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
Vvi19g1194 Blo04g00450 Blo13g00612 . . . . Bma08g00829 . . . . . . . . . . Bhi05g01975 Tan02g0011 . . . . . . . . . . . . . . . . . Csa07g01227 . . . . . . Bpe15g00932 . Bma03g00483 . . . . . . . . Cpe15g00914 . . . . . . . . . . . . . . . . . Chy01g00832 Cme01g01486
Vvi19g1195 Blo04g00448 . . . . . . . . . . . . . . . . . . . . . . . Cla02g01848 Cam02g1954 Cec02g1982 Cco02g2020 Clacu02g1936 Cmu02g1885 Cre02g2196 . . . . . . . Cme11g01668 . . . . Bpe15g00933 . . . Sed05g3326 . . . . . . . Cpe05g01019 Bhi10g00909 Tan05g0565 Cmetu11g0290 . Hepe08g0666 . . . . . . . . . . Csa06g01132 Chy11g01062 .
Vvi19g1196 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa07g01233 . . . . . . . . . . . . . . . . . Cpe15g00917 . . . . . . . . . . . . . . . . . . .
Vvi19g1197 Blo04g00447 Blo13g00613 . . . . Bma08g00830 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe15g00934 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy01g00828 Cme01g01479
Vvi19g1198 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1199 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1200 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 60868876 60879888 - XM_039032826.1 Bhi05g01975 1975
10 18584928 18593089 - XM_039044427.1 Bhi10g00909 909
4 3690617 3698011 + BLOR13359 Blo04g00447 447
4 3699656 3704867 - BLOR13360 Blo04g00448 448
4 3710985 3715904 - BLOR13362 Blo04g00450 450
13 28536186 28540126 + BLOR19664 Blo13g00612 612
13 28547654 28549522 - BLOR19665 Blo13g00613 613
3 3752240 3770301 - Bma016767.1 Bma03g00483 483
8 46131513 46136871 + Bma028225.2 Bma08g00829 829
8 46144396 46146522 - Bma028226.1 Bma08g00830 830
15 19089342 19105323 + Bpe024593 Bpe15g00932 932
15 19106190 19111071 + Bpe001855.1 Bpe15g00933 933
15 19111582 19112964 - Bpe001856.1 Bpe15g00934 934
2 32661758 32669416 + CaPI482276_02g019540.1 Cam02g1954 1954
2 33173019 33180659 + CcPI632755_02g020200.1 Cco02g2020 2020
2 37673171 37680827 + CePI673135_02g019820.1 Cec02g1982 1982
1 6991070 6995410 - Chy1G008280.1 Chy01g00828 828
1 7105374 7116169 - Chy1G008320.1 Chy01g00832 832
11 15137070 15144446 + Chy11G196420.1 Chy11g01062 1062
2 32913602 32921243 + ClG42_02g0193600.10 Clacu02g1936 1936
2 33629903 33637777 + ClCG02G018890.1 Cla02g01848 1848
1 19241451 19243312 - MELO3C012573.2.1 Cme01g01479 1479
1 19397689 19414257 - MELO3C012579.2.1 Cme01g01486 1486
11 24645008 24652643 + MELO3C019602.2.1 Cme11g01668 1668
11 8183146 8198256 - PI0005033.2 Cmetu11g0290 290
2 32775983 32785504 + CmPI595203_02g018850.1 Cmu02g1885 1885
5 6646097 6652730 - Cp4.1LG05g10170.1 Cpe05g01019 1019
15 8766417 8775052 + Cp4.1LG15g09110.1 Cpe15g00914 914
15 8797513 8804468 + Cp4.1LG15g09100.1 Cpe15g00917 917
2 35628427 35637910 + CrPI670011_02g021960.1 Cre02g2196 2196
6 9400380 9408214 - CsaV3_6G013300.1 Csa06g01132 1132
7 12133310 12152944 + CsaV3_7G023160.1 Csa07g01227 1227
7 12209869 12218518 + CsaV3_7G023220.1 Csa07g01233 1233
8 5961984 5971630 + Hsped.08g06660.1 Hepe08g0666 666
5 42594114 42600237 + Sed0019803.1 Sed05g3326 3326
2 379620 418172 - Tan0015051.3 Tan02g0011 11
5 4005822 4018875 - Tan0022322.1 Tan05g0565 565
19 23853479 23873991 + Vvi19g1194 Vvi19g1194 1194
19 23874563 23889349 + Vvi19g1195 Vvi19g1195 1195
19 23921593 23931529 + Vvi19g1196 Vvi19g1196 1196
19 23954167 23955962 - Vvi19g1197 Vvi19g1197 1197
19 23985951 23997831 + Vvi19g1198 Vvi19g1198 1198
19 23998363 23999284 + Vvi19g1199 Vvi19g1199 1199
19 24013270 24013696 + Vvi19g1200 Vvi19g1200 1200
       

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