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
Vvi19g894 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g895 . . . . . . . . Cmo16g00488 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda05g00817 . . . . . . . . . Cma16g00452 . Car16g00410 Cpe14g00382 . . . . . . . . Cla07g00994 Cam07g1069 Cec07g1141 Cco07g1119 Clacu07g1042 Cmu07g1034 Cre07g1410 . . Chy07g01012 .
Vvi19g896 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g897 . . . . . . . . . Cmo04g00699 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma04g00649 . Car04g00603 . . Cpe01g00585 . . . . . . . . . . . . . . . . . .
Vvi19g898 . . . . . . . . Cmo16g00489 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma16g00453 . Car16g00411 Cpe14g00383 . . . . . . . . Cla07g00995 Cam07g1070 Cec07g1142 Cco07g1120 Clacu07g1044 Cmu07g1035 Cre07g1411 . . Chy07g01013 .
Vvi19g899 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g900 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g901 . . . . . . . Bma13g00908 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g902 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g903 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 56667192 56668934 + Bda021975.1 Bda05g00817 817
13 39453922 39458595 + Bma009984.1 Bma13g00908 908
7 25029430 25032301 + CaPI482276_07g010690.1 Cam07g1069 1069
7 25071171 25072753 + CaPI482276_07g010700.1 Cam07g1070 1070
4 3456379 3457675 - Carg13102-RA Car04g00603 603
16 2545072 2546859 + Carg11377-RA Car16g00410 410
16 2556179 2557445 + Carg11378-RA Car16g00411 411
7 24727808 24730405 + CcPI632755_07g011190.1 Cco07g1119 1119
7 24777319 24778888 + CcPI632755_07g011200.1 Cco07g1120 1120
7 26628683 26631386 + CePI673135_07g011410.1 Cec07g1141 1141
7 26680243 26681806 + CePI673135_07g011420.1 Cec07g1142 1142
7 14901909 14903693 + Chy7G138420.1 Chy07g01012 1012
7 14931474 14932951 + Chy7G138430.1 Chy07g01013 1013
7 24824821 24826605 + ClG42_07g0104200.10 Clacu07g1042 1042
7 24868613 24870202 + ClG42_07g0104400.10 Clacu07g1044 1044
7 26153989 26155773 + ClCG07G010450.2 Cla07g00994 994
7 26197965 26199548 + ClCG07G010460.1 Cla07g00995 995
4 3321297 3322998 - CmaCh04G006490.1 Cma04g00649 649
16 2258319 2260106 + CmaCh16G004520.1 Cma16g00452 452
16 2269857 2271606 + CmaCh16G004530.1 Cma16g00453 453
4 3463934 3465435 - CmoCh04G006990.1 Cmo04g00699 699
16 2341707 2343494 + CmoCh16G004880.1 Cmo16g00488 488
16 2353890 2355617 + CmoCh16G004890.1 Cmo16g00489 489
7 25069349 25071133 + CmPI595203_07g010340.1 Cmu07g1034 1034
7 25113308 25114911 + CmPI595203_07g010350.1 Cmu07g1035 1035
1 3388963 3390723 - Cp4.1LG01g00820.1 Cpe01g00585 585
14 2336485 2338272 + Cp4.1LG14g03400.1 Cpe14g00382 382
14 2348256 2350141 + Cp4.1LG14g03420.1 Cpe14g00383 383
7 29005127 29007727 + CrPI670011_07g014100.1 Cre07g1410 1410
7 29046583 29048150 + CrPI670011_07g014110.1 Cre07g1411 1411
19 15309712 15310119 + Vvi19g894 Vvi19g894 894
19 15403003 15406647 + Vvi19g895 Vvi19g895 895
19 15466460 15470255 - Vvi19g896 Vvi19g896 896
19 15497728 15499650 + Vvi19g897 Vvi19g897 897
19 15603206 15604930 + Vvi19g898 Vvi19g898 898
19 15646368 15646734 + Vvi19g899 Vvi19g899 899
19 15663550 15663916 + Vvi19g900 Vvi19g900 900
19 15754697 15779104 + Vvi19g901 Vvi19g901 901
19 15779469 15780216 - Vvi19g902 Vvi19g902 902
19 15810820 15811240 + Vvi19g903 Vvi19g903 903
       

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