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
Vvi5g1049 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone18ag0907 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1050 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1051 . . . . . . . . Cmo08g00838 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi12g02119 . . . Hepe03g0632 . Lcy13g0892 Cla07g01594 Cam07g1691 Cec07g1787 Cco07g1749 Clacu07g1674 Cmu07g1641 Cre07g2015 Lsi09g01618 . . Cme11g02216
Vvi5g1052 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1053 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1054 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1055 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1056 . . . . . . . . Cmo08g00839 . . . . . . . . . . . . . . . . . . . . . . Cone14ag0540 Cone15ag0563 Cone18ag0904 . . . . . Blo02g00397 . . . . . . . . . . Cma08g00869 . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1057 . . . . . . . . Cmo08g00840 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme06g00859 . . . . . . . . . . . Cma08g00870 . . . . . Bhi12g02118 . . . . . Lcy13g0890 . . . . . . . Lsi09g01617 . . Cme11g02215
Vvi5g1058 . . . . . . . . Cmo08g00841 . . . . . . Cpe08g00103 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma08g00871 . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
12 65938450 65941637 + XM_039019566.1 Bhi12g02118 2118
12 65951892 65953760 - XM_039020078.1 Bhi12g02119 2119
2 4865536 4866939 + BLOR10127 Blo02g00397 397
7 31606061 31613215 - CaPI482276_07g016910.1 Cam07g1691 1691
7 31592371 31599651 - CcPI632755_07g017490.1 Cco07g1749 1749
7 33520530 33526272 - CePI673135_07g017870.1 Cec07g1787 1787
7 31457004 31464048 - ClG42_07g0167400.10 Clacu07g1674 1674
7 33244503 33251624 - ClCG07G016730.2 Cla07g01594 1594
8 5366642 5367982 - CmaCh08G008690.1 Cma08g00869 869
8 5372284 5374051 + CmaCh08G008700.1 Cma08g00870 870
8 5376350 5378721 - CmaCh08G008710.1 Cma08g00871 871
6 5877707 5883650 + MELO3C006779.2.1 Cme06g00859 859
11 29388679 29390871 - MELO3C021156.2.1 Cme11g02215 2215
11 29392496 29393976 + MELO3C021155.2.1 Cme11g02216 2216
8 5391991 5393340 - CmoCh08G008380.1 Cmo08g00838 838
8 5403120 5404702 + CmoCh08G008390.1 Cmo08g00839 839
8 5407125 5410105 - CmoCh08G008400.1 Cmo08g00840 840
8 5416717 5419290 - CmoCh08G008410.1 Cmo08g00841 841
7 31708953 31716034 - CmPI595203_07g016410.1 Cmu07g1641 1641
14 2692900 2694667 - Conep14aG0055100.1 Cone14ag0540 540
15 2825761 2827131 - Conep15aG0057500.1 Cone15ag0563 563
18 6420828 6422246 - Conep18aG0093000.1 Cone18ag0904 904
18 6448222 6449485 - Conep18aG0093300.1 Cone18ag0907 907
8 655968 657455 + Cp4.1LG08g05750.1 Cpe08g00103 103
7 35710948 35718137 - CrPI670011_07g020150.1 Cre07g2015 2015
3 12957521 12960331 - Hsped.03g06320.1 Hepe03g0632 632
13 15691039 15692798 - Maker00026349 Lcy13g0890 890
13 15714389 15717176 + Maker00026373 Lcy13g0892 892
9 24379542 24381682 + Lsi09G016170.1 Lsi09g01617 1617
9 24383717 24386566 - Lsi09G016180.1 Lsi09g01618 1618
5 18772177 18773897 - Vvi5g1049 Vvi5g1049 1049
5 18779196 18794608 + Vvi5g1050 Vvi5g1050 1050
5 18853398 18854607 - Vvi5g1051 Vvi5g1051 1051
5 18881482 18890603 - Vvi5g1052 Vvi5g1052 1052
5 18907192 18915663 - Vvi5g1053 Vvi5g1053 1053
5 18915856 18918978 + Vvi5g1054 Vvi5g1054 1054
5 18925517 18926513 - Vvi5g1055 Vvi5g1055 1055
5 18933763 18935456 + Vvi5g1056 Vvi5g1056 1056
5 18955955 18957477 + Vvi5g1057 Vvi5g1057 1057
5 18984606 19001277 + Vvi5g1058 Vvi5g1058 1058
       

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