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
Vvi4g702 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g703 . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00833 Cam01g0858 Cec01g0858 Cco01g0883 Clacu01g0849 Cmu01g0816 Cre09g1692 . . . . . . . . . Blo18g00242 . Bda13g01817 Bpe14g00060 . . Bma02g00565 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g704 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g705 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe14g00059 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g706 . . . . . Bpe02g00195 . . . . . . . . . . . . . . . . . . Cla01g00838 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g707 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo18g00216 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g708 . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00840 Cam01g0865 Cec01g0865 Cco01g0892 Clacu01g0854 Cmu01g0823 Cre09g1687 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g709 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g710 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g711 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
13 42098715 42103164 + Bda000706.2 Bda13g01817 1817
18 2122330 2142763 - BLOR08704 Blo18g00216 216
18 2384779 2394133 + BLOR08730 Blo18g00242 242
2 11710197 11714749 + Bma015094.1 Bma02g00565 565
2 1365753 1369338 - Bpe008045.2 Bpe02g00195 195
14 952941 964885 + Bpe024956 Bpe14g00059 59
14 980623 985081 - Bpe006715.1 Bpe14g00060 60
1 9961742 9967181 + CaPI482276_01g008580.1 Cam01g0858 858
1 10038010 10039443 - CaPI482276_01g008650.1 Cam01g0865 865
1 9760676 9766203 + CcPI632755_01g008830.1 Cco01g0883 883
1 9839604 9840981 - CcPI632755_01g008920.1 Cco01g0892 892
1 9807327 9812820 + CePI673135_01g008580.1 Cec01g0858 858
1 9880472 9881921 - CePI673135_01g008650.1 Cec01g0865 865
1 9612018 9617517 + ClG42_01g0084900.10 Clacu01g0849 849
1 9678876 9685646 - ClG42_01g0085400.10 Clacu01g0854 854
1 10100519 10106389 + ClCG01G008480.1 Cla01g00833 833
1 10148080 10152164 - ClCG01G008530.1 Cla01g00838 838
1 10176907 10178337 - ClCG01G008550.1 Cla01g00840 840
1 9576620 9582122 + CmPI595203_01g008160.1 Cmu01g0816 816
1 9648931 9650361 - CmPI595203_01g008230.1 Cmu01g0823 823
9 34714983 34716451 + CrPI670011_09g016870.1 Cre09g1687 1687
9 34807257 34812852 - CrPI670011_09g016920.1 Cre09g1692 1692
4 10470252 10475343 - Vvi4g702 Vvi4g702 702
4 10519231 10523018 + Vvi4g703 Vvi4g703 703
4 10548707 10552163 - Vvi4g704 Vvi4g704 704
4 10608982 10628087 + Vvi4g705 Vvi4g705 705
4 10642873 10646839 - Vvi4g706 Vvi4g706 706
4 10683929 10694055 - Vvi4g707 Vvi4g707 707
4 10795506 10796386 - Vvi4g708 Vvi4g708 708
4 10818525 10828335 - Vvi4g709 Vvi4g709 709
4 10832626 10833305 - Vvi4g710 Vvi4g710 710
4 10836815 10849302 + Vvi4g711 Vvi4g711 711
       

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