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
Vvi17g926 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g927 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g928 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g929 . . . . . . . . . Cmo18g00080 . . . . . . . . . . . . . . . . . . . . . . . . . . Csa01g00756 . . . . . . . . . . . . . . Cma18g00104 . . Cpe09g01087 . . . . . . . . . . . . . . . . . . .
Vvi17g930 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00281 . . . . . . . . . . . . . . . . . . . . Bhi08g01361 . . Lac10g0334 . . . . . . . . . . . . . .
Vvi17g931 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00280 . . . . . . . . . . . Sed08g2588 . . . . . . . . Bhi08g01360 Tan05g2129 Cmetu12g1923 Lac10g0333 . . . . . . . . . . . . . .
Vvi17g932 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g933 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00279 . . . . . . . . . . . . . . . . . . . . Bhi08g01359 . . Lac10g0332 . . . . . . . . . . . . . .
Vvi17g934 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g935 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 40829563 40830514 - XM_039039471.1 Bhi08g01359 1359
8 40846706 40847657 + XM_039039468.1 Bhi08g01360 1360
8 40851755 40852454 + XM_039037728.1 Bhi08g01361 1361
18 495407 497314 + CmaCh18G001040.1 Cma18g00104 104
12 1865106 1865721 - PI0022861.1 Cmetu12g1923 1923
18 540939 546540 + CmoCh18G000800.1 Cmo18g00080 80
9 9407768 9411250 - Cp4.1LG09g10910.1 Cpe09g01087 1087
1 4807125 4809674 + CsaV3_1G007560.1 Csa01g00756 756
10 2607023 2607637 - Lag0024377.1 Lac10g0332 332
10 2611553 2612146 - Lag0024378.1 Lac10g0333 333
10 2614280 2614897 - Lag0024379.1 Lac10g0334 334
2 2360483 2361100 - Lsi02G002790.1 Lsi02g00279 279
2 2365341 2365970 - Lsi02G002800.1 Lsi02g00280 280
2 2370976 2394905 - Lsi02G002810.1 Lsi02g00281 281
8 38290041 38290836 - Sed0020580.1 Sed08g2588 2588
5 71982101 72001926 + Tan0014729.1 Tan05g2129 2129
17 13346702 13350089 - Vvi17g926 Vvi17g926 926
17 13360169 13384785 - Vvi17g927 Vvi17g927 927
17 13442115 13442208 - Vvi17g928 Vvi17g928 928
17 13468911 13471520 + Vvi17g929 Vvi17g929 929
17 13472782 13473557 - Vvi17g930 Vvi17g930 930
17 13575608 13588502 + Vvi17g931 Vvi17g931 931
17 13601783 13602643 - Vvi17g932 Vvi17g932 932
17 13671503 13671863 + Vvi17g933 Vvi17g933 933
17 13677842 13680844 + Vvi17g934 Vvi17g934 934
17 13685061 13685812 - Vvi17g935 Vvi17g935 935
       

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