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
Vvi2g372 . . . . . . . . . . . . . Car15g01087 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g373 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g374 . . . Bda08g00332 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g375 . . Bda06g00076 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone9ag0758 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g376 . . . . . . . Bma14g00584 . Cmo16g01061 . . . . . . Cpe05g00311 . . . . . . . . . . . . . . . . . . . . . . . . . Bda09g00049 . . . . . . . . . . . . . Bhi12g00209 . . Lac11g2129 Hepe06g1577 . Lcy12g1689 . . . . . . . . . . .
Vvi2g377 . . . . Bpe05g00631 . . . . Cmo16g01059 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma05g00808 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g378 . . . . . . . . Cmo06g01129 Cmo16g01058 . . . . . Cpe14g00834 . Bhi11g00237 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma12g00096 . . . Cma06g01102 . Car06g00939 Car16g00969 Cpe08g00516 . . . . . . . . . . . . . . . . . . .
Vvi2g379 . . . . . Bpe07g00120 . . . . . . . . . . . Bhi11g00366 . . . . . . . . . . . . . . . Cone6ag0757 . . . . . . . . . . . . . . . . Cma06g00723 . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g380 . . . . . . . . . . Cma02g01477 . Car02g01238 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g381 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 756668 764878 + Bda023247.1 Bda06g00076 76
8 3407379 3412932 - Bda024770.1 Bda08g00332 332
9 714590 716312 + Bda030572.1 Bda09g00049 49
11 5731806 5738404 + XM_039047205.1 Bhi11g00237 237
11 8692058 8708627 + XM_039047298.1 Bhi11g00366 366
12 6721599 6724305 - XM_039018763.1 Bhi12g00209 209
5 45416612 45418453 - Bma021911.1 Bma05g00808 808
12 1629114 1631506 - Bma006967.1 Bma12g00096 96
14 6342254 6345417 - Bma011020.1 Bma14g00584 584
5 20196570 20198400 - Bpe018047.2 Bpe05g00631 631
7 853122 867895 - Bpe020932.1 Bpe07g00120 120
2 8381003 8383482 + Carg02510-RA Car02g01238 1238
6 7258309 7261808 - Carg24955-RA Car06g00939 939
15 8537163 8540169 - Carg16655-RA Car15g01087 1087
16 8084760 8091807 - Carg25214-RA Car16g00969 969
2 8463688 8465457 + CmaCh02G014770.1 Cma02g01477 1477
6 3646150 3666643 - CmaCh06G007230.1 Cma06g00723 723
6 7440315 7443484 - CmaCh06G011020.1 Cma06g01102 1102
6 8677999 8680953 - CmoCh06G011290.1 Cmo06g01129 1129
16 7427147 7434657 - CmoCh16G010580.1 Cmo16g01058 1058
16 7436229 7443521 + CmoCh16G010590.1 Cmo16g01059 1059
16 7447423 7451865 + CmoCh16G010610.1 Cmo16g01061 1061
6 3847251 3857398 + Conep06aG0078000.1 Cone6ag0757 757
9 3628198 3631611 + Conep09aG0077500.1 Cone9ag0758 758
5 1735860 1739963 - Cp4.1LG05g03670.1 Cpe05g00311 311
8 3336974 3340525 + Cp4.1LG08g01630.1 Cpe08g00516 516
14 6771794 6778915 - Cp4.1LG14g08390.1 Cpe14g00834 834
6 66521449 66523943 + Hsped.06g15770.1 Hepe06g1577 1577
11 37329767 37332075 + Lag0032767.1 Lac11g2129 2129
12 37373106 37375549 + Maker00003084 Lcy12g1689 1689
2 3594086 3614388 - Vvi2g372 Vvi2g372 372
2 3615151 3630010 - Vvi2g373 Vvi2g373 373
2 3631706 3639546 + Vvi2g374 Vvi2g374 374
2 3644700 3649060 + Vvi2g375 Vvi2g375 375
2 3651996 3655704 - Vvi2g376 Vvi2g376 376
2 3662067 3666803 - Vvi2g377 Vvi2g377 377
2 3670618 3678500 + Vvi2g378 Vvi2g378 378
2 3679350 3708506 + Vvi2g379 Vvi2g379 379
2 3716499 3720934 - Vvi2g380 Vvi2g380 380
2 3722060 3723122 - Vvi2g381 Vvi2g381 381
       

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