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
Vvi1g1151 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1152 . . Bda01g02188 . . . . . . Cmo18g00702 . Cma18g00715 . Car18g00660 . Cpe09g00576 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma01g00022 . . . . . . . . . . . . . . . . . Cla11g01359 Cam11g1415 Cec11g1444 Cco11g1440 Clacu11g1574 Cmu11g1394 Cre11g1815 . . . .
Vvi1g1153 . . . . . . . . . . . . . . . Cpe09g00575 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1154 . . . . . . . Bma15g00241 . . . . . . . Cpe09g00574 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1155 . . . . . Bpe10g00780 . . . . . . . . . Cpe09g00573 . Bhi07g01878 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1156 . . . . . . . . . . . . . . . Cpe09g00572 . . . . . . . . . . . . . . . . . . . . . . . Blo06g00823 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1157 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda07g01391 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1158 Blo01g00370 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0730 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1159 . Blo16g01189 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1160 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57847805 57850603 - Bda004529.2 Bda01g02188 2188
7 16719847 16725469 + Bda026596.1 Bda07g01391 1391
7 50861423 50864340 + XM_039035405.1 Bhi07g01878 1878
1 4310938 4320238 - BLOR00370 Blo01g00370 370
6 31485719 31496287 + BLOR17406 Blo06g00823 823
16 40417315 40419556 - BLOR21976 Blo16g01189 1189
1 345531 348334 - Bma000192.3 Bma01g00022 22
15 2421345 2424143 + Bma013227.1 Bma15g00241 241
10 13980490 13982501 + Bpe003086.1 Bpe10g00780 780
11 26857887 26862846 - CaPI482276_11g014150.1 Cam11g1415 1415
18 7844803 7846346 - Carg21243-RA Car18g00660 660
11 27176003 27182869 - CcPI632755_11g014400.1 Cco11g1440 1440
11 28606514 28611483 - CePI673135_11g014440.1 Cec11g1444 1444
11 26883467 26888416 - ClG42_11g0157400.10 Clacu11g1574 1574
11 27088155 27094275 - ClCG11G013870.2 Cla11g01359 1359
18 6477536 6480390 - CmaCh18G007150.1 Cma18g00715 715
18 8870450 8873310 - CmoCh18G007020.1 Cmo18g00702 702
11 26135550 26147760 - CmPI595203_11g013940.1 Cmu11g1394 1394
8 7327720 7333574 + Conep08aG0075400.1 Cone8ag0730 730
9 3951925 3960284 + Cp4.1LG09g06170.1 Cpe09g00572 572
9 3961304 3964171 + Cp4.1LG09g06180.1 Cpe09g00573 573
9 3964469 3972081 - Cp4.1LG09g06070.1 Cpe09g00574 574
9 3973500 3976247 + Cp4.1LG09g06120.1 Cpe09g00575 575
9 3977814 3983685 + Cp4.1LG09g06140.1 Cpe09g00576 576
11 29755793 29760752 - CrPI670011_11g018150.1 Cre11g1815 1815
1 19601974 19607050 - Vvi1g1151 Vvi1g1151 1151
1 19607085 19617233 - Vvi1g1152 Vvi1g1152 1152
1 19617238 19617692 - Vvi1g1153 Vvi1g1153 1153
1 19621572 19632678 + Vvi1g1154 Vvi1g1154 1154
1 19632805 19637702 - Vvi1g1155 Vvi1g1155 1155
1 19639324 19647921 - Vvi1g1156 Vvi1g1156 1156
1 19653031 19663798 + Vvi1g1157 Vvi1g1157 1157
1 19670400 19679603 - Vvi1g1158 Vvi1g1158 1158
1 19685492 19688706 + Vvi1g1159 Vvi1g1159 1159
1 19699206 19700709 - Vvi1g1160 Vvi1g1160 1160
       

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