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
Vvi2g892 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g893 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g894 . . . . . . . Bma14g00116 . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0531 . . . . . . . Blo03g00846 . Bda07g00133 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g895 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo03g00847 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g896 . . . . . . . Bma14g00117 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo03g00849 . Bda07g00132 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g897 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo03g00852 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g898 . . . . . . . Bma14g00118 Cmo06g00604 Cmo16g01265 . . . . . Cpe14g01008 . . . . . . . . Cla10g00097 Cam10g0095 Cec10g0100 Cco10g0101 Clacu10g0096 Cmu10g0943 Cre10g0357 Cone8ag0533 Cone12ag0535 . . . . . Cme06g02406 . . Bda07g00131 . . . . . . . . Cma06g00598 Cma16g01222 Car06g00532 Car16g01149 . . . . . . . . . . . . . . . . . Csa03g00101 Chy06g02204 .
Vvi2g899 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0538 Cone12ag0536 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g900 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g901 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0537 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 1670854 1671961 + Bda025196.1 Bda07g00131 131
7 1674521 1676184 + Bda025197.1 Bda07g00132 132
7 1677497 1680030 + Bda025198.1 Bda07g00133 133
3 34222685 34223311 - BLOR12027 Blo03g00846 846
3 34224924 34226279 - BLOR12028 Blo03g00847 847
3 34272852 34274318 - BLOR12030 Blo03g00849 849
3 34306755 34308221 - BLOR12033 Blo03g00852 852
14 1518408 1518935 - Bma010520.1 Bma14g00116 116
14 1520374 1521840 - Bma010521.1 Bma14g00117 117
14 1533852 1534279 - Bma030644 Bma14g00118 118
10 2538501 2540084 - CaPI482276_10g000950.1 Cam10g0095 95
6 2990533 2991403 - Carg16284-RA Car06g00532 532
16 9796146 9797565 + Carg19492-RA Car16g01149 1149
10 941775 943354 - CcPI632755_10g001010.1 Cco10g0101 101
10 971198 972779 - CePI673135_10g001000.1 Cec10g0100 100
6 26251507 26253361 + Chy6G127320.1 Chy06g02204 2204
10 1261228 1262810 - ClG42_10g0009600.10 Clacu10g0096 96
10 983209 986440 - ClCG10G000940.2 Cla10g00097 97
6 2885724 2887459 - CmaCh06G005980.1 Cma06g00598 598
16 9233826 9235023 + CmaCh16G012220.1 Cma16g01222 1222
6 31222019 31224273 - MELO3C031937.2.1 Cme06g02406 2406
6 2976171 2977172 - CmoCh06G006040.1 Cmo06g00604 604
16 9015366 9016819 + CmoCh16G012650.1 Cmo16g01265 1265
10 1412736 1414318 - CmPI595203_10g009430.1 Cmu10g0943 943
8 3896268 3898212 - Conep08aG0055200.1 Cone8ag0531 531
8 3906587 3908290 + Conep08aG0055400.1 Cone8ag0533 533
8 3959203 3962870 + Conep08aG0055900.1 Cone8ag0538 538
12 3735130 3736733 + Conep12aG0055600.1 Cone12ag0535 535
12 3746526 3750250 - Conep12aG0055700.1 Cone12ag0536 536
12 3764208 3774302 + Conep12aG0055800.1 Cone12ag0537 537
14 8489729 8491145 + Cp4.1LG14g10020.1 Cpe14g01008 1008
10 2378776 2380359 - CrPI670011_10g003570.1 Cre10g0357 357
3 792311 794552 - CsaV3_3G001010.1 Csa03g00101 101
2 16675911 16678634 + Vvi2g892 Vvi2g892 892
2 16680943 16682001 - Vvi2g893 Vvi2g893 893
2 16688397 16693728 - Vvi2g894 Vvi2g894 894
2 16704243 16707373 - Vvi2g895 Vvi2g895 895
2 16737478 16740699 - Vvi2g896 Vvi2g896 896
2 16750684 16752537 - Vvi2g897 Vvi2g897 897
2 16785800 16791758 + Vvi2g898 Vvi2g898 898
2 16795323 16798580 + Vvi2g899 Vvi2g899 899
2 16801816 16819506 - Vvi2g900 Vvi2g900 900
2 16853296 16878858 + Vvi2g901 Vvi2g901 901
       

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