010 Vvi3g1010 1010
3 16649673 16650636 + Vvi3g1011 Vvi3g1011 1011
3 16654191 16659203 + Vvi3g1012 Vvi3g1012 1012
3 16670413 16670960 + Vvi3g1013 Vvi3g1013 1013
3 16692711 16702257 - Vvi3g1014 Vvi3g1014 1014
3 16716642 16718686 - Vvi3g1015 Vvi3g1015 1015
       

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