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
Vvi3g836 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g837 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi10g00268 . . . . . . . . . . . . . . . . . . . . Bhi10g01644 . . . . . . Cla09g01628 . . . . . . . . . .
Vvi3g838 . . . . . . . . . . . . . . . . . . . . . . . . Cla10g00943 Cam10g0965 Cec10g1000 Cco10g0961 Clacu10g0988 Cmu10g1771 Cre10g1145 . . . Cone10ag1087 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi03g00982 . . .
Vvi3g839 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g840 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g841 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g842 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g843 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g844 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g845 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
10 41630869 41633721 + XM_039046514.1 Bhi10g01644 1644
10 21688410 21689623 - CaPI482276_10g009650.1 Cam10g0965 965
10 20860110 20876684 - CcPI632755_10g009610.1 Cco10g0961 961
10 22568604 22575334 - CePI673135_10g010000.1 Cec10g1000 1000
10 21301629 21308381 - ClG42_10g0098800.10 Clacu10g0988 988
9 32497667 32499787 - ClCG09G016600.1 Cla09g01628 1628
10 22268981 22283191 - ClCG10G009840.2 Cla10g00943 943
10 21909588 21916342 - CmPI595203_10g017710.1 Cmu10g1771 1771
10 7536536 7540059 - Conep10aG0111400.1 Cone10ag1087 1087
10 23605955 23613930 - CrPI670011_10g011450.1 Cre10g1145 1145
3 18966933 18972686 + Lsi03G009820.1 Lsi03g00982 982
10 4303464 4312165 + Lsi10G002680.1 Lsi10g00268 268
3 9774608 9789444 - Vvi3g836 Vvi3g836 836
3 9826459 9827998 - Vvi3g837 Vvi3g837 837
3 9989269 10030836 + Vvi3g838 Vvi3g838 838
3 10091913 10092024 + Vvi3g839 Vvi3g839 839
3 10125779 10126001 + Vvi3g840 Vvi3g840 840
3 10137656 10139644 + Vvi3g841 Vvi3g841 841
3 10150393 10151378 - Vvi3g842 Vvi3g842 842
3 10217206 10217764 + Vvi3g843 Vvi3g843 843
3 10227597 10230155 + Vvi3g844 Vvi3g844 844
3 10230648 10232611 - Vvi3g845 Vvi3g845 845
       

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