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
Vvi1g1041 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme10g01393 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1042 . . . . . . . . . . . . . . Sed04g3062 . . Bhi07g00120 Tan04g1675 Cmetu10g0133 Lac13g1644 Hepe01g0395 . . . . . . . . . . . . . . . Chy10g00117 Cme10g01102 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01019 . .
Vvi1g1043 . . . . . . . . . . . . . . Sed06g0251 . . Bhi07g00129 Tan04g1677 Cmetu10g0260 . . . . . . . . . . . . . . . . . Chy10g00107 Cme10g01116 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01015 . .
Vvi1g1044 . . . . . . . . . . . . . . . . . Bhi07g00139 . . Lac13g1653 . . . . . . . . . . . . . . . . Chy10g00104 Cme10g01121 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01011 . .
Vvi1g1045 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1046 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1047 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1048 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1049 . . . . . . . . . Cmo18g00258 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1050 . . . . . . . . . Cmo18g00261 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 7035461 7043718 - XM_039035472.1 Bhi07g00120 120
7 7531630 7536353 + XM_039037346.1 Bhi07g00129 129
7 7660263 7699245 - XM_039035935.1 Bhi07g00139 139
10 2549467 2595966 + Chy10G172980.1 Chy10g00104 104
10 2689074 2693859 - Chy10G173010.1 Chy10g00107 107
10 2850337 2854535 + Chy10G173110.1 Chy10g00117 117
10 10120019 10126612 - MELO3C026796.2.1 Cme10g01102 1102
10 10295550 10300433 + MELO3C020030.2.1 Cme10g01116 1116
10 10387421 10416355 - MELO3C020035.2.1 Cme10g01121 1121
10 16359669 16374782 + MELO3C022613.2.1 Cme10g01393 1393
10 9364663 9369779 + PI0009172.1 Cmetu10g0133 133
10 9452538 9457549 + PI0019473.2 Cmetu10g0260 260
18 1713640 1718878 - CmoCh18G002580.1 Cmo18g00258 258
18 1733948 1739173 + CmoCh18G002610.1 Cmo18g00261 261
5 9559126 9583343 + CsaV3_5G013170.1 Csa05g01011 1011
5 9648412 9654068 - CsaV3_5G013210.1 Csa05g01015 1015
5 9700050 9705858 + CsaV3_5G013250.1 Csa05g01019 1019
1 55232084 55239431 + Hsped.01g03950.1 Hepe01g0395 395
13 17892601 17897828 - Lag0041440.1 Lac13g1644 1644
13 18083887 18097065 - Lag0041449.1 Lac13g1653 1653
4 41662658 41666379 - Sed0002621.1 Sed04g3062 3062
6 2050740 2056089 + Sed0015909.2 Sed06g0251 251
4 35924956 35937441 - Tan0000081.1 Tan04g1675 1675
4 36076559 36081536 + Tan0016751.1 Tan04g1677 1677
1 16927369 16938407 - Vvi1g1041 Vvi1g1041 1041
1 16963232 16970228 + Vvi1g1042 Vvi1g1042 1042
1 16970764 16987400 + Vvi1g1043 Vvi1g1043 1043
1 17019946 17056744 + Vvi1g1044 Vvi1g1044 1044
1 17127120 17127644 - Vvi1g1045 Vvi1g1045 1045
1 17166276 17167723 - Vvi1g1046 Vvi1g1046 1046
1 17179383 17239791 - Vvi1g1047 Vvi1g1047 1047
1 17248218 17248647 + Vvi1g1048 Vvi1g1048 1048
1 17280658 17300963 - Vvi1g1049 Vvi1g1049 1049
1 17305087 17308607 - Vvi1g1050 Vvi1g1050 1050
       

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