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
Vvi3g896 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g897 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g898 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g899 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g900 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g901 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g902 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g903 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g904 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g905 . Blo03g00035 Bda06g01133 . . . . . Cmo19g00508 Cmo11g01451 . . . . . Cpe04g00360 Cpe15g00386 Bhi05g00956 . . . . . . . . . . . . . . . . . Lsi03g00681 Csa07g00619 . Cme01g00179 . . . . . . . . . . . Cma11g01676 Cma19g00490 Car11g01167 Car19g00367 . . . . . . . . . Cla09g01596 . . . . . . . . Chy01g00189 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 40212318 40214414 - Bda022929.1 Bda06g01133 1133
5 33762262 33764984 + XM_039032949.1 Bhi05g00956 956
3 1523286 1523825 - BLOR11216 Blo03g00035 35
11 9358980 9361022 + Carg23061-RA Car11g01167 1167
19 5531262 5533424 + Carg22797-RA Car19g00367 367
1 1286559 1288676 - Chy1G001890.1 Chy01g00189 189
9 31993165 31996539 - ClCG09G016260.2 Cla09g01596 1596
11 11041783 11044997 - CmaCh11G016760.1 Cma11g01676 1676
19 5826667 5828820 + CmaCh19G004900.1 Cma19g00490 490
1 1254289 1256569 + MELO3C018578.2.1 Cme01g00179 179
11 10206715 10208757 + CmoCh11G014510.1 Cmo11g01451 1451
19 6018940 6021102 + CmoCh19G005080.1 Cmo19g00508 508
4 4231589 4233813 + Cp4.1LG04g07290.1 Cpe04g00360 360
15 5085194 5100577 + Cp4.1LG15g03810.1 Cpe15g00386 386
7 4495826 4498233 - CsaV3_7G007180.1 Csa07g00619 619
3 8641436 8643557 - Lsi03G006810.1 Lsi03g00681 681
3 11875118 11877082 - Vvi3g896 Vvi3g896 896
3 11884520 11885474 - Vvi3g897 Vvi3g897 897
3 11895009 11895610 - Vvi3g898 Vvi3g898 898
3 11911753 11922553 - Vvi3g899 Vvi3g899 899
3 11939927 11940490 - Vvi3g900 Vvi3g900 900
3 12160725 12163148 + Vvi3g901 Vvi3g901 901
3 12166242 12166828 - Vvi3g902 Vvi3g902 902
3 12184511 12184804 - Vvi3g903 Vvi3g903 903
3 12187829 12194131 + Vvi3g904 Vvi3g904 904
3 12199842 12207930 - Vvi3g905 Vvi3g905 905
       

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