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
Vvi5g859 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g860 . . . . . Bpe14g01299 . . . . Cma06g01261 Cma14g01879 Car06g01084 Car14g01681 . Cpe08g00385 Cpe03g01576 . . . . . . . . . . . . . . . . . Cone4ag0387 . . . Cme06g00401 . . . Bda13g00022 . . . . . Cmo06g01270 Cmo14g01927 . . . . . . . . . . . . . Cla05g00366 Cam05g0399 Cec05g0404 Cco05g0404 Clacu05g0394 Cmu05g0379 Cre05g0441 . Csa03g01120 Chy06g00388 .
Vvi5g861 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g862 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag0392 . . . . . . . . . . Bma02g00736 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g863 . . Bda03g01152 . . Bpe14g01304 . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0222 Cone15ag0239 . . . . . . . . . . . . Bma02g00735 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g864 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g865 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g866 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g867 . . . . . . . . . Cmo17g00115 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car08g00907 Car17g00098 . . . . . . . . . . . . . . . . . . . .
Vvi5g868 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 12554389 12555030 - Bda017209.1 Bda03g01152 1152
13 408314 430509 + Bda000864.1 Bda13g00022 22
2 37732870 37734366 + Bma015435.1 Bma02g00735 735
2 37735258 37737470 - Bma015436.1 Bma02g00736 736
14 9930872 9938977 - Bpe014655.1 Bpe14g01299 1299
14 10022647 10034178 + Bpe014660.1 Bpe14g01304 1304
5 3664715 3680536 + CaPI482276_05g003990.1 Cam05g0399 399
6 8137225 8142289 + Carg06275-RA Car06g01084 1084
8 6079577 6087007 - Carg11017-RA Car08g00907 907
14 13371690 13377027 - Carg16506-RA Car14g01681 1681
17 574457 582503 - Carg10134-RA Car17g00098 98
5 3318396 3334246 + CcPI632755_05g004040.1 Cco05g0404 404
5 3310532 3326742 + CePI673135_05g004040.1 Cec05g0404 404
6 2614593 2620560 + Chy6G109160.1 Chy06g00388 388
5 3378757 3394519 + ClG42_05g0039400.10 Clacu05g0394 394
5 3329869 3346376 + ClCG05G003530.2 Cla05g00366 366
6 8381605 8389450 + CmaCh06G012610.1 Cma06g01261 1261
14 13306893 13312692 - CmaCh14G018790.1 Cma14g01879 1879
6 2566388 2572809 + MELO3C006331.2.1 Cme06g00401 401
6 9580820 9586552 + CmoCh06G012700.1 Cmo06g01270 1270
14 14291973 14298246 - CmoCh14G019270.1 Cmo14g01927 1927
17 614191 622057 - CmoCh17G001150.1 Cmo17g00115 115
5 3216746 3232502 + CmPI595203_05g003790.1 Cmu05g0379 379
4 1756989 1760681 - Conep04aG0040000.1 Cone4ag0387 387
4 1784047 1786702 - Conep04aG0040600.1 Cone4ag0392 392
14 1023399 1028242 + Conep14aG0022700.1 Cone14ag0222 222
15 1126291 1130850 + Conep15aG0024400.1 Cone15ag0239 239
3 12190608 12197543 - Cp4.1LG03g18190.1 Cpe03g01576 1576
8 2413842 2419619 - Cp4.1LG08g02860.1 Cpe08g00385 385
5 4000165 4015960 + CrPI670011_05g004410.1 Cre05g0441 441
3 8836703 8843358 + CsaV3_3G011200.1 Csa03g01120 1120
5 11812245 11816013 + Vvi5g859 Vvi5g859 859
5 11894247 11921267 + Vvi5g860 Vvi5g860 860
5 11954398 11969257 + Vvi5g861 Vvi5g861 861
5 11976258 11986353 + Vvi5g862 Vvi5g862 862
5 12014629 12073403 - Vvi5g863 Vvi5g863 863
5 12124245 12124599 - Vvi5g864 Vvi5g864 864
5 12156029 12156413 - Vvi5g865 Vvi5g865 865
5 12188266 12188410 + Vvi5g866 Vvi5g866 866
5 12189928 12193060 - Vvi5g867 Vvi5g867 867
5 12193112 12218103 - Vvi5g868 Vvi5g868 868
       

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