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
Vvi5g569 . Blo12g00345 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g570 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g571 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g572 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g573 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g574 . . Bda03g00859 . Bpe04g00812 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g575 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g576 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g577 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g578 . . . . . . . . . . Cma06g01356 . Car06g01177 . Sed02g1355 . . Bhi01g00747 Tan10g0777 Cmetu06g1274 . Hepe05g1595 . Lcy11g1592 . . . . . . . . . . . Lsi05g01648 . . Cme06g00565 . . . . . . . . . Cmo06g01371 . . . . . . . . . . . . . . . . . . . . . . Csa03g01281 Chy06g00533 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 7442225 7444555 - Bda016850.1 Bda03g00859 859
1 14142973 14145885 - XM_039025523.1 Bhi01g00747 747
12 19397056 19404560 + BLOR04364 Blo12g00345 345
4 5343498 5346847 - Bpe015472.1 Bpe04g00812 812
6 8648280 8651748 - Carg06180-RA Car06g01177 1177
6 3623106 3625796 - Chy6G110610.1 Chy06g00533 533
6 8885696 8887726 - CmaCh06G013560.1 Cma06g01356 1356
6 3566514 3569730 - MELO3C006492.2.1 Cme06g00565 565
6 3821156 3824290 - PI0025067.1 Cmetu06g1274 1274
6 10107444 10109456 - CmoCh06G013710.1 Cmo06g01371 1371
3 9783757 9787642 - CsaV3_3G012810.1 Csa03g01281 1281
5 65622583 65626112 + Hsped.05g15950.1 Hepe05g1595 1595
11 39761547 39764626 + Maker00031337 Lcy11g1592 1592
5 24123857 24132411 + Lsi05G016480.1 Lsi05g01648 1648
2 49838159 49841601 + Sed0006870.2 Sed02g1355 1355
10 6439587 6443000 - Tan0010730.1 Tan10g0777 777
5 5884387 5899015 - Vvi5g569 Vvi5g569 569
5 5920945 5929612 + Vvi5g570 Vvi5g570 570
5 5938848 5945621 + Vvi5g571 Vvi5g571 571
5 5954822 6022326 - Vvi5g572 Vvi5g572 572
5 6022841 6024227 + Vvi5g573 Vvi5g573 573
5 6025513 6051172 - Vvi5g574 Vvi5g574 574
5 6052179 6053937 + Vvi5g575 Vvi5g575 575
5 6056508 6156452 - Vvi5g576 Vvi5g576 576
5 6187478 6188292 + Vvi5g577 Vvi5g577 577
5 6206913 6210538 + Vvi5g578 Vvi5g578 578
       

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