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
Vvi5g119 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi12g01892 . . . . . . . . . . . . . . . . .
Vvi5g120 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g121 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g122 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g123 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g124 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi09g01464 . . .
Vvi5g125 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g126 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy11g01543 . . . . . . . . . . . . . . Car08g01124 . . . . . . . . . . . . . . . . . Lsi09g01463 . . Cme11g02051
Vvi5g127 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe17g00045 . . . . . . . . . . . . . . . . . .
Vvi5g128 . . . . . . . . Cmo08g01222 Cmo17g00337 . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy11g01542 . . . . . . Bpe13g00680 . . . . . Cma08g01251 Cma17g00349 . Car17g00320 Cpe12g00298 . . . . . . . . . . . . . . . Lsi09g01462 . . Cme11g02050
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
12 60538040 60539433 - XM_039050680.1 Bhi12g01892 1892
13 13499353 13499920 - Bpe010381.1 Bpe13g00680 680
8 7609519 7610430 + Carg18866-RA Car08g01124 1124
17 1997243 1998454 + Carg05526-RA Car17g00320 320
11 21981463 21983192 - Chy11G201220.1 Chy11g01542 1542
11 21986193 21987414 + Chy11G201230.1 Chy11g01543 1543
8 7643435 7644361 + CmaCh08G012510.1 Cma08g01251 1251
17 1907566 1908896 + CmaCh17G003490.1 Cma17g00349 349
11 28265343 28266801 - MELO3C021294.2.1 Cme11g02050 2050
11 28265400 28266801 - MELO3C034928.2.1 Cme11g02051 2051
8 7757470 7758369 + CmoCh08G012220.1 Cmo08g01222 1222
17 2039548 2040919 + CmoCh17G003370.1 Cmo17g00337 337
12 1980900 1982416 + Cp4.1LG12g02820.1 Cpe12g00298 298
17 293620 294354 + Cp4.1LG17g00490.1 Cpe17g00045 45
9 22608043 22610078 - Lsi09G014620.1 Lsi09g01462 1462
9 22611219 22616097 + Lsi09G014630.1 Lsi09g01463 1463
9 22616247 22622036 + Lsi09G014640.1 Lsi09g01464 1464
5 1246770 1247714 - Vvi5g119 Vvi5g119 119
5 1251025 1252742 + Vvi5g120 Vvi5g120 120
5 1260026 1260999 + Vvi5g121 Vvi5g121 121
5 1271443 1272482 + Vvi5g122 Vvi5g122 122
5 1282251 1288085 + Vvi5g123 Vvi5g123 123
5 1288590 1289336 + Vvi5g124 Vvi5g124 124
5 1295956 1296900 + Vvi5g125 Vvi5g125 125
5 1298334 1299312 + Vvi5g126 Vvi5g126 126
5 1301717 1302621 + Vvi5g127 Vvi5g127 127
5 1304983 1305784 + Vvi5g128 Vvi5g128 128
       

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