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
Vvi19g314 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g315 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1097 Cone15ag1107 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g316 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g317 . . . . . . . . . . . . . . . . Cpe02g00728 . . . . . . . Cla11g01809 Cam11g1875 Cec11g1898 Cco11g1906 Clacu11g2039 Cmu11g1844 Cre11g2249 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g318 . . Bda07g00267 . . . . . . . . . . . . Cpe06g00723 . . . . . . . . . . . . . . . . . . . Lsi04g01275 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g319 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g320 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g321 . . . . . . . . . . . . . . . Cpe06g00725 . . . . . . . . Cla11g01811 Cam11g1877 Cec11g1900 Cco11g1908 Clacu11g2041 Cmu11g1846 Cre11g2251 Cone6ag0106 Cone9ag0126 . . Lsi04g01273 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g322 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g323 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 3744726 3751136 + Bda025347.2 Bda07g00267 267
11 31306336 31320159 - CaPI482276_11g018750.1 Cam11g1875 1875
11 31326805 31331384 + CaPI482276_11g018770.1 Cam11g1877 1877
11 31762627 31776380 - CcPI632755_11g019060.1 Cco11g1906 1906
11 31783120 31787706 + CcPI632755_11g019080.1 Cco11g1908 1908
11 33210277 33221428 - CePI673135_11g018980.1 Cec11g1898 1898
11 33227982 33232577 + CePI673135_11g019000.1 Cec11g1900 1900
11 31346156 31359794 - ClG42_11g0203900.10 Clacu11g2039 2039
11 31366361 31370949 + ClG42_11g0204100.10 Clacu11g2041 2041
11 31749574 31763972 - ClCG11G018570.1 Cla11g01809 1809
11 31770123 31774924 + ClCG11G018590.2 Cla11g01811 1811
11 30596026 30609661 - CmPI595203_11g018440.1 Cmu11g1844 1844
11 30616232 30620820 + CmPI595203_11g018460.1 Cmu11g1846 1846
6 516455 519856 - Conep06aG0010600.1 Cone6ag0106 106
9 553482 556630 - Conep09aG0012600.1 Cone9ag0126 126
14 9168980 9170938 - Conep14aG0111900.1 Cone14ag1097 1097
15 9057548 9059186 - Conep15aG0113300.1 Cone15ag1107 1107
2 4636696 4651584 - Cp4.1LG02g01310.1 Cpe02g00728 728
6 4502731 4514408 - Cp4.1LG06g07390.1 Cpe06g00723 723
6 4516962 4524065 + Cp4.1LG06g07270.1 Cpe06g00725 725
11 34267530 34281282 - CrPI670011_11g022490.1 Cre11g2249 2249
11 34287983 34292569 + CrPI670011_11g022510.1 Cre11g2251 2251
4 20081665 20087285 - Lsi04G012730.1 Lsi04g01273 1273
4 20111837 20125653 + Lsi04G012750.1 Lsi04g01275 1275
19 3938937 3941145 + Vvi19g314 Vvi19g314 314
19 3942746 3944969 - Vvi19g315 Vvi19g315 315
19 3952948 3953062 + Vvi19g316 Vvi19g316 316
19 4088498 4092360 - Vvi19g317 Vvi19g317 317
19 4092387 4097206 - Vvi19g318 Vvi19g318 318
19 4097210 4097885 - Vvi19g319 Vvi19g319 319
19 4110587 4155161 - Vvi19g320 Vvi19g320 320
19 4163203 4172299 + Vvi19g321 Vvi19g321 321
19 4181540 4182679 + Vvi19g322 Vvi19g322 322
19 4190150 4190744 + Vvi19g323 Vvi19g323 323
       

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