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
Vvi3g756 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g757 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g758 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g759 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g760 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g761 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g762 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1035 Cone8ag1066 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g763 Blo02g00922 Blo03g00061 . . . . . . Cmo19g00555 . . . . . . . Cpe15g00430 . . . . . . . Cla02g00696 Cam02g0729 Cec02g0744 Cco02g0768 Clacu02g0740 Cmu02g0735 Cre02g1048 . . Cone3ag1042 . Lsi03g00598 Csa07g00671 . Cme01g00133 . . . . . . . . Sed07g1141 Cmo04g00467 . . Cma19g00541 . Car19g00398 . . Bhi11g01118 Tan01g0612 Cmetu07g1601 . . Mch10g0413 . . . . . . . . . . Chy01g00144 Cme07g02206
Vvi3g764 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g765 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 32635203 32636119 + XM_039049678.1 Bhi11g01118 1118
2 35557218 35559865 + BLOR10652 Blo02g00922 922
3 2228755 2229249 + BLOR11242 Blo03g00061 61
2 8826273 8830790 - CaPI482276_02g007290.1 Cam02g0729 729
19 5894357 5900476 + Carg16319-RA Car19g00398 398
2 8131116 8135702 - CcPI632755_02g007680.1 Cco02g0768 768
2 8093862 8098422 - CePI673135_02g007440.1 Cec02g0744 744
1 970796 975225 - Chy1G001440.1 Chy01g00144 144
2 7828896 7833460 - ClG42_02g0074000.10 Clacu02g0740 740
2 8194305 8198869 - ClCG02G007120.2 Cla02g00696 696
19 6226516 6232059 + CmaCh19G005410.1 Cma19g00541 541
1 956515 960761 - MELO3C018530.2.1 Cme01g00133 133
7 26290225 26290845 - MELO3C018021.2.1 Cme07g02206 2206
7 308074 309071 + PI0020027.1 Cmetu07g1601 1601
4 2332800 2333276 + CmoCh04G004670.1 Cmo04g00467 467
19 6393515 6399411 + CmoCh19G005550.1 Cmo19g00555 555
2 7737099 7741636 - CmPI595203_02g007350.1 Cmu02g0735 735
3 29219887 29220700 - Conep03aG0154300.1 Cone3ag1042 1042
8 9685925 9689350 + Conep08aG0109500.1 Cone8ag1066 1066
12 8656140 8659016 + Conep12aG0106400.1 Cone12ag1035 1035
15 5444568 5455402 + Cp4.1LG15g04260.1 Cpe15g00430 430
2 8370815 8375410 - CrPI670011_02g010480.1 Cre02g1048 1048
7 4798189 4801084 + CsaV3_7G007700.1 Csa07g00671 671
3 7436108 7446147 - Lsi03G005980.1 Lsi03g00598 598
10 2724306 2725336 + MC10g0340 Mch10g0413 413
7 8557472 8558175 - Sed0014293.1 Sed07g1141 1141
1 5594347 5595318 + Tan0004847.1 Tan01g0612 612
3 8229083 8232564 - Vvi3g756 Vvi3g756 756
3 8232627 8239401 + Vvi3g757 Vvi3g757 757
3 8239783 8241124 - Vvi3g758 Vvi3g758 758
3 8241137 8242407 - Vvi3g759 Vvi3g759 759
3 8242464 8244586 - Vvi3g760 Vvi3g760 760
3 8244779 8251952 - Vvi3g761 Vvi3g761 761
3 8252531 8257124 - Vvi3g762 Vvi3g762 762
3 8281114 8302826 - Vvi3g763 Vvi3g763 763
3 8315151 8316025 - Vvi3g764 Vvi3g764 764
3 8326556 8335645 - Vvi3g765 Vvi3g765 765
       

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