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
Vvi16g774 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g775 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g776 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g777 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g778 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g779 . . . . . . . . . . . . . . Sed13g0543 . . Bhi01g01589 Tan01g0786 . . . Mch10g0553 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g780 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g781 . . Bda05g00095 . Bpe03g00261 . Bma10g01257 . Cmo16g00102 . . . . . . . . Bhi01g01413 . . . . . . . . . . . . . Cone1ag1196 . . . Lsi05g01187 . . . Blo07g00371 . . . . . . . . . . Cma16g00095 . Car16g00085 . . . . . . . . . . Cla05g00920 Cam05g1008 Cec05g1012 Cco05g1008 Clacu05g0996 . . . Csa03g01753 Chy06g00982 .
Vvi16g782 . . . . . . . . Cmo16g00100 . . . . . . . Cpe14g00079 . . . . . . . . . . . . . . . . . Cone15ag0059 . . . . . . . . . . . . . . . Cma16g00094 . Car16g00084 . . . . . . . . . . . . . . . . . . . . .
Vvi16g783 . . . . . . Bma10g01259 . Cmo16g00099 Cmo18g01306 . . . . Sed13g0111 . Cpe14g00078 Bhi01g01416 Tan01g0184 Cmetu06g0411 . Hepe07g0116 Mch10g0119 . . . . . . . . Cone1ag1197 Cone5ag0895 . . Lsi05g01185 . . . Blo07g00370 . . . . . . . . . . Cma16g00093 Cma18g01275 Car16g00083 Car18g01188 Cpe09g00062 . . . . . . . . Cla05g00922 Cam05g1010 Cec05g1014 Cco05g1010 Clacu05g0998 Cmu05g0952 Cre05g1033 . Csa03g01755 Chy06g00984 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 4914632 4922865 + Bda020700.1 Bda05g00095 95
1 28871436 28878456 + XM_039024536.1 Bhi01g01413 1413
1 28883774 28895020 - XM_039024549.1 Bhi01g01416 1416
1 32864861 32877059 - XM_039030876.1 Bhi01g01589 1589
7 6019102 6023302 + BLOR18302 Blo07g00370 370
7 6023821 6037218 - BLOR18303 Blo07g00371 371
10 44598895 44612023 + Bma005351.2 Bma10g01257 1257
10 44620122 44625330 - Bma005353.1 Bma10g01259 1259
3 3555141 3572335 - Bpe012114.2 Bpe03g00261 261
5 9102216 9110039 + CaPI482276_05g010080.1 Cam05g1008 1008
5 9114126 9124536 - CaPI482276_05g010100.1 Cam05g1010 1010
16 519756 527747 + Carg15102-RA Car16g00083 83
16 529287 530645 - Carg15103-RA Car16g00084 84
16 531756 538083 - Carg15104-RA Car16g00085 85
18 11498413 11503954 - Carg22136-RA Car18g01188 1188
5 8867133 8873006 + CcPI632755_05g010080.1 Cco05g1008 1008
5 8877735 8888077 - CcPI632755_05g010100.1 Cco05g1010 1010
5 8847600 8854697 + CePI673135_05g010120.1 Cec05g1012 1012
5 8859448 8869835 - CePI673135_05g010140.1 Cec05g1014 1014
6 7267519 7273135 + Chy6G115100.1 Chy06g00982 982
6 7278728 7291425 - Chy6G115120.1 Chy06g00984 984
5 8818853 8826009 + ClG42_05g0099600.10 Clacu05g0996 996
5 8830723 8841141 - ClG42_05g0099800.10 Clacu05g0998 998
5 9108517 9116435 + ClCG05G008450.1 Cla05g00920 920
5 9120788 9133341 - ClCG05G008470.2 Cla05g00922 922
16 410970 418390 + CmaCh16G000930.1 Cma16g00093 93
16 417986 421303 - CmaCh16G000940.1 Cma16g00094 94
16 422820 428730 - CmaCh16G000950.1 Cma16g00095 95
18 9885048 9893082 - CmaCh18G012750.1 Cma18g01275 1275
6 7551781 7556273 - PI0014966.1 Cmetu06g0411 411
16 456410 459129 + CmoCh16G000990.1 Cmo16g00099 99
16 458601 462083 - CmoCh16G001000.1 Cmo16g00100 100
16 463609 470594 - CmoCh16G001020.1 Cmo16g00102 102
18 12503904 12511745 - CmoCh18G013060.1 Cmo18g01306 1306
5 8676031 8686432 - CmPI595203_05g009520.1 Cmu05g0952 952
1 55868766 55873756 + Conep01aG0124500.1 Cone1ag1196 1196
1 55874353 55878306 - Conep01aG0124600.1 Cone1ag1197 1197
5 3845643 3849589 - Conep05aG0092100.1 Cone5ag0895 895
15 346754 349128 - Conep15aG0006100.1 Cone15ag0059 59
9 369009 378512 + Cp4.1LG09g00550.1 Cpe09g00062 62
14 424381 431541 + Cp4.1LG14g06480.1 Cpe14g00078 78
14 431188 441519 - Cp4.1LG14g06350.1 Cpe14g00079 79
5 9560599 9571005 - CrPI670011_05g010330.1 Cre05g1033 1033
3 13127493 13135745 + CsaV3_3G017530.1 Csa03g01753 1753
3 13139930 13162136 - CsaV3_3G017550.1 Csa03g01755 1755
7 1077014 1088075 + Hsped.07g01160.1 Hepe07g0116 116
5 19759017 19772232 + Lsi05G011850.1 Lsi05g01185 1185
5 19775602 19782274 - Lsi05G011870.1 Lsi05g01187 1187
10 697386 713898 + MC10g0101 Mch10g0119 119
10 3644332 3645371 + MC10g0450 Mch10g0553 553
13 743146 751894 + Sed0017638.1 Sed13g0111 111
13 3748283 3753125 - Sed0018121.1 Sed13g0543 543
1 1695974 1704440 + Tan0018405.1 Tan01g0184 184
1 7496048 7500773 + Tan0007360.2 Tan01g0786 786
16 18165084 18179221 + Vvi16g774 Vvi16g774 774
16 18215065 18216904 + Vvi16g775 Vvi16g775 775
16 18222302 18224981 + Vvi16g776 Vvi16g776 776
16 18233567 18235457 - Vvi16g777 Vvi16g777 777
16 18247256 18248671 + Vvi16g778 Vvi16g778 778
16 18255108 18256261 + Vvi16g779 Vvi16g779 779
16 18275438 18276955 - Vvi16g780 Vvi16g780 780
16 18304762 18312966 + Vvi16g781 Vvi16g781 781
16 18315824 18317281 + Vvi16g782 Vvi16g782 782
16 18317817 18324441 - Vvi16g783 Vvi16g783 783
       

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