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
Vvi19g1134 . Blo13g00598 . . . . Bma08g00820 . . . . . . . . Cpe04g00863 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe15g00900 . . . . . . . . . . . . . . . . . . .
Vvi19g1135 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1136 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1137 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1138 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme11g01629 Blo15g00635 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy11g01039 .
Vvi19g1139 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa07g01201 . . Blo15g00636 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1140 . . . . . . . . . . . . . . . . . . . . . . . . Cla02g01825 Cam02g1933 Cec02g1959 Cco02g2000 Clacu02g1914 Cmu02g1862 Cre02g2177 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1141 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1142 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1143 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi10g00944 . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
10 19272591 19280187 - XM_039046811.1 Bhi10g00944 944
13 28405543 28407955 - BLOR19650 Blo13g00598 598
15 16670171 16684389 + BLOR07029 Blo15g00635 635
15 16685979 16689083 - BLOR07030 Blo15g00636 636
8 45896902 45899245 - Bma031461 Bma08g00820 820
2 32441153 32446126 - CaPI482276_02g019330.1 Cam02g1933 1933
2 32960115 32963764 - CcPI632755_02g020000.1 Cco02g2000 2000
2 37458746 37462382 - CePI673135_02g019590.1 Cec02g1959 1959
11 14853980 14873435 - Chy11G196190.1 Chy11g01039 1039
2 32701844 32705482 - ClG42_02g0191400.10 Clacu02g1914 1914
2 33405777 33409825 - ClCG02G018650.2 Cla02g01825 1825
11 24153346 24169546 - MELO3C019635.2.1 Cme11g01629 1629
2 32564111 32567749 - CmPI595203_02g018620.1 Cmu02g1862 1862
4 7933630 7935381 - Cp4.1LG04g02230.1 Cpe04g00863 863
15 8663631 8667957 - Cp4.1LG15g08970.1 Cpe15g00900 900
2 35412094 35415745 - CrPI670011_02g021770.1 Cre02g2177 2177
7 11805491 11813743 + CsaV3_7G022900.1 Csa07g01201 1201
19 22763854 22769558 + Vvi19g1134 Vvi19g1134 1134
19 22805627 22810184 + Vvi19g1135 Vvi19g1135 1135
19 22830807 22834737 + Vvi19g1136 Vvi19g1136 1136
19 22835274 22848066 + Vvi19g1137 Vvi19g1137 1137
19 22854357 22885790 + Vvi19g1138 Vvi19g1138 1138
19 22886898 22896623 - Vvi19g1139 Vvi19g1139 1139
19 22897110 22905063 + Vvi19g1140 Vvi19g1140 1140
19 22905486 22906558 - Vvi19g1141 Vvi19g1141 1141
19 22906564 22924143 - Vvi19g1142 Vvi19g1142 1142
19 22924598 22935504 - Vvi19g1143 Vvi19g1143 1143
       

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