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
Vvi4g882 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0952 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g883 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone10ag0588 Cone3ag0615 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla03g00982 Cam03g1036 Cec03g1033 Cco03g1032 Clacu03g1014 Cmu03g1600 Cre03g1303 Lsi06g00675 . . .
Vvi4g884 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone10ag0587 Cone3ag0614 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi07g00219 . . .
Vvi4g885 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0954 . Cone10ag0586 Cone3ag0613 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi06g00660 . . .
Vvi4g886 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0761 . . . . . . . . . . . . . . Sed02g0840 . . . . . . . . Bhi10g02238 Tan07g1016 Cmetu11g1488 . Hepe10g0820 . . . . . . . . . . . . .
Vvi4g887 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag0612 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g888 . . Bda04g00081 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag0611 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g889 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g890 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g891 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone5ag0959 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 1626211 1629507 + Bda018731.1 Bda04g00081 81
10 58207746 58211050 + XM_039046865.1 Bhi10g02238 2238
3 18841512 18865792 - CaPI482276_03g010360.1 Cam03g1036 1036
3 17754874 17776679 - CcPI632755_03g010320.1 Cco03g1032 1032
3 21298319 21320201 - CePI673135_03g010330.1 Cec03g1033 1033
3 17713804 17737764 - ClG42_03g0101400.10 Clacu03g1014 1014
3 18494080 18520031 - ClCG03G010290.2 Cla03g00982 982
11 29745111 29747731 + PI0016499.1 Cmetu11g1488 1488
3 18100521 18122594 - CmPI595203_03g016000.1 Cmu03g1600 1600
3 3033151 3035440 + Conep03aG0062900.1 Cone3ag0611 611
3 3035396 3038819 - Conep03aG0063000.1 Cone3ag0612 612
3 3038961 3040859 + Conep03aG0063100.1 Cone3ag0613 613
3 3042319 3046533 + Conep03aG0063200.1 Cone3ag0614 614
3 3046517 3048835 - Conep03aG0063300.1 Cone3ag0615 615
5 4065048 4069522 - Conep05aG0097800.1 Cone5ag0952 952
5 4072111 4073636 - Conep05aG0098000.1 Cone5ag0954 954
5 4087514 4096223 - Conep05aG0098500.1 Cone5ag0959 959
10 2749645 2750959 + Conep10aG0060300.1 Cone10ag0586 586
10 2752731 2758394 + Conep10aG0060400.1 Cone10ag0587 587
10 2756489 2758394 - Conep10aG0060500.1 Cone10ag0588 588
12 7015882 7018060 - Conep12aG0078400.1 Cone12ag0761 761
3 22680886 22696033 - CrPI670011_03g013030.1 Cre03g1303 1303
10 16910943 16914150 - Hsped.10g08200.1 Hepe10g0820 820
6 10022364 10030411 - Lsi06G006600.1 Lsi06g00660 660
6 10450695 10466783 - Lsi06G006750.1 Lsi06g00675 675
7 2357801 2359429 + Lsi07G002190.1 Lsi07g00219 219
2 46016247 46020658 - Sed0004945.1 Sed02g0840 840
7 25234471 25237462 - Tan0004942.1 Tan07g1016 1016
4 17203387 17213431 - Vvi4g882 Vvi4g882 882
4 17227364 17237592 + Vvi4g883 Vvi4g883 883
4 17237680 17249747 - Vvi4g884 Vvi4g884 884
4 17250290 17259108 - Vvi4g885 Vvi4g885 885
4 17261345 17265845 + Vvi4g886 Vvi4g886 886
4 17272093 17283855 + Vvi4g887 Vvi4g887 887
4 17285215 17297138 - Vvi4g888 Vvi4g888 888
4 17297744 17299565 - Vvi4g889 Vvi4g889 889
4 17321649 17322027 - Vvi4g890 Vvi4g890 890
4 17331794 17344656 - Vvi4g891 Vvi4g891 891
       

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