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
Vvi5g1289 . Blo12g00266 Bda03g00971 . . . . . . . Cma06g01698 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme07g01952 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1290 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1291 . . . . Bpe04g00897 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1292 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1293 . . . . . . . . . . Cma06g01697 Cma14g01428 . Car14g01258 . . Cpe03g01200 . . . . . . . . . . . . . . . . . Cone11ag0666 . . . Cme07g01951 . . . . . . . . . . Cmo14g01464 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1294 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1295 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1296 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1297 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1298 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 8776867 8778437 - Bda016981.1 Bda03g00971 971
12 16095030 16097607 + BLOR04285 Blo12g00266 266
4 6016063 6017613 - Bpe015560.1 Bpe04g00897 897
14 10832663 10840923 + Carg06579-RA Car14g01258 1258
6 10429201 10433462 - CmaCh06G016970.1 Cma06g01697 1697
6 10434993 10442118 - CmaCh06G016980.1 Cma06g01698 1698
14 10960965 10969243 + CmaCh14G014280.1 Cma14g01428 1428
7 24660224 24669018 - MELO3C017774.2.1 Cme07g01951 1951
7 24669811 24673000 - MELO3C017775.2.1 Cme07g01952 1952
14 11858049 11865918 + CmoCh14G014640.1 Cmo14g01464 1464
11 4446361 4451654 + Conep11aG0068300.1 Cone11ag0666 666
3 9814523 9822698 + Cp4.1LG03g13110.1 Cpe03g01200 1200
5 23489772 23496002 + Vvi5g1289 Vvi5g1289 1289
5 23496191 23498289 + Vvi5g1290 Vvi5g1290 1290
5 23498291 23501139 + Vvi5g1291 Vvi5g1291 1291
5 23503052 23506585 - Vvi5g1292 Vvi5g1292 1292
5 23508601 23514920 + Vvi5g1293 Vvi5g1293 1293
5 23520465 23524730 + Vvi5g1294 Vvi5g1294 1294
5 23524734 23526631 + Vvi5g1295 Vvi5g1295 1295
5 23526663 23528119 + Vvi5g1296 Vvi5g1296 1296
5 23528811 23532402 - Vvi5g1297 Vvi5g1297 1297
5 23547819 23548882 + Vvi5g1298 Vvi5g1298 1298
       

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