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
Vvi4g1162 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1163 . . . . . . . . . . . . . . . . . . . . . . . . Cla01g01542 Cam01g1613 Cec04g1258 Cco04g1331 Clacu01g1638 Cmu01g1525 Cre04g1203 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1164 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1165 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1166 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1167 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1168 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1169 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1170 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1171 . Blo16g00100 Bda04g00359 . . . . Bma15g00900 . . . . . . Sed14g0208 Cpe19g00547 . Bhi03g01403 Tan03g1361 Cmetu08g1663 . Hepe04g1138 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi07g01069 Csa06g02816 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 49719895 49721588 - Bda019284.1 Bda04g00359 359
3 29431048 29437995 + XM_039025542.1 Bhi03g01403 1403
16 2411820 2413131 + BLOR07348 Blo16g00100 100
15 30941085 30942947 - Bma014103.1 Bma15g00900 900
1 29713113 29720493 + CaPI482276_01g016130.1 Cam01g1613 1613
4 28661699 28668986 + CcPI632755_04g013310.1 Cco04g1331 1331
4 32203023 32210375 + CePI673135_04g012580.1 Cec04g1258 1258
1 28513125 28519299 + ClG42_01g0163800.10 Clacu01g1638 1638
1 30068923 30075765 + ClCG01G015760.1 Cla01g01542 1542
8 18699264 18706251 + PI0021496.1 Cmetu08g1663 1663
1 28862400 28869768 + CmPI595203_01g015250.1 Cmu01g1525 1525
19 4637473 4642653 + Cp4.1LG19g12200.1 Cpe19g00547 547
4 30722317 30729683 + CrPI670011_04g012030.1 Cre04g1203 1203
6 24583973 24591181 + CsaV3_6G042020.1 Csa06g02816 2816
4 66506582 66511926 + Hsped.04g11380.1 Hepe04g1138 1138
7 16051697 16058420 - Lsi07G010690.1 Lsi07g01069 1069
14 2351148 2357638 + Sed0026791.1 Sed14g0208 208
3 70069167 70076478 + Tan0014114.1 Tan03g1361 1361
4 20392623 20394981 + Vvi4g1162 Vvi4g1162 1162
4 20405865 20426069 + Vvi4g1163 Vvi4g1163 1163
4 20426686 20444676 + Vvi4g1164 Vvi4g1164 1164
4 20444700 20445124 + Vvi4g1165 Vvi4g1165 1165
4 20445938 20454938 + Vvi4g1166 Vvi4g1166 1166
4 20459876 20462249 + Vvi4g1167 Vvi4g1167 1167
4 20462868 20473622 + Vvi4g1168 Vvi4g1168 1168
4 20474491 20475588 + Vvi4g1169 Vvi4g1169 1169
4 20475611 20476783 + Vvi4g1170 Vvi4g1170 1170
4 20478860 20481294 - Vvi4g1171 Vvi4g1171 1171
       

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