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
Vvi16g824 . . . . . . . . . . . . . . . . . Bhi01g01561 Tan01g0806 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g825 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g826 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g827 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g828 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g829 . . . . . . . . . . . . . . . . . Bhi01g01547 . . . . Mch10g0565 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g830 . Blo15g00103 . . . Bpe07g01002 . . . . . . . . . . . . . . . . . . Cla01g00074 Cam01g0074 . Cco01g0075 Clacu01g0075 Cmu01g0076 Cre09g2433 . . . . . Csa05g00086 . . . . Bda06g00771 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi09g00056 . . .
Vvi16g831 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g832 . . . . . . . . . . Cma02g01168 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma12g01187 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g833 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 10708070 10716072 - Bda024092.2 Bda06g00771 771
1 31685529 31688681 + XM_039022171.1 Bhi01g01547 1547
1 32083874 32096206 - XM_039023072.1 Bhi01g01561 1561
15 861941 870660 + BLOR06497 Blo15g00103 103
12 44708235 44716232 - Bma008546.2 Bma12g01187 1187
7 15704453 15713691 - Bpe021846.3 Bpe07g01002 1002
1 1039120 1047386 + CaPI482276_01g000740.1 Cam01g0074 74
1 553556 561979 + CcPI632755_01g000750.1 Cco01g0075 75
1 648173 656459 + ClG42_01g0007500.10 Clacu01g0075 75
1 610062 619703 + ClCG01G000730.1 Cla01g00074 74
2 6884428 6887382 + CmaCh02G011680.1 Cma02g01168 1168
1 592961 601254 + CmPI595203_01g000760.1 Cmu01g0076 76
9 43718328 43726649 - CrPI670011_09g024330.1 Cre09g2433 2433
5 420728 429410 + CsaV3_5G000860.1 Csa05g00086 86
9 464476 473778 + Lsi09G000560.1 Lsi09g00056 56
10 3754147 3756789 + MC10g0461 Mch10g0565 565
1 7807230 7808948 - Tan0008948.1 Tan01g0806 806
16 18986473 18988399 - Vvi16g824 Vvi16g824 824
16 19005965 19006693 - Vvi16g825 Vvi16g825 825
16 19015881 19017151 + Vvi16g826 Vvi16g826 826
16 19045738 19045972 - Vvi16g827 Vvi16g827 827
16 19047646 19073952 - Vvi16g828 Vvi16g828 828
16 19081474 19085375 - Vvi16g829 Vvi16g829 829
16 19092047 19094299 - Vvi16g830 Vvi16g830 830
16 19098148 19102682 - Vvi16g831 Vvi16g831 831
16 19109675 19118799 - Vvi16g832 Vvi16g832 832
16 19119205 19119992 - Vvi16g833 Vvi16g833 833
       

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