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
Vvi4g512 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g513 . . Bda01g00767 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g514 . . Bda01g00768 . . . . . . . . . . . Sed11g1146 . . Bhi04g00043 Tan02g2758 Cmetu03g1431 . Hepe10g0221 . Lcy13g1826 . . . . . . . . . . . . . . . . . . Bda13g01245 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme07g00112
Vvi4g515 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g516 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g517 . . . . . . . . . . . . . . . . . Bhi04g00042 Tan02g2757 . . . . Lcy13g1825 . . . . . . . . . . . . . . . . Blo18g00012 . Bda13g01246 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g518 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g519 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g520 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo18g00011 . . . . . . . . . . . . . . . Bhi09g02991 Tan01g3577 . . . . . . . . . . . . . . . .
Vvi4g521 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi09g02986 . . . . . . . . . . . . . . . . Cme07g00110
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 34973525 34976822 + Bda002813.1 Bda01g00767 767
1 34986157 34987851 - Bda002814.1 Bda01g00768 768
13 34855875 34856735 - Bda000053.1 Bda13g01245 1245
13 34899322 34900146 + Bda000054.1 Bda13g01246 1246
4 1028774 1030381 - XM_039029623.1 Bhi04g00042 42
4 1151633 1154843 + XM_039028105.1 Bhi04g00043 43
9 77420812 77435509 - XM_039041827.1 Bhi09g02986 2986
9 77634563 77640649 - XM_039042440.1 Bhi09g02991 2991
18 132508 138201 - BLOR08499 Blo18g00011 11
18 139181 140005 + BLOR08500 Blo18g00012 12
7 686726 701976 - MELO3C016973.2.1 Cme07g00110 110
7 710653 717940 - MELO3C016971.2.1 Cme07g00112 112
3 4568153 4572137 + PI0004850.3 Cmetu03g1431 1431
10 2321033 2324136 - Hsped.10g02210.1 Hepe10g0221 221
13 37189891 37192101 - Maker00034243 Lcy13g1825 1825
13 37213120 37216501 + Maker00034175 Lcy13g1826 1826
11 27351193 27354200 - Sed0019085.1 Sed11g1146 1146
1 100812118 100818225 + Tan0017079.2 Tan01g3577 3577
2 95846262 95849924 - Tan0013983.1 Tan02g2757 2757
2 95872285 95875729 + Tan0012645.1 Tan02g2758 2758
4 5399281 5403785 - Vvi4g512 Vvi4g512 512
4 5409057 5416309 + Vvi4g513 Vvi4g513 513
4 5421563 5424000 - Vvi4g514 Vvi4g514 514
4 5443111 5446547 + Vvi4g515 Vvi4g515 515
4 5458049 5460205 + Vvi4g516 Vvi4g516 516
4 5460207 5460736 - Vvi4g517 Vvi4g517 517
4 5460761 5461802 - Vvi4g518 Vvi4g518 518
4 5478407 5482629 + Vvi4g519 Vvi4g519 519
4 5486283 5510561 + Vvi4g520 Vvi4g520 520
4 5518758 5591661 + Vvi4g521 Vvi4g521 521
       

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