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
Vvi19g964 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g965 . . . . . . . . . . . . . . . . . . . . . . . . Cla11g01586 Cam11g1653 Cec11g1681 Cco11g1678 Clacu11g1810 Cmu11g1624 Cre11g2040 Cone6ag0288 Cone9ag0323 . . . . . . Blo07g01000 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g966 . . . . . . . . . . . . . . . . . . . . . . . . Cla11g01587 Cam11g1654 Cec11g1682 Cco11g1679 Clacu11g1811 Cmu11g1625 Cre11g2041 Cone6ag0287 Cone9ag0322 . . Lsi04g01865 . . Cme07g00767 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g967 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g01182 . .
Vvi19g968 . . . . Bpe09g00292 . . . . . . Cma09g00748 . Car09g00656 Sed05g1856 . . Bhi05g02031 Tan02g0066 Cmetu01g2586 Lac12g0881 Hepe02g0032 . . Cla11g01588 . . . . . . . . . Cone15ag0980 Lsi04g01867 . . Cme07g00766 . . . . . . . . . . Cmo09g00740 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g969 . . . . . . . . . . . Cma09g00747 . Car09g00655 . . . . . . . . . . Cla11g01589 Cam11g1656 Cec11g1684 Cco11g1681 Clacu11g1813 Cmu11g1627 Cre11g2043 Cone6ag0286 Cone9ag0321 . . Lsi04g01868 . . Cme07g00762 . . . . . . . . . . Cmo09g00739 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g970 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g971 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g972 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g973 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 62319939 62321538 - XM_039032925.1 Bhi05g02031 2031
7 29587962 29589559 - BLOR18932 Blo07g01000 1000
9 2330595 2334785 + Bpe023962.1 Bpe09g00292 292
11 29233769 29238186 + CaPI482276_11g016530.1 Cam11g1653 1653
11 29238328 29244220 - CaPI482276_11g016540.1 Cam11g1654 1654
11 29257836 29269317 - CaPI482276_11g016560.1 Cam11g1656 1656
9 3836619 3846131 + Carg20062-RA Car09g00655 655
9 3851782 3855958 + Carg20063-RA Car09g00656 656
11 29612859 29617484 + CcPI632755_11g016780.1 Cco11g1678 1678
11 29617504 29623400 - CcPI632755_11g016790.1 Cco11g1679 1679
11 29637801 29649115 - CcPI632755_11g016810.1 Cco11g1681 1681
11 31069676 31074164 + CePI673135_11g016810.1 Cec11g1681 1681
11 31074306 31080146 - CePI673135_11g016820.1 Cec11g1682 1682
11 31094260 31105223 - CePI673135_11g016840.1 Cec11g1684 1684
11 29254422 29254770 + ClG42_11g0181000.10 Clacu11g1810 1810
11 29258659 29264870 - ClG42_11g0181100.10 Clacu11g1811 1811
11 29278677 29290127 - ClG42_11g0181300.10 Clacu11g1813 1813
11 29555839 29560241 + ClCG11G016280.2 Cla11g01586 1586
11 29559656 29566351 - ClCG11G016290.2 Cla11g01587 1587
11 29567642 29572633 - ClCG11G016300.2 Cla11g01588 1588
11 29578833 29591193 - ClCG11G016310.1 Cla11g01589 1589
9 3566489 3574964 + CmaCh09G007470.1 Cma09g00747 747
9 3576934 3584824 + CmaCh09G007480.1 Cma09g00748 748
7 6955546 6971064 + MELO3C010557.2.1 Cme07g00762 762
7 6979883 6986131 + MELO3C010555.2.1 Cme07g00766 766
7 7019261 7024594 + MELO3C010554.2.1 Cme07g00767 767
1 7554086 7556285 - PI0025577.1 Cmetu01g2586 2586
9 3694462 3701764 + CmoCh09G007390.1 Cmo09g00739 739
9 3708981 3713236 + CmoCh09G007400.1 Cmo09g00740 740
11 28507636 28507984 + CmPI595203_11g016240.1 Cmu11g1624 1624
11 28511891 28518128 - CmPI595203_11g016250.1 Cmu11g1625 1625
11 28531928 28542974 - CmPI595203_11g016270.1 Cmu11g1627 1627
6 1311415 1316676 + Conep06aG0028800.1 Cone6ag0286 286
6 1323600 1327692 + Conep06aG0028900.1 Cone6ag0287 287
6 1329789 1330924 - Conep06aG0029000.1 Cone6ag0288 288
9 1393365 1398584 + Conep09aG0032400.1 Cone9ag0321 321
9 1400858 1407596 + Conep09aG0032500.1 Cone9ag0322 322
9 1409268 1412538 - Conep09aG0032600.1 Cone9ag0323 323
15 7829933 7834101 - Conep15aG0100100.1 Cone15ag0980 980
11 32168155 32172737 + CrPI670011_11g020400.1 Cre11g2040 2040
11 32172879 32178780 - CrPI670011_11g020410.1 Cre11g2041 2041
11 32193071 32210035 - CrPI670011_11g020430.1 Cre11g2043 2043
6 9988814 9990198 + CsaV3_6G013800.1 Csa06g01182 1182
2 478310 479809 - Hsped.02g00320.1 Hepe02g0032 32
12 9169252 9170468 + Lag0015253.1 Lac12g0881 881
4 25777554 25785942 - Lsi04G018650.1 Lsi04g01865 1865
4 25796060 25802378 - Lsi04G018670.1 Lsi04g01867 1867
4 25809788 25829141 - Lsi04G018680.1 Lsi04g01868 1868
5 32009812 32012127 - Sed0026558.1 Sed05g1856 1856
2 867886 869672 - Tan0008912.1 Tan02g0066 66
19 18679153 18679264 - Vvi19g964 Vvi19g964 964
19 18708698 18709996 + Vvi19g965 Vvi19g965 965
19 18712457 18722886 - Vvi19g966 Vvi19g966 966
19 18754505 18762882 + Vvi19g967 Vvi19g967 967
19 18785289 18790280 - Vvi19g968 Vvi19g968 968
19 18803651 18822202 - Vvi19g969 Vvi19g969 969
19 18872619 18880961 - Vvi19g970 Vvi19g970 970
19 18966009 18966189 - Vvi19g971 Vvi19g971 971
19 18967467 18968195 - Vvi19g972 Vvi19g972 972
19 18990269 19006513 - Vvi19g973 Vvi19g973 973
       

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