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
Vvi5g999 . Blo12g00111 Bda03g01130 . Bpe04g01073 . . . . . Cma06g01698 . Car06g01440 . . . . . . . . . . . . . . . . . . . . . . . Csa02g00896 . . . . . . . . . . . . . . . . Car17g00072 Cpe12g00072 . Bhi12g01464 . . . Hepe03g0386 . . . . . . . . . Lsi09g01112 . . .
Vvi5g1000 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00346 . . Bpe13g00860 . Bma06g01280 . . . . . . . . Cpe17g00305 . . . . . . . . . . . . . . . . . .
Vvi5g1002 . Blo12g00114 Bda03g01129 . Bpe04g01072 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1003 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1004 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1005 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1006 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1007 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1008 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 11874338 11882168 - Bda017180.3 Bda03g01129 1129
3 11912212 11916743 + Bda017181.1 Bda03g01130 1130
11 3865693 3873100 - Bda005078.1 Bda11g00346 346
12 47456088 47462120 + XM_039019733.1 Bhi12g01464 1464
12 7951492 7956661 - BLOR04130 Blo12g00111 111
12 8064139 8067745 + BLOR04133 Blo12g00114 114
6 49889016 49903895 - Bma024389.1 Bma06g01280 1280
4 8178957 8182415 - Bpe015744.1 Bpe04g01072 1072
4 8215201 8219676 + Bpe015745.1 Bpe04g01073 1073
13 14771340 14777078 + Bpe010548.1 Bpe13g00860 860
6 10239775 10243925 - Carg15435-RA Car06g01440 1440
17 418096 422887 + Carg10160-RA Car17g00072 72
6 10434993 10442118 - CmaCh06G016980.1 Cma06g01698 1698
12 426482 431576 + Cp4.1LG12g00660.1 Cpe12g00072 72
17 2068622 2076756 + Cp4.1LG17g02690.1 Cpe17g00305 305
2 8344387 8352074 + CsaV3_2G011120.1 Csa02g00896 896
3 5586563 5592537 + Hsped.03g03860.1 Hepe03g0386 386
9 17836340 17842292 + Lsi09G011120.1 Lsi09g01112 1112
5 17358931 17387128 - Vvi5g999 Vvi5g999 999
5 17395111 17395321 - Vvi5g1000 Vvi5g1000 1000
5 17396352 17430590 - Vvi5g1001 Vvi5g1001 1001
5 17443712 17468487 + Vvi5g1002 Vvi5g1002 1002
5 17471045 17472850 + Vvi5g1003 Vvi5g1003 1003
5 17485622 17488917 - Vvi5g1004 Vvi5g1004 1004
5 17537905 17558726 + Vvi5g1005 Vvi5g1005 1005
5 17560596 17561510 - Vvi5g1006 Vvi5g1006 1006
5 17569693 17570482 + Vvi5g1007 Vvi5g1007 1007
5 17575003 17582060 - Vvi5g1008 Vvi5g1008 1008
       

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