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
Vvi18g630 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1621 Cone7ag1327 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g631 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g632 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g633 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g634 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g635 . . . . . . . . . . Cma01g01780 . Car01g01388 . . . . . . . . . . . . . . . . . . . Cone7ag1328 . . Lsi04g01476 Csa04g02486 . . . . . Bda01g01639 Bpe02g01082 . . . . Cmo01g01838 . . . . . . Cpe02g00226 Bhi09g03221 . . . . . . Cla05g02112 . . Cco05g2327 . Cmu05g2124 . . . Chy07g00195 .
Vvi18g636 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g637 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g638 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g639 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 52340459 52343807 - Bda032966 Bda01g01639 1639
9 82839583 82845108 - XM_039041223.1 Bhi09g03221 3221
2 13961062 13963672 - Bpe025117 Bpe02g01082 1082
1 12140357 12143727 - Carg10649-RA Car01g01388 1388
5 31814960 31818509 + CcPI632755_05g023270.1 Cco05g2327 2327
7 1584618 1587691 + Chy7G130250.1 Chy07g00195 195
5 32712175 32715522 + ClCG05G020670.2 Cla05g02112 2112
1 11931026 11934396 - CmaCh01G017800.1 Cma01g01780 1780
1 13426818 13429971 - CmoCh01G018380.1 Cmo01g01838 1838
5 30737107 30742150 + CmPI595203_05g021240.1 Cmu05g2124 2124
4 12297026 12298011 + Conep04aG0167300.1 Cone4ag1621 1621
7 9715746 9716902 - Conep07aG0136700.1 Cone7ag1327 1327
7 9718315 9721168 - Conep07aG0136800.1 Cone7ag1328 1328
2 1159077 1162322 + Cp4.1LG02g06450.1 Cpe02g00226 226
4 24771435 24774514 + CsaV3_4G035120.1 Csa04g02486 2486
4 22496938 22503303 - Lsi04G014760.1 Lsi04g01476 1476
18 7435494 7436733 - Vvi18g630 Vvi18g630 630
18 7438729 7439704 + Vvi18g631 Vvi18g631 631
18 7443688 7448671 - Vvi18g632 Vvi18g632 632
18 7464763 7465436 + Vvi18g633 Vvi18g633 633
18 7471548 7473041 - Vvi18g634 Vvi18g634 634
18 7474793 7480633 - Vvi18g635 Vvi18g635 635
18 7484812 7485994 - Vvi18g636 Vvi18g636 636
18 7499913 7512039 - Vvi18g637 Vvi18g637 637
18 7515407 7516048 + Vvi18g638 Vvi18g638 638
18 7519685 7520846 + Vvi18g639 Vvi18g639 639
       

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