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
Vvi4g1192 . . . . . . . Bma15g00888 . . Cma03g00623 Cma07g00385 Car03g00578 Car07g00337 . Cpe19g00897 Cpe10g00714 . . . . . . . . . . . . . . . Cone12ag0866 . . Lsi01g00530 . . . . Blo06g00274 . . Bpe10g00194 . . . . . Cmo07g00378 . . . . . . . . . . . . . . . . . . . . . . Chy02g00506 .
Vvi4g1193 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1194 . . . . Bpe15g00371 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0895 Cone12ag0867 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1195 . . Bda04g00215 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0896 Cone12ag0868 . . . . . . Blo05g00676 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1196 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0897 Cone12ag0869 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi07g01056 . . .
Vvi4g1197 Blo04g00862 . . . Bpe15g00498 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0899 Cone12ag0870 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1198 Blo04g00861 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0900 Cone12ag0871 . . . . . . . . Bda11g01810 . . . Bma03g00929 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1199 . Blo16g00107 . . . Bpe13g00389 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma06g00075 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1200 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0901 Cone12ag0872 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1201 . . . . . . . Bma15g00886 . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0874 . . . . . . . Blo06g00254 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi07g01046 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 8289131 8289933 - Bda018509.1 Bda04g00215 215
11 53260196 53264622 + Bda008739.1 Bda11g01810 1810
4 9480033 9489654 + BLOR13773 Blo04g00861 861
4 9490541 9503715 + BLOR13774 Blo04g00862 862
5 22241159 22246268 - BLOR15638 Blo05g00676 676
6 13264311 13265341 - BLOR16837 Blo06g00254 254
6 14949871 14950644 + BLOR16857 Blo06g00274 274
16 2484489 2486263 - BLOR07355 Blo16g00107 107
3 9648699 9652638 + Bma017255.1 Bma03g00929 929
6 1177395 1185428 + Bma022687.1 Bma06g00075 75
15 30130171 30154281 + Bma014078.2 Bma15g00886 886
15 30199743 30200516 + Bma014080.1 Bma15g00888 888
10 6180931 6181698 + Bpe002515.1 Bpe10g00194 194
13 11643208 11644921 + Bpe006513.1 Bpe13g00389 389
15 15256207 15259084 - Bpe001308.2 Bpe15g00371 371
15 16223024 16238942 - Bpe001431.1 Bpe15g00498 498
3 5509421 5510191 + Carg00538-RA Car03g00578 578
7 1691214 1691984 + Carg07917-RA Car07g00337 337
2 3089587 3091289 - Chy2G027730.1 Chy02g00506 506
3 5419952 5421986 + CmaCh03G006230.1 Cma03g00623 623
7 1651525 1652295 + CmaCh07G003850.1 Cma07g00385 385
7 1735733 1742746 + CmoCh07G003780.1 Cmo07g00378 378
8 8713993 8720264 - Conep08aG0092100.1 Cone8ag0895 895
8 8722294 8723979 + Conep08aG0092200.1 Cone8ag0896 896
8 8725091 8725964 + Conep08aG0092300.1 Cone8ag0897 897
8 8730311 8736459 - Conep08aG0092500.1 Cone8ag0899 899
8 8741647 8746533 + Conep08aG0092600.1 Cone8ag0900 900
8 8752098 8754410 + Conep08aG0092700.1 Cone8ag0901 901
12 7738271 7740478 - Conep12aG0089100.1 Cone12ag0866 866
12 7741036 7744278 - Conep12aG0089200.1 Cone12ag0867 867
12 7749914 7751526 + Conep12aG0089300.1 Cone12ag0868 868
12 7752125 7753569 + Conep12aG0089400.1 Cone12ag0869 869
12 7755393 7761665 - Conep12aG0089500.1 Cone12ag0870 870
12 7768604 7772541 + Conep12aG0089600.1 Cone12ag0871 871
12 7779041 7781944 + Conep12aG0089800.1 Cone12ag0872 872
12 7796985 7806808 - Conep12aG0090000.1 Cone12ag0874 874
10 4085903 4090529 - Cp4.1LG10g10320.1 Cpe10g00714 714
19 6539530 6542210 - Cp4.1LG19g08500.1 Cpe19g00897 897
1 4343875 4344645 - Lsi01G005300.1 Lsi01g00530 530
7 15853078 15858005 + Lsi07G010460.1 Lsi07g01046 1046
7 15926784 15931862 + Lsi07G010560.1 Lsi07g01056 1056
4 20771153 20773249 + Vvi4g1192 Vvi4g1192 1192
4 20782109 20782409 - Vvi4g1193 Vvi4g1193 1193
4 20787047 20791102 - Vvi4g1194 Vvi4g1194 1194
4 20801266 20803199 + Vvi4g1195 Vvi4g1195 1195
4 20804640 20807243 + Vvi4g1196 Vvi4g1196 1196
4 20807988 20822529 - Vvi4g1197 Vvi4g1197 1197
4 20833740 20841170 + Vvi4g1198 Vvi4g1198 1198
4 20843707 20847365 + Vvi4g1199 Vvi4g1199 1199
4 20861324 20865130 + Vvi4g1200 Vvi4g1200 1200
4 20870207 20881776 - Vvi4g1201 Vvi4g1201 1201
       

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