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
Vvi19g54 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g55 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g56 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g57 . . . . . . . . . . . . . . . . . Bhi09g03546 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car04g00590 . . Cpe01g00528 . . . . . . . . . . . . . . . . . .
Vvi19g58 . . . . . . . . . . Cma01g01265 . . . . . . Bhi09g03545 . . . . Mch11g0985 . . . . . . . . . . . . Lsi04g01990 . . . Blo07g00985 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g59 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g60 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g61 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g62 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g63 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo07g00984 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
9 89226706 89241834 + XM_039044180.1 Bhi09g03545 3545
9 89226706 89241834 + XM_039044181.1 Bhi09g03546 3546
7 29359276 29363109 - BLOR18916 Blo07g00984 984
7 29371926 29376363 - BLOR18917 Blo07g00985 985
4 3365743 3368526 + Carg13115-RA Car04g00590 590
1 9117332 9125495 + CmaCh01G012650.1 Cma01g01265 1265
1 3031762 3039916 - Cp4.1LG01g01320.1 Cpe01g00528 528
4 27014043 27020125 + Lsi04G019900.1 Lsi04g01990 1990
11 6756616 6766679 - MC11g_new0178 Mch11g0985 985
19 580767 594553 + Vvi19g54 Vvi19g54 54
19 600124 606739 + Vvi19g55 Vvi19g55 55
19 611535 620235 + Vvi19g56 Vvi19g56 56
19 621202 638780 - Vvi19g57 Vvi19g57 57
19 639170 641698 - Vvi19g58 Vvi19g58 58
19 649745 649913 + Vvi19g59 Vvi19g59 59
19 655788 657245 - Vvi19g60 Vvi19g60 60
19 657406 658074 + Vvi19g61 Vvi19g61 61
19 661688 663430 + Vvi19g62 Vvi19g62 62
19 669184 677944 + Vvi19g63 Vvi19g63 63
       

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