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
Vvi5g659 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi05g01709 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g660 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag0317 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g01227 . .
Vvi5g661 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi05g01712 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g662 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo06g01341 . . . . . . . . . . . . . . . . . . . . . . Csa03g01226 . .
Vvi5g663 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi05g01713 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g664 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo06g01340 . . . . . . . . . . . . . . . . . . . . . . Csa03g01225 . .
Vvi5g665 . . . . . . . . . . Cma06g01336 . . . . . . . . . . . . . . . . . . . . . . . . Lsi05g01715 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g666 . . . . . . . . Cmo08g01067 . . . Car06g01146 . . . . . . . . . . . . . . . . . . . . . . . . . Cme06g00509 . . . . . . . . . Cmo06g01339 . . . . . . . . . . . . . . . . . . . . . . Csa03g01224 . .
Vvi5g667 . . . . . . . . . . Cma06g01335 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g668 . . . . . . . Bma05g01073 Cmo08g01066 . . . Car06g01145 . . . . . . . . . . . . . . . . . . . . . . . Csa02g01076 Chy05g00336 Cme06g00508 . . . . Bpe05g00863 Bpe13g00564 . . . Cmo06g01338 . Cma08g01091 . Car08g00966 . . . . . . . . . . . . . . . . . Lsi09g01246 Csa03g01223 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 49470710 49473426 - Bma022240.2 Bma05g01073 1073
5 21837675 21839415 - Bpe018276.1 Bpe05g00863 863
13 12827594 12828902 - Bpe010267.1 Bpe13g00564 564
6 8492165 8493891 + Carg06212-RA Car06g01145 1145
6 8493914 8499679 - Carg06211-RA Car06g01146 1146
8 6442410 6446112 - Carg10956-RA Car08g00966 966
5 3460704 3463122 - Chy5G093820.1 Chy05g00336 336
6 8769765 8772827 - CmaCh06G013350.1 Cma06g01335 1335
6 8773673 8775643 - CmaCh06G013360.1 Cma06g01336 1336
8 6804306 6806000 - CmaCh08G010910.1 Cma08g01091 1091
6 3203334 3204945 - MELO3C006438.2.1 Cme06g00508 508
6 3208838 3210528 - MELO3C006439.2.1 Cme06g00509 509
6 9947011 9948759 + CmoCh06G013380.1 Cmo06g01338 1338
6 9948977 9950753 - CmoCh06G013390.1 Cmo06g01339 1339
6 9951638 9953414 - CmoCh06G013400.1 Cmo06g01340 1340
6 9954185 9955958 - CmoCh06G013410.1 Cmo06g01341 1341
8 6886895 6888505 - CmoCh08G010660.1 Cmo08g01066 1066
8 6889377 6890767 - CmoCh08G010670.1 Cmo08g01067 1067
4 1442966 1443979 + Conep04aG0032900.1 Cone4ag0317 317
2 10486203 10488514 - CsaV3_2G012920.1 Csa02g01076 1076
3 9428438 9430680 - CsaV3_3G012230.1 Csa03g01223 1223
3 9431286 9433103 - CsaV3_3G012240.1 Csa03g01224 1224
3 9435557 9437009 - CsaV3_3G012250.1 Csa03g01225 1225
3 9438806 9440125 - CsaV3_3G012260.1 Csa03g01226 1226
3 9441109 9442415 - CsaV3_3G012270.1 Csa03g01227 1227
5 24600794 24602402 + Lsi05G017090.1 Lsi05g01709 1709
5 24614752 24616117 + Lsi05G017120.1 Lsi05g01712 1712
5 24624034 24626092 + Lsi05G017130.1 Lsi05g01713 1713
5 24631657 24634037 + Lsi05G017150.1 Lsi05g01715 1715
9 20093881 20106864 - Lsi09G012460.1 Lsi09g01246 1246
5 7368011 7369801 - Vvi5g659 Vvi5g659 659
5 7382400 7384116 + Vvi5g660 Vvi5g660 660
5 7384131 7393730 + Vvi5g661 Vvi5g661 661
5 7405375 7407224 + Vvi5g662 Vvi5g662 662
5 7409855 7411681 + Vvi5g663 Vvi5g663 663
5 7413731 7415180 + Vvi5g664 Vvi5g664 664
5 7417579 7444624 + Vvi5g665 Vvi5g665 665
5 7444853 7446921 + Vvi5g666 Vvi5g666 666
5 7455360 7457511 + Vvi5g667 Vvi5g667 667
5 7461184 7463778 + Vvi5g668 Vvi5g668 668
       

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