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
Vvi1g1291 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1292 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe17g01020 . . . . . . . . . . . . . . . . . . .
Vvi1g1293 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0654 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1294 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1295 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1296 Blo01g00172 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00297 . . . . . . . . . . . . . . . . . . Cpe03g01220 . . . . . . . . . . . . . . . . . .
Vvi1g1297 Blo01g00171 . . . . . . . . . . . . . . . . . . . . . . . Cla06g00185 Cam06g0026 Cec06g0203 Cco06g0198 Clacu06g0202 Cmu06g0195 Cre06g0968 . . . . . . Chy11g01805 Cme11g02338 . . . . . . . . Sed07g0107 . . . . . . . . Bhi12g02426 Tan06g1492 Cmetu11g2271 . Hepe03g1138 . . . . . . . . . . . . .
Vvi1g1298 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo02g00197 . . . Bpe14g00802 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1299 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1300 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
12 76532078 76562158 - XM_039019188.1 Bhi12g02426 2426
1 2373105 2375457 + BLOR00171 Blo01g00171 171
1 2377287 2379350 + BLOR00172 Blo01g00172 172
2 1792369 1795430 + BLOR09927 Blo02g00197 197
14 6047503 6051004 + Bpe025522 Bpe14g00802 802
6 2090747 2100875 + CaPI482276_06g000260.1 Cam06g0026 26
6 2080391 2088350 - CcPI632755_06g001980.1 Cco06g0198 198
6 2110505 2112368 - CePI673135_06g002030.1 Cec06g0203 203
11 24403538 24408029 + Chy11G203850.1 Chy11g01805 1805
6 2262250 2266603 - ClG42_06g0020200.10 Clacu06g0202 202
6 2144079 2154018 - ClCG06G002010.2 Cla06g00185 185
11 30417472 30418870 + MELO3C022329.2.1 Cme11g02338 2338
11 1657168 1659454 - PI0010898.1 Cmetu11g2271 2271
6 2057815 2062155 - CmPI595203_06g001950.1 Cmu06g0195 195
14 3284979 3287503 - Conep14aG0066800.1 Cone14ag0654 654
3 9939119 9942179 + Cp4.1LG03g12940.1 Cpe03g01220 1220
17 7722341 7726267 + Cp4.1LG17g10130.1 Cpe17g01020 1020
6 3153551 3154655 - CrPI670011_06g009680.1 Cre06g0968 968
4 1843442 1846106 + CsaV3_4G002970.1 Csa04g00297 297
3 64529838 64532922 + Hsped.03g11380.1 Hepe03g1138 1138
7 997903 1000328 + Sed0009950.1 Sed07g0107 107
6 20406416 20409848 - Tan0012061.1 Tan06g1492 1492
1 21705191 21716307 + Vvi1g1291 Vvi1g1291 1291
1 21717510 21724801 - Vvi1g1292 Vvi1g1292 1292
1 21736727 21739613 + Vvi1g1293 Vvi1g1293 1293
1 21739812 21740747 - Vvi1g1294 Vvi1g1294 1294
1 21761881 21762187 + Vvi1g1295 Vvi1g1295 1295
1 21766670 21769961 - Vvi1g1296 Vvi1g1296 1296
1 21773086 21777218 - Vvi1g1297 Vvi1g1297 1297
1 21855815 21861685 + Vvi1g1298 Vvi1g1298 1298
1 21864294 21867415 + Vvi1g1299 Vvi1g1299 1299
1 21867974 21876241 + Vvi1g1300 Vvi1g1300 1300
       

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