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
Vvi18g700 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g701 . . . . . . Bma04g00149 . . . . Cma09g00262 . . . Cpe06g00181 . . . . . . . . . . . . . . . Cone4ag1600 Cone7ag1349 . . Lsi04g01515 Csa04g02449 . . . . . . . . . . . . Cmo09g00256 . . . Car09g00220 . . Bhi09g03270 . . . . . . Cla05g02080 Cam05g2231 Cec05g2250 Cco05g2291 Clacu05g2225 Cmu05g2091 Cre05g2216 . . Chy07g00165 .
Vvi18g702 . . . Bda03g00196 . . . Bma01g02260 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g703 . . . . . Bpe04g00168 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g704 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g705 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g706 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g707 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g708 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g709 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 1569272 1571653 + Bda016141.1 Bda03g00196 196
9 83721219 83729675 + XM_039041504.1 Bhi09g03270 3270
1 79766295 79768658 + Bma003116.1 Bma01g02260 2260
4 1289845 1293915 + Bma018594.2 Bma04g00149 149
4 1092368 1094752 + Bpe014888.3 Bpe04g00168 168
5 30571701 30577699 - CaPI482276_05g022310.1 Cam05g2231 2231
9 1086093 1088501 - Carg26298-RA Car09g00220 220
5 31590975 31596904 - CcPI632755_05g022910.1 Cco05g2291 2291
5 33949199 33955187 - CePI673135_05g022500.1 Cec05g2250 2250
7 1383430 1388590 - Chy7G129950.1 Chy07g00165 165
5 30773667 30779637 - ClG42_05g0222500.10 Clacu05g2225 2225
5 32458676 32464853 - ClCG05G020270.2 Cla05g02080 2080
9 1096003 1101691 - CmaCh09G002620.1 Cma09g00262 262
9 1145044 1151335 - CmoCh09G002560.1 Cmo09g00256 256
5 30508062 30514033 - CmPI595203_05g020910.1 Cmu05g2091 2091
4 12186832 12189492 - Conep04aG0165200.1 Cone4ag1600 1600
7 9813603 9817566 + Conep07aG0139000.1 Cone7ag1349 1349
6 979481 985402 - Cp4.1LG06g01790.1 Cpe06g00181 181
5 33843285 33849261 - CrPI670011_05g022160.1 Cre05g2216 2216
4 24579665 24585179 - CsaV3_4G034740.1 Csa04g02449 2449
4 22776799 22788326 + Lsi04G015150.1 Lsi04g01515 1515
18 8077179 8078488 - Vvi18g700 Vvi18g700 700
18 8092083 8129064 + Vvi18g701 Vvi18g701 701
18 8135121 8137527 + Vvi18g702 Vvi18g702 702
18 8151294 8153837 + Vvi18g703 Vvi18g703 703
18 8157248 8159843 - Vvi18g704 Vvi18g704 704
18 8166274 8168677 + Vvi18g705 Vvi18g705 705
18 8171670 8173596 - Vvi18g706 Vvi18g706 706
18 8174091 8185174 - Vvi18g707 Vvi18g707 707
18 8190898 8193301 + Vvi18g708 Vvi18g708 708
18 8196677 8199086 - Vvi18g709 Vvi18g709 709
       

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