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
Vvi4g562 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g563 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g564 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g565 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g04496 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g566 . . . . . . . . . . Cma01g01519 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo18g00018 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g567 . . . . . . . . . . . . . . Sed04g0126 . . Bhi04g00018 Tan02g2366 Cmetu03g2209 . Hepe10g0521 . Lcy13g1583 . . . . . . . . . . . . . . . . . . Bda13g01252 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g568 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda13g01253 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g569 . . Bda01g00751 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g570 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g571 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 34753437 34756563 + Bda002790.1 Bda01g00751 751
13 34944065 34948415 - Bda032807 Bda13g01252 1252
13 34948908 34949963 - Bda000059.1 Bda13g01253 1253
4 367230 372900 + XM_039030589.1 Bhi04g00018 18
18 156665 160081 - BLOR08506 Blo18g00018 18
1 10643119 10645347 + CmaCh01G015190.1 Cma01g01519 1519
3 5125543 5129602 - PI0028600.1 Cmetu03g2209 2209
3 39156157 39160789 - CsaV3_3G048020.1 Csa03g04496 4496
10 6040993 6045799 - Hsped.10g05210.1 Hepe10g0521 521
13 34697370 34701346 - Maker00034008 Lcy13g1583 1583
4 795394 799955 + Sed0008739.4 Sed04g0126 126
2 92289617 92293647 + Tan0018613.1 Tan02g2366 2366
4 6281236 6283155 + Vvi4g562 Vvi4g562 562
4 6284452 6286825 + Vvi4g563 Vvi4g563 563
4 6327028 6327610 + Vvi4g564 Vvi4g564 564
4 6370072 6380258 + Vvi4g565 Vvi4g565 565
4 6381531 6389548 - Vvi4g566 Vvi4g566 566
4 6390423 6401066 - Vvi4g567 Vvi4g567 567
4 6408874 6414336 - Vvi4g568 Vvi4g568 568
4 6416367 6424588 - Vvi4g569 Vvi4g569 569
4 6428659 6430028 - Vvi4g570 Vvi4g570 570
4 6434195 6447365 + Vvi4g571 Vvi4g571 571
       

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