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
Vvi5g1029 . . . . . . . . Cmo08g00107 . . . . . . . . . . . . . . . . . . . . . . Cone14ag0543 Cone15ag0565 . . . . . . . . . . . . . . . . . . . Car08g00085 . . Cpe17g01008 . . . . . . . . . . . . . . . . . .
Vvi5g1030 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1031 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00359 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1032 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0542 Cone15ag0564 . . . . . . . . . . Bpe05g01077 . . . Sed09g0007 . . . . . . . . Bhi12g02122 Tan06g1933 Cmetu11g0962 . . . Lcy13g0900 . . . . . . . . . . Cme11g02218
Vvi5g1033 . Blo12g00157 . . . . . . . . . . . . . . . Bhi01g02664 . . . . . Lcy11g1163 . . . . . . . . . . . . . . . . . . . . . Bma02g01009 . . . . . . . . . . . . . . . . . . . . . . . . Lsi09g01621 . . .
Vvi5g1034 . . . . . . . . . . . . . . . . . Bhi01g01167 . . . . . Lcy11g1279 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi09g01620 . . .
Vvi5g1035 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1036 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g1037 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone11ag0602 . . . . . . . . . . . . . . . . . . . . . Bhi12g02121 . . . . . Lcy13g0895 . . . . . . . . . . .
Vvi5g1038 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 3987323 3988145 - Bda005094.1 Bda11g00359 359
1 22888445 22890971 + XM_039036842.1 Bhi01g01167 1167
1 66308246 66311552 + XM_039048377.1 Bhi01g02664 2664
12 66071087 66072699 + XM_039019358.1 Bhi12g02121 2121
12 66105998 66110038 + XM_039050979.1 Bhi12g02122 2122
12 10554026 10555501 + BLOR04176 Blo12g00157 157
2 51196215 51197618 - Bma015824.1 Bma02g01009 1009
5 23269845 23273140 - Bpe018492.2 Bpe05g01077 1077
8 520615 523985 + Carg04928-RA Car08g00085 85
11 29399964 29405071 + MELO3C021153.2.1 Cme11g02218 2218
11 2721272 2724652 - PI0004339.1 Cmetu11g0962 962
8 561635 565069 + CmoCh08G001070.1 Cmo08g00107 107
11 3697507 3698940 - Conep11aG0061800.1 Cone11ag0602 602
14 2701991 2705458 - Conep14aG0055300.1 Cone14ag0542 542
14 2705855 2708428 - Conep14aG0055400.1 Cone14ag0543 543
15 2827955 2831744 - Conep15aG0057600.1 Cone15ag0564 564
15 2832229 2834661 - Conep15aG0057700.1 Cone15ag0565 565
17 7654280 7661427 + Cp4.1LG17g10110.1 Cpe17g01008 1008
11 34023102 34024556 - Maker00005166 Lcy11g1163 1163
11 36094577 36096836 - Maker00005269 Lcy11g1279 1279
13 15760465 15761787 + Maker00026337 Lcy13g0895 895
13 15971423 15975586 + Maker00026434 Lcy13g0900 900
9 24402039 24403394 - Lsi09G016200.1 Lsi09g01620 1620
9 24409212 24410582 - Lsi09G016210.1 Lsi09g01621 1621
9 74086 83621 - Sed0014888.1 Sed09g0007 7
6 59431326 59435666 - Tan0019778.1 Tan06g1933 1933
5 18370275 18379815 + Vvi5g1029 Vvi5g1029 1029
5 18396876 18398637 + Vvi5g1030 Vvi5g1030 1030
5 18409763 18411439 + Vvi5g1031 Vvi5g1031 1031
5 18412760 18422972 - Vvi5g1032 Vvi5g1032 1032
5 18422989 18423385 + Vvi5g1033 Vvi5g1033 1033
5 18426698 18461920 + Vvi5g1034 Vvi5g1034 1034
5 18465142 18465277 + Vvi5g1035 Vvi5g1035 1035
5 18465325 18470664 + Vvi5g1036 Vvi5g1036 1036
5 18470724 18474810 + Vvi5g1037 Vvi5g1037 1037
5 18478180 18479876 + Vvi5g1038 Vvi5g1038 1038
       

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