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
Vvi5g169 Blo01g00068 . . Bda08g00296 . . . Bma05g01028 Cmo08g01207 Cmo17g00324 . . . . . . . . . . . . . . Cla06g00470 Cam06g0504 Cec06g0506 Cco06g0507 Clacu06g0488 Cmu06g0490 Cre06g1262 . . . . . Csa06g01797 Chy11g01521 . . . . . Bpe05g00829 . . . . . . Cma08g01232 Cma17g00335 . Car17g00308 Cpe12g00284 Cpe17g00031 Bhi12g02042 Tan06g2691 . Lac11g0848 Hepe03g0093 . Lcy12g0741 . . . . . . . Lsi09g01441 . . Cme11g02022
Vvi5g170 . . . . . . . . . . Cma06g01578 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g171 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g172 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g173 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g174 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g175 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g176 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g177 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g178 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 3102144 3109605 - Bda024730.1 Bda08g00296 296
12 63665325 63671926 + XM_039019478.1 Bhi12g02042 2042
1 860406 871510 + BLOR00068 Blo01g00068 68
5 48846367 48856538 + Bma022187.1 Bma05g01028 1028
5 21550221 21557706 + Bpe018242.1 Bpe05g00829 829
6 7130072 7136338 + CaPI482276_06g005040.1 Cam06g0504 504
17 1917616 1922937 - Carg05514-RA Car17g00308 308
6 5540731 5547017 + CcPI632755_06g005070.1 Cco06g0507 507
6 5662418 5668700 + CePI673135_06g005060.1 Cec06g0506 506
11 21829290 21834454 - Chy11G201010.1 Chy11g01521 1521
6 5671218 5677463 + ClG42_06g0048800.10 Clacu06g0488 488
6 5720605 5727355 + ClCG06G005030.1 Cla06g00470 470
6 9874913 9880406 + CmaCh06G015780.1 Cma06g01578 1578
8 7561331 7566369 - CmaCh08G012320.1 Cma08g01232 1232
17 1830773 1834228 - CmaCh17G003350.1 Cma17g00335 335
11 28072147 28078179 - MELO3C021318.2.1 Cme11g02022 2022
8 7666246 7672863 - CmoCh08G012070.1 Cmo08g01207 1207
17 1957136 1963741 - CmoCh17G003240.1 Cmo17g00324 324
6 5473183 5479429 + CmPI595203_06g004900.1 Cmu06g0490 490
12 1899179 1906092 - Cp4.1LG12g02970.1 Cpe12g00284 284
17 207294 214828 - Cp4.1LG17g00610.1 Cpe17g00031 31
6 6535135 6541399 + CrPI670011_06g012620.1 Cre06g1262 1262
6 15876471 15881581 + CsaV3_6G023910.1 Csa06g01797 1797
3 1147748 1155099 + Hsped.03g00930.1 Hepe03g0093 93
11 9078831 9085803 - Lag0031486.1 Lac11g0848 848
12 9404684 9411963 - Maker00024708 Lcy12g0741 741
9 22398310 22405183 - Lsi09G014410.1 Lsi09g01441 1441
6 79328087 79336786 - Tan0018304.2 Tan06g2691 2691
5 1683016 1690188 + Vvi5g169 Vvi5g169 169
5 1690233 1699142 - Vvi5g170 Vvi5g170 170
5 1699773 1706856 - Vvi5g171 Vvi5g171 171
5 1707275 1708873 - Vvi5g172 Vvi5g172 172
5 1710650 1716408 - Vvi5g173 Vvi5g173 173
5 1730893 1734419 + Vvi5g174 Vvi5g174 174
5 1748258 1750088 + Vvi5g175 Vvi5g175 175
5 1771675 1772123 + Vvi5g176 Vvi5g176 176
5 1772316 1774184 - Vvi5g177 Vvi5g177 177
5 1782797 1783564 + Vvi5g178 Vvi5g178 178
       

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