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
Vvi4g672 . Blo12g00965 . Bda03g00205 . . Bma04g00155 Bma01g02264 . . Cma01g01575 . . . . . . . . . . . . . . . . . . . . Cone4ag1861 Cone7ag1766 . . . Csa03g04408 Chy04g00294 . . . . . . Bpe04g00173 . . Sed08g0447 . . Cma09g00530 . . . . . Bhi09g02375 Tan01g3739 Cmetu04g1319 . Hepe01g2092 Mch11g0630 . . . . . . . . . . . Cme04g00334
Vvi4g673 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g674 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g675 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g676 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g677 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda01g01334 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g678 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag0938 Cone20ag0281 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g679 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g680 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g681 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone19ag1126 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 49023935 49024445 + Bda003570.1 Bda01g01334 1334
3 1615820 1616772 - Bda016149.1 Bda03g00205 205
9 64793315 64795437 - XM_039043961.1 Bhi09g02375 2375
12 27764937 27766080 - BLOR04984 Blo12g00965 965
1 79806697 79807886 + Bma003120.1 Bma01g02264 2264
4 1345202 1346380 + Bma018600.6 Bma04g00155 155
4 1125445 1126620 + Bpe014893.1 Bpe04g00173 173
4 2650264 2651870 + Chy4G070120.1 Chy04g00294 294
1 10882048 10884101 - CmaCh01G015750.1 Cma01g01575 1575
9 2358729 2360437 - CmaCh09G005300.1 Cma09g00530 530
4 2660995 2663678 + MELO3C003622.2.1 Cme04g00334 334
4 30705278 30707548 - PI0026425.1 Cmetu04g1319 1319
4 13342698 13344413 - Conep04aG0192000.1 Cone4ag1861 1861
7 11645922 11647867 - Conep07aG0181900.1 Cone7ag1766 1766
17 7335319 7336872 - Conep17aG0096500.1 Cone17ag0938 938
19 8076803 8078475 + Conep19aG0116000.1 Cone19ag1126 1126
20 1257309 1258399 - Conep20aG0029400.1 Cone20ag0281 281
3 38433423 38436416 - CsaV3_3G047140.1 Csa03g04408 4408
1 85524699 85526613 - Hsped.01g20920.1 Hepe01g2092 2092
11 4053570 4055956 - MC11g0524 Mch11g0630 630
8 2773120 2775752 - Sed0003080.1 Sed08g0447 447
1 102159890 102162088 - Tan0003663.1 Tan01g3739 3739
4 9363168 9365026 - Vvi4g672 Vvi4g672 672
4 9378967 9386209 - Vvi4g673 Vvi4g673 673
4 9387926 9388566 + Vvi4g674 Vvi4g674 674
4 9388595 9395789 + Vvi4g675 Vvi4g675 675
4 9395798 9397432 - Vvi4g676 Vvi4g676 676
4 9399943 9400803 - Vvi4g677 Vvi4g677 677
4 9409804 9411286 - Vvi4g678 Vvi4g678 678
4 9417304 9419688 + Vvi4g679 Vvi4g679 679
4 9420386 9426072 - Vvi4g680 Vvi4g680 680
4 9458117 9459081 + Vvi4g681 Vvi4g681 681
       

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