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
Vvi5g1109 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1110 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1111 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1112 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1113 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1114 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1115 Blo01g00237 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag1361 . . . . . . . . . . . Bpe05g01024 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1116 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1117 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1118 . . . . . . . . . . . Cma14g01498 . Car14g01330 . . Cpe03g01258 Bhi01g02630 . . . Hepe05g1275 . . . . . . . . . . . . . . . . Cme07g01854 . . . . . . . . . . Cmo14g01533 . . . . . . . . . . . . . Cla07g01582 Cam07g1679 Cec07g1774 Cco07g1737 Clacu07g1663 Cmu07g1629 Cre07g2003 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 65304440 65313217 + XM_039027704.1 Bhi01g02630 2630
1 2939872 2941458 + BLOR00237 Blo01g00237 237
5 22861063 22862649 + Bpe018435.1 Bpe05g01024 1024
7 31412875 31421623 - CaPI482276_07g016790.1 Cam07g1679 1679
14 11246969 11254410 - Carg22441-RA Car14g01330 1330
7 31400042 31407992 - CcPI632755_07g017370.1 Cco07g1737 1737
7 33320440 33329209 - CePI673135_07g017740.1 Cec07g1774 1774
7 31261304 31272655 - ClG42_07g0166300.10 Clacu07g1663 1663
7 33030625 33042350 - ClCG07G016600.2 Cla07g01582 1582
14 11338083 11344675 - CmaCh14G014980.1 Cma14g01498 1498
7 24014166 24023152 + MELO3C017683.2.1 Cme07g01854 1854
14 12247970 12255032 - CmoCh14G015330.1 Cmo14g01533 1533
7 31513072 31520962 - CmPI595203_07g016290.1 Cmu07g1629 1629
1 56592634 56593933 + Conep01aG0141800.1 Cone1ag1361 1361
3 10195735 10203778 - Cp4.1LG03g12460.1 Cpe03g01258 1258
7 35522198 35530149 - CrPI670011_07g020030.1 Cre07g2003 2003
5 60286076 60295113 - Hsped.05g12750.1 Hepe05g1275 1275
5 20219549 20228364 - Vvi5g1109 Vvi5g1109 1109
5 20228611 20244419 - Vvi5g1110 Vvi5g1110 1110
5 20251496 20251637 - Vvi5g1111 Vvi5g1111 1111
5 20260088 20261162 + Vvi5g1112 Vvi5g1112 1112
5 20265976 20266435 + Vvi5g1113 Vvi5g1113 1113
5 20269992 20270547 + Vvi5g1114 Vvi5g1114 1114
5 20273517 20276507 - Vvi5g1115 Vvi5g1115 1115
5 20312696 20315158 + Vvi5g1116 Vvi5g1116 1116
5 20325548 20328541 - Vvi5g1117 Vvi5g1117 1117
5 20344507 20353316 - Vvi5g1118 Vvi5g1118 1118
       

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