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
Vvi18g1770 Blo01g01693 . . . Bpe02g00249 . . Bma01g02458 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00913 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1771 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1772 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1773 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1774 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1775 . . . . . . . Bma01g02459 . . Cma01g00887 . Car01g00809 . . Cpe06g00945 . . . . . . . . Cla08g00187 . . . . . . . . . . . . . Cme09g00127 . . . . . . . . . Cmo01g00932 Cmo09g01202 . . . Car09g01072 . Cpe02g00978 Bhi06g00105 . . . . . . . . . . . . . . . . .
Vvi18g1776 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1777 Blo01g01695 . . . Bpe02g00247 . . Bma01g02461 . . . . . . . . . . . . . . . . Cla08g00194 . Cec08g0043 Cco08g0264 . Cmu08g0181 Cre08g0169 . . . . . . . Cme09g00132 . . Bda11g00909 . . . . . Sed10g1659 . Cmo09g01192 . . . . . Cpe02g00975 Bhi06g00098 Tan10g1823 Cmetu09g0513 . . . . . . . . . . . . . . .
Vvi18g1778 Blo01g01696 . . . Bpe02g00246 . . Bma01g02462 . . . . . . . . . . . . . . . . Cla08g00196 . Cec08g0041 Cco08g0266 . Cmu08g0182 Cre08g0171 . . . . . . . Cme09g00133 . . Bda11g00908 . . . . . . . Cmo09g01191 . . . . . . Bhi06g00097 Tan10g1822 . . . . . . . . . . . . . . . .
Vvi18g1779 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 8903359 8905907 + Bda005662.1 Bda11g00908 908
11 8906510 8907852 + Bda005663.1 Bda11g00909 909
11 8936580 8941856 + Bda005668.1 Bda11g00913 913
6 2698374 2708212 + XM_039033165.1 Bhi06g00097 97
6 2711474 2713885 + XM_039034015.1 Bhi06g00098 98
6 2876115 2884593 - XM_039034337.1 Bhi06g00105 105
1 56627242 56631666 - BLOR01693 Blo01g01693 1693
1 56640994 56642366 - BLOR01695 Blo01g01695 1695
1 56643028 56645297 - BLOR01696 Blo01g01696 1696
1 82172443 82177125 - Bma003328.1 Bma01g02458 2458
1 82179449 82180872 + Bma003329.1 Bma01g02459 2459
1 82186277 82187569 - Bma003331.1 Bma01g02461 2461
1 82188198 82189958 - Bma003332.1 Bma01g02462 2462
2 1686996 1688865 + Bpe008091.1 Bpe02g00246 246
2 1689502 1690840 + Bpe008092.1 Bpe02g00247 247
2 1699003 1703697 + Bpe008094.1 Bpe02g00249 249
1 5442881 5444500 + Carg27123-RA Car01g00809 809
9 9678555 9681260 - Carg27920-RA Car09g01072 1072
8 4743934 4746402 - CcPI632755_08g002640.1 Cco08g0264 264
8 4789722 4793036 - CcPI632755_08g002660.1 Cco08g0266 266
8 764865 768265 + CePI673135_08g000410.1 Cec08g0041 41
8 798001 800577 + CePI673135_08g000430.1 Cec08g0043 43
8 3840670 3844494 + ClCG08G001870.2 Cla08g00187 187
8 3955913 3958634 - ClCG08G001920.2 Cla08g00194 194
8 3994422 3998243 - ClCG08G001940.2 Cla08g00196 196
1 5107016 5108950 + CmaCh01G008870.1 Cma01g00887 887
9 953358 957725 + MELO3C022117.2.1 Cme09g00127 127
9 974790 977114 - MELO3C022113.2.1 Cme09g00132 132
9 978151 981530 - MELO3C022112.2.1 Cme09g00133 133
9 20843388 20845541 + PI0016361.1 Cmetu09g0513 513
1 5364232 5365825 + CmoCh01G009320.1 Cmo01g00932 932
9 8738281 8745477 + CmoCh09G011910.1 Cmo09g01191 1191
9 8748631 8752870 + CmoCh09G011920.1 Cmo09g01192 1192
9 8977626 8980357 - CmoCh09G012020.1 Cmo09g01202 1202
8 3890002 3892564 - CmPI595203_08g001810.1 Cmu08g0181 181
8 3926111 3929499 - CmPI595203_08g001820.1 Cmu08g0182 182
2 8747885 8749265 - Cp4.1LG02g09780.1 Cpe02g00975 975
2 8786511 8788089 - Cp4.1LG02g09760.1 Cpe02g00978 978
6 7738020 7740698 - Cp4.1LG06g09740.1 Cpe06g00945 945
8 3848296 3850830 - CrPI670011_08g001690.1 Cre08g0169 169
8 3885503 3888908 - CrPI670011_08g001710.1 Cre08g0171 171
10 33259814 33262332 - Sed0007613.1 Sed10g1659 1659
10 56877051 56886856 + Tan0015920.2 Tan10g1822 1822
10 56891961 56895897 + Tan0022571.1 Tan10g1823 1823
18 28940631 28948447 - Vvi18g1770 Vvi18g1770 1770
18 28949935 28951701 - Vvi18g1771 Vvi18g1771 1771
18 28984712 28986077 + Vvi18g1772 Vvi18g1772 1772
18 28988812 28989566 + Vvi18g1773 Vvi18g1773 1773
18 28991562 29014023 + Vvi18g1774 Vvi18g1774 1774
18 29018756 29021753 + Vvi18g1775 Vvi18g1775 1775
18 29046999 29058675 - Vvi18g1776 Vvi18g1776 1776
18 29067482 29070189 - Vvi18g1777 Vvi18g1777 1777
18 29070858 29074288 - Vvi18g1778 Vvi18g1778 1778
18 29077207 29084742 + Vvi18g1779 Vvi18g1779 1779
       

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