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
Vvi18g1320 . . . . . . . . Cmo04g02579 . . . . . Sed11g1378 . . Bhi04g01745 Tan11g1099 . . Hepe02g2814 . Lcy10g1371 Cla08g00746 Cam08g1173 Cec08g0763 Cco08g0870 Clacu08g0879 . Cre08g0681 . . . Cone20ag0364 . . . Cme03g01053 Blo17g00133 . . Bda13g01417 . . . Bma02g00153 . . . . . Car04g02372 . Cpe01g02133 . . . . . . . . . . . . . . . Lsi08g00575 . Chy03g00488 .
Vvi18g1321 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1322 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1323 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1324 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1325 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1326 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1327 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1328 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0363 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1329 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
13 36870264 36885177 - Bda000244.1 Bda13g01417 1417
4 42429132 42445002 + XM_039029394.1 Bhi04g01745 1745
17 1225206 1231530 - BLOR15954 Blo17g00133 133
2 1343558 1353348 - Bma014608.1 Bma02g00153 153
8 18060027 18068585 + CaPI482276_08g011730.1 Cam08g1173 1173
4 19030040 19039589 - Carg15807-RA Car04g02372 2372
8 20545368 20555036 + CcPI632755_08g008700.1 Cco08g0870 870
8 19336580 19346433 + CePI673135_08g007630.1 Cec08g0763 763
3 6749093 6755706 + Chy3G054680.1 Chy03g00488 488
8 18848828 18857396 + ClG42_08g0087900.10 Clacu08g0879 879
8 19746899 19755559 + ClCG08G007340.2 Cla08g00746 746
3 19809899 19827887 - MELO3C019977.2.1 Cme03g01053 1053
4 18867318 18875874 - CmoCh04G025790.1 Cmo04g02579 2579
20 1632197 1634366 + Conep20aG0037700.1 Cone20ag0363 363
20 1637882 1643603 - Conep20aG0037800.1 Cone20ag0364 364
1 17986689 17995606 - Cp4.1LG01g21320.1 Cpe01g02133 2133
8 19757653 19766235 + CrPI670011_08g006810.1 Cre08g0681 681
2 77223366 77233584 - Hsped.02g28140.1 Hepe02g2814 2814
10 36920944 36931708 - Maker00008667 Lcy10g1371 1371
8 14017264 14027577 - Lsi08G005750.1 Lsi08g00575 575
11 29786111 29795485 - Sed0007537.1 Sed11g1378 1378
11 8711257 8721803 + Tan0009084.1 Tan11g1099 1099
18 18789155 18832323 + Vvi18g1320 Vvi18g1320 1320
18 18833384 18834436 - Vvi18g1321 Vvi18g1321 1321
18 18834450 18840157 + Vvi18g1322 Vvi18g1322 1322
18 18840210 18858436 - Vvi18g1323 Vvi18g1323 1323
18 18858919 18864380 - Vvi18g1324 Vvi18g1324 1324
18 18882117 18882775 - Vvi18g1325 Vvi18g1325 1325
18 18902686 18908850 + Vvi18g1326 Vvi18g1326 1326
18 18915283 18918742 - Vvi18g1327 Vvi18g1327 1327
18 18930308 18934653 - Vvi18g1328 Vvi18g1328 1328
18 18948925 18949435 - Vvi18g1329 Vvi18g1329 1329
       

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