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
Vvi18g1670 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1671 . . . . . . . . . . . Cma09g01302 . . . . . Bhi04g02576 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma02g00296 . . . . . . . . . . . . . . . . Cla11g00842 Cam11g0873 Cec11g0873 Cco11g0869 Clacu11g0989 Cmu11g0840 Cre11g1317 . . . .
Vvi18g1672 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1673 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1674 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1675 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1676 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1677 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1678 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1679 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 69245951 69248494 - XM_039030762.1 Bhi04g02576 2576
2 3429978 3431521 - Bma014748.1 Bma02g00296 296
11 11941305 11943071 - CaPI482276_11g008730.1 Cam11g0873 873
11 10857190 10859217 - CcPI632755_11g008690.1 Cco11g0869 869
11 11269387 11271404 - CePI673135_11g008730.1 Cec11g0873 873
11 11363489 11365286 + ClG42_11g0098900.10 Clacu11g0989 989
11 12897813 12899610 - ClCG11G008780.2 Cla11g00842 842
9 9068457 9084292 - CmaCh09G013020.1 Cma09g01302 1302
11 10691424 10693221 + CmPI595203_11g008400.1 Cmu11g0840 840
11 12787785 12789825 - CrPI670011_11g013170.1 Cre11g1317 1317
18 27377307 27377568 + Vvi18g1670 Vvi18g1670 1670
18 27385313 27387315 - Vvi18g1671 Vvi18g1671 1671
18 27396664 27397644 - Vvi18g1672 Vvi18g1672 1672
18 27402302 27404654 - Vvi18g1673 Vvi18g1673 1673
18 27404734 27407557 + Vvi18g1674 Vvi18g1674 1674
18 27407572 27411680 + Vvi18g1675 Vvi18g1675 1675
18 27419480 27419627 - Vvi18g1676 Vvi18g1676 1676
18 27426690 27430888 + Vvi18g1677 Vvi18g1677 1677
18 27434976 27437128 - Vvi18g1678 Vvi18g1678 1678
18 27437275 27443136 + Vvi18g1679 Vvi18g1679 1679
       

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