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
Vvi19g924 . . . . . . . . Cmo16g00499 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy07g01038 .
Vvi19g925 . . . . . . . . Cmo16g00500 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00707 . . . . . . . . . Cma04g00641 . . . . . . . . . . . . . . . . . . . . . Chy07g01039 .
Vvi19g926 . . . . . . . . Cmo16g00501 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00706 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy07g01042 .
Vvi19g927 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00705 . . . . . . . . . Cma04g00640 . . . . . . . . . . . . . . . . . . . . . Chy07g01043 .
Vvi19g928 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00702 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g929 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00699 . . . . . . . . . Cma04g00639 . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g930 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g931 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00697 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g932 . . . . . . . . . . . . . Car09g00657 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g933 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00695 Bda05g00801 . . . . . . . . Cma04g00638 . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 56458421 56459258 + Bda021957.1 Bda05g00801 801
10 22298221 22299175 + BLOR02485 Blo10g00695 695
10 22337960 22344201 + BLOR02487 Blo10g00697 697
10 22376806 22377817 + BLOR02489 Blo10g00699 699
10 22466544 22467509 - BLOR02492 Blo10g00702 702
10 22558030 22558962 - BLOR02495 Blo10g00705 705
10 22568544 22579536 - BLOR02496 Blo10g00706 706
10 22588267 22589229 - BLOR02497 Blo10g00707 707
9 3857637 3860845 - Carg20064-RA Car09g00657 657
7 15329299 15330071 + Chy7G138680.1 Chy07g01038 1038
7 15331807 15332627 + Chy7G138690.1 Chy07g01039 1039
7 15362524 15363803 + Chy7G138720.1 Chy07g01042 1042
7 15369291 15376043 + Chy7G138730.1 Chy07g01043 1043
4 3268691 3269778 - CmaCh04G006380.1 Cma04g00638 638
4 3269916 3271375 - CmaCh04G006390.1 Cma04g00639 639
4 3271577 3272321 - CmaCh04G006400.1 Cma04g00640 640
4 3273122 3286431 - CmaCh04G006410.1 Cma04g00641 641
16 2411394 2414595 + CmoCh16G004990.1 Cmo16g00499 499
16 2417204 2417551 + CmoCh16G005000.1 Cmo16g00500 500
16 2417740 2418027 + CmoCh16G005010.1 Cmo16g00501 501
19 16626399 16627945 + Vvi19g924 Vvi19g924 924
19 16675413 16687774 - Vvi19g925 Vvi19g925 925
19 16803107 16803919 + Vvi19g926 Vvi19g926 926
19 16876920 16878081 + Vvi19g927 Vvi19g927 927
19 16915104 16916114 - Vvi19g928 Vvi19g928 928
19 17054530 17055451 - Vvi19g929 Vvi19g929 929
19 17070454 17071827 - Vvi19g930 Vvi19g930 930
19 17114057 17114848 + Vvi19g931 Vvi19g931 931
19 17116245 17118711 - Vvi19g932 Vvi19g932 932
19 17210240 17211505 + Vvi19g933 Vvi19g933 933
       

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