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
Vvi2g922 . . . . . . Bma07g01222 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda09g00464 Bpe08g01064 . . . . . . . . . . . Cpe06g00590 . . . . . . . . . . . . . . . . . .
Vvi2g923 . . . . . . Bma07g01221 . . . . . . . . . Cpe02g00590 . . . . . . . . . . . . . . . . Cone6ag0875 Cone9ag0881 . . . . . . . Bda09g00465 Bpe08g01063 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g924 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g925 Blo02g01168 . . . . . . . . Cmo16g00568 . . . . . Cpe14g00442 . . . . . . . . . . . . . . . . . Cone6ag0876 . . . . . . . . . . . . . . . . . Cma16g00522 . . Cpe01g00529 . . . . . . . . . . . . . . . . Csa04g00694 . .
Vvi2g926 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe01g00531 . . . . . . . . . . . . . . . . Csa04g00695 . .
Vvi2g927 . . . Bda08g00656 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g928 Blo02g01169 . . . . . . . . Cmo16g00566 . . . . . Cpe14g00440 . . . . . . . . . . . . . . . . . Cone6ag0878 Cone9ag0883 . . . . . . . . . . . . . . . . Cma16g00520 . . . . . . . . . . . . . . . . . . . Csa04g00698 . .
Vvi2g929 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g930 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g931 Blo02g01170 . . Bda08g00445 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe01g00532 . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 4557098 4558552 - Bda024895.2 Bda08g00445 445
8 6855311 6856663 + Bda029117.1 Bda08g00656 656
9 6053306 6053844 - Bda031054.1 Bda09g00464 464
9 6065706 6069267 - Bda031055.1 Bda09g00465 465
2 43359872 43362342 - BLOR10898 Blo02g01168 1168
2 43362689 43365222 + BLOR10899 Blo02g01169 1169
2 43366358 43367809 + BLOR10900 Blo02g01170 1170
7 47127657 47131737 + Bma026472.2 Bma07g01221 1221
7 47132669 47135925 + Bma026473.2 Bma07g01222 1222
8 12802020 12805615 + Bpe023188.1 Bpe08g01063 1063
8 12806334 12809579 + Bpe023189.3 Bpe08g01064 1064
16 2659970 2662866 - CmaCh16G005200.1 Cma16g00520 520
16 2667114 2668418 + CmaCh16G005220.1 Cma16g00522 522
16 2755340 2758113 - CmoCh16G005660.1 Cmo16g00566 566
16 2762979 2764283 + CmoCh16G005680.1 Cmo16g00568 568
6 4471860 4474517 - Conep06aG0090200.1 Cone6ag0875 875
6 4475114 4476379 - Conep06aG0090300.1 Cone6ag0876 876
6 4482171 4484024 + Conep06aG0090500.1 Cone6ag0878 878
9 4301807 4304619 - Conep09aG0090300.1 Cone9ag0881 881
9 4309948 4311597 + Conep09aG0090500.1 Cone9ag0883 883
1 3040921 3042826 - Cp4.1LG01g01340.1 Cpe01g00529 529
1 3044048 3059896 - Cp4.1LG01g01440.1 Cpe01g00531 531
1 3063974 3065437 + Cp4.1LG01g01420.1 Cpe01g00532 532
2 3531737 3536161 + Cp4.1LG02g02910.1 Cpe02g00590 590
6 3614432 3619483 - Cp4.1LG06g05920.1 Cpe06g00590 590
14 2753742 2756350 - Cp4.1LG14g02820.1 Cpe14g00440 440
14 2761556 2762860 + Cp4.1LG14g02710.1 Cpe14g00442 442
4 4708709 4710001 - CsaV3_4G006940.1 Csa04g00694 694
4 4712922 4714214 - CsaV3_4G006950.1 Csa04g00695 695
4 4725093 4728621 + CsaV3_4G006980.1 Csa04g00698 698
2 17382960 17393010 - Vvi2g922 Vvi2g922 922
2 17393636 17408885 - Vvi2g923 Vvi2g923 923
2 17415539 17416971 + Vvi2g924 Vvi2g924 924
2 17430557 17432766 - Vvi2g925 Vvi2g925 925
2 17439360 17448268 - Vvi2g926 Vvi2g926 926
2 17478429 17482898 - Vvi2g927 Vvi2g927 927
2 17515271 17517964 + Vvi2g928 Vvi2g928 928
2 17518995 17520457 - Vvi2g929 Vvi2g929 929
2 17566263 17566545 - Vvi2g930 Vvi2g930 930
2 17582980 17584459 - Vvi2g931 Vvi2g931 931
       

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