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
Vvi18g1790 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1791 Blo01g01700 . . . Bpe02g00244 . . Bma01g02476 . . Cma01g00891 . Car01g00813 . . . . . . . . . . . Cla08g00197 . Cec08g0338 Cco08g0268 . Cmu08g0183 Cre08g0172 . . . . . . . Cme09g00134 . . Bda11g00904 . . . . . Sed10g1662 Cmo01g00936 . . . . . . Cpe02g00974 Bhi06g00095 Tan10g1820 Cmetu09g1691 . . . . . . . . . . . Lsi08g00192 . . .
Vvi18g1792 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1793 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1794 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1795 . Blo12g00803 . Bda03g00369 . Bpe04g00332 Bma04g00347 . . . Cma01g00893 . Car01g00814 . . . . . . . . . . . Cla08g00207 . . . . . Cre08g0181 . . . . . . . . . . . . . . . . . Cmo01g00937 . . . . . . Cpe02g00973 . . . . . . . . . . . . . . Lsi08g00193 . . .
Vvi18g1796 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g2 . . . . . . . . . . Cma01g01278 . Car01g01093 Car09g00605 Sed04g2513 Cpe06g00537 . Bhi09g03588 Tan01g4237 Cmetu07g0669 . Hepe01g1479 Mch11g0969 . . . . . . . . . . . . . . . . . . . . . . . . . Cmo01g01331 Cmo09g00669 . . . . . . . . . . . . . . . . . . . . . Csa04g00829 . .
Vvi19g3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 3104841 3105137 + Bda016332.1 Bda03g00369 369
11 8850235 8851286 + Bda005658.1 Bda11g00904 904
6 2684034 2690239 + XM_039035096.1 Bhi06g00095 95
9 89703116 89704252 + XM_039043388.1 Bhi09g03588 3588
1 56758143 56761594 - BLOR01700 Blo01g01700 1700
12 26419912 26421455 - BLOR04822 Blo12g00803 803
1 82491508 82493748 - Bma003350.1 Bma01g02476 2476
4 2818265 2820127 + Bma018806.1 Bma04g00347 347
2 1670558 1673133 + Bpe008088.1 Bpe02g00244 244
4 2115713 2117574 + Bpe015028.1 Bpe04g00332 332
1 5495686 5500772 - Carg27119-RA Car01g00813 813
1 5502771 5508236 + Carg27118-RA Car01g00814 814
1 10229290 10230145 + Carg14758-RA Car01g01093 1093
9 3431988 3434850 - Carg03088-RA Car09g00605 605
8 4809834 4819843 - CcPI632755_08g002680.1 Cco08g0268 268
8 8174899 8185838 - CePI673135_08g003380.1 Cec08g0338 338
8 4011729 4025515 - ClCG08G001950.1 Cla08g00197 197
8 4185622 4190564 + ClCG08G002000.1 Cla08g00207 207
1 5139715 5145984 - CmaCh01G008910.1 Cma01g00891 891
1 5151235 5152699 + CmaCh01G008930.1 Cma01g00893 893
1 9200080 9201280 + CmaCh01G012780.1 Cma01g01278 1278
9 983156 986306 - MELO3C022111.2.1 Cme09g00134 134
7 21064862 21066219 - PI0020010.1 Cmetu07g0669 669
9 20834547 20838265 + PI0006526.1 Cmetu09g1691 1691
1 5419814 5425029 - CmoCh01G009360.1 Cmo01g00936 936
1 5426737 5432200 + CmoCh01G009370.1 Cmo01g00937 937
1 10568061 10578870 + CmoCh01G013310.1 Cmo01g01331 1331
9 3340757 3341386 + CmoCh09G006690.1 Cmo09g00669 669
8 3943528 3958824 - CmPI595203_08g001830.1 Cmu08g0183 183
2 8731069 8735408 - Cp4.1LG02g09790.1 Cpe02g00973 973
2 8741664 8746601 + Cp4.1LG02g09700.1 Cpe02g00974 974
6 3205273 3208336 - Cp4.1LG06g05380.1 Cpe06g00537 537
8 3905824 3908956 - CrPI670011_08g001720.1 Cre08g0172 172
8 4089095 4093400 + CrPI670011_08g001810.1 Cre08g0181 181
4 5813261 5815722 + CsaV3_4G008290.1 Csa04g00829 829
1 80084014 80085044 + Hsped.01g14790.1 Hepe01g1479 1479
8 4045145 4047279 - Lsi08G001920.1 Lsi08g00192 192
8 4071702 4077706 - Lsi08G001930.1 Lsi08g00193 193
11 6646195 6647544 - MC11g_new0172 Mch11g0969 969
4 38073953 38074885 + Sed0010429.2 Sed04g2513 2513
10 33268492 33279047 - Sed0003038.1 Sed10g1662 1662
1 107186096 107187286 - Tan0010115.1 Tan01g4237 4237
10 56768160 56784622 + Tan0012304.1 Tan10g1820 1820
18 29243609 29244818 - Vvi18g1790 Vvi18g1790 1790
18 29249151 29263470 - Vvi18g1791 Vvi18g1791 1791
18 29276687 29278041 - Vvi18g1792 Vvi18g1792 1792
18 29278844 29285761 - Vvi18g1793 Vvi18g1793 1793
18 29309059 29310270 - Vvi18g1794 Vvi18g1794 1794
18 29311048 29315400 - Vvi18g1795 Vvi18g1795 1795
18 29341757 29342811 + Vvi18g1796 Vvi18g1796 1796
19 1175 19554 + Vvi19g1 Vvi19g1 1
19 20818 28405 + Vvi19g2 Vvi19g2 2
19 30920 35512 + Vvi19g3 Vvi19g3 3
       

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