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
Vvi1g951 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g952 . . . . . . . Bma15g00144 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo06g00918 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g953 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g954 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g955 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo15g00895 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g956 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g957 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag0562 Cone9ag0569 . . . . . . . . . . . . . . . . . . . . Cpe07g00643 . . . . . . . . . . . . . . . . . .
Vvi1g958 . Blo16g01104 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0934 Cone19ag0927 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g959 . . . Bda11g01202 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01202 . Bpe02g02329 . Bma06g00708 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g960 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0935 . . . . . . . . . . . . . . . . . . . . . . . Cpe07g00146 . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 12345453 12347649 - Bda007702.1 Bda11g01202 1202
6 32438208 32441776 + BLOR17501 Blo06g00918 918
16 39531690 39536147 + BLOR21891 Blo16g01104 1104
6 37376180 37378415 + Bma023689.1 Bma06g00708 708
15 1501899 1505402 - Bma013123.1 Bma15g00144 144
2 23897801 23899260 - Bpe010145.1 Bpe02g02329 2329
15 4523668 4528225 + CmoCh15G008950.1 Cmo15g00895 895
6 2756537 2758393 - Conep06aG0057500.1 Cone6ag0562 562
9 2683978 2686331 - Conep09aG0057900.1 Cone9ag0569 569
13 8097746 8107627 + Conep13aG0096200.1 Cone13ag0934 934
13 8108005 8112401 + Conep13aG0096300.1 Cone13ag0935 935
19 7148842 7153570 + Conep19aG0095500.1 Cone19ag0927 927
7 811137 816572 - Cp4.1LG07g01490.1 Cpe07g00146 146
7 4590253 4591717 + Cp4.1LG07g06520.1 Cpe07g00643 643
1 13805284 13806679 + Vvi1g951 Vvi1g951 951
1 13829610 13833472 + Vvi1g952 Vvi1g952 952
1 13836988 13837108 + Vvi1g953 Vvi1g953 953
1 13887153 13887515 + Vvi1g954 Vvi1g954 954
1 13887516 13910631 + Vvi1g955 Vvi1g955 955
1 13917483 13917951 + Vvi1g956 Vvi1g956 956
1 13920147 13926541 + Vvi1g957 Vvi1g957 957
1 13949444 13973750 + Vvi1g958 Vvi1g958 958
1 13976630 13980385 - Vvi1g959 Vvi1g959 959
1 13988501 14007397 + Vvi1g960 Vvi1g960 960
       

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