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
Vvi3g996 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g997 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g998 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g999 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1000 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1002 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo16g00460 . . . . Cpe14g00361 Cpe01g00592 . . . . . . . . . . . . . . . . . .
Vvi3g1003 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0280 Cone9ag0316 . Cone15ag0954 . . . . . . . . . . . . . . . . . . . . Cpe01g00557 . . . . . . . . . . . . . . . . . .
Vvi3g1004 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1005 . . . . . . . . . Cmo11g01481 . . . . . Cpe04g00376 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo16g00251 . . Car11g01184 . Cpe14g00192 . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 9588282 9592383 + Carg26459-RA Car11g01184 1184
11 10472368 10475662 + CmoCh11G014810.1 Cmo11g01481 1481
16 1112133 1114876 + CmoCh16G002510.1 Cmo16g00251 251
16 2210073 2212455 - CmoCh16G004600.1 Cmo16g00460 460
6 1295971 1300334 + Conep06aG0028200.1 Cone6ag0280 280
9 1377787 1382147 + Conep09aG0031900.1 Cone9ag0316 316
15 7566400 7574960 + Conep15aG0097400.1 Cone15ag0954 954
1 3229013 3238863 + Cp4.1LG01g01050.1 Cpe01g00557 557
1 3421344 3423687 + Cp4.1LG01g00730.1 Cpe01g00592 592
4 4416690 4419787 + Cp4.1LG04g07140.1 Cpe04g00376 376
14 1093133 1095859 + Cp4.1LG14g05230.1 Cpe14g00192 192
14 2196371 2199592 - Cp4.1LG14g03480.1 Cpe14g00361 361
3 16194422 16196702 + Vvi3g996 Vvi3g996 996
3 16198325 16210046 - Vvi3g997 Vvi3g997 997
3 16245390 16254121 - Vvi3g998 Vvi3g998 998
3 16254646 16267837 - Vvi3g999 Vvi3g999 999
3 16267840 16268915 - Vvi3g1000 Vvi3g1000 1000
3 16302153 16303017 - Vvi3g1001 Vvi3g1001 1001
3 16336054 16343696 + Vvi3g1002 Vvi3g1002 1002
3 16344078 16360673 - Vvi3g1003 Vvi3g1003 1003
3 16377477 16379930 + Vvi3g1004 Vvi3g1004 1004
3 16414992 16420516 - Vvi3g1005 Vvi3g1005 1005
       

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