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
Vvi3g516 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g517 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g518 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g519 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g520 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g521 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g522 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g523 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g524 . . . . . . . . Cmo19g00649 Cmo11g01332 . . . . Sed10g2064 Cpe04g00256 . Bhi05g01166 Tan02g0861 Cmetu01g0313 . Hepe02g0554 . . Cla02g00566 Cam02g0596 Cec02g0596 Cco02g0607 Clacu02g0591 Cmu02g0589 Cre02g0919 . . Cone3ag1124 Cone10ag1133 . Csa07g00812 . . Blo04g00497 . . . . . . . . . . Cma11g01778 Cma19g00634 Car11g01072 Car19g00483 . . . . . . . . . . . . . . . . Lsi11g01043 . Chy01g00017 .
Vvi3g525 . . . . . . . . . . . Cma20g00881 . Car20g00759 . . . . . . . . . . . . . . . . . . . . . Lsi10g00324 . Chy11g00422 . . . . . . . . . . . Cmo20g00889 . . . . . . Bhi10g02063 . . . Hepe08g1050 . . Cla09g01732 Cam09g1827 Cec09g1887 Cco09g1980 . . Cre01g0682 . Csa02g01213 . Cme11g00489
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 41682735 41684187 - XM_039031558.1 Bhi05g01166 1166
10 51602614 51619123 - XM_039045903.1 Bhi10g02063 2063
4 4137210 4138115 - BLOR13409 Blo04g00497 497
2 6791662 6792498 + CaPI482276_02g005960.1 Cam02g0596 596
9 32729195 32765594 + CaPI482276_09g018270.1 Cam09g1827 1827
11 8313420 8314247 + Carg20165-RA Car11g01072 1072
19 6449452 6450288 - Carg22041-RA Car19g00483 483
20 4454757 4475920 - Carg23624-RA Car20g00759 759
2 5957260 5958096 + CcPI632755_02g006070.1 Cco02g0607 607
9 33997589 33997825 + CcPI632755_09g019800.1 Cco09g1980 1980
2 5851558 5852394 + CePI673135_02g005960.1 Cec02g0596 596
9 35699464 35699700 + CePI673135_09g018870.1 Cec09g1887 1887
1 136645 137478 + Chy1G000170.1 Chy01g00017 17
11 4072286 4092293 - Chy11G190020.1 Chy11g00422 422
2 5765226 5770405 + ClG42_02g0059100.10 Clacu02g0591 591
2 6037899 6038735 + ClCG02G005530.1 Cla02g00566 566
9 34635424 34672084 + ClCG09G017690.2 Cla09g01732 1732
11 11899012 11899839 - CmaCh11G017780.1 Cma11g01778 1778
19 6786481 6787320 - CmaCh19G006340.1 Cma19g00634 634
20 4216463 4236759 - CmaCh20G008810.1 Cma20g00881 881
11 4813298 4833227 - MELO3C021931.2.1 Cme11g00489 489
1 177169 178005 + PI0020318.1 Cmetu01g0313 313
11 9197820 9198647 + CmoCh11G013320.1 Cmo11g01332 1332
19 7001979 7002869 - CmoCh19G006490.1 Cmo19g00649 649
20 4487120 4508358 - CmoCh20G008890.1 Cmo20g00889 889
2 5671971 5677146 + CmPI595203_02g005890.1 Cmu02g0589 589
3 29811487 29812284 - Conep03aG0162800.1 Cone3ag1124 1124
10 8149637 8150542 - Conep10aG0116500.1 Cone10ag1133 1133
4 3170132 3174932 + Cp4.1LG04g08380.1 Cpe04g00256 256
1 6314825 6349390 - CrPI670011_01g006820.1 Cre01g0682 682
2 6282021 6282857 + CrPI670011_02g009190.1 Cre02g0919 919
2 11920558 11947853 + CsaV3_2G014290.1 Csa02g01213 1213
7 5703331 5704167 - CsaV3_7G010100.1 Csa07g00812 812
2 5608193 5609385 + Hsped.02g05540.1 Hepe02g0554 554
8 10114516 10138756 - Hsped.08g10500.1 Hepe08g1050 1050
10 5191047 5214720 + Lsi10G003240.1 Lsi10g00324 324
11 17983365 17985520 - Lsi11G010430.1 Lsi11g01043 1043
10 37147641 37149099 - Sed0025947.1 Sed10g2064 2064
2 9567297 9569354 + Tan0015620.1 Tan02g0861 861
3 4990920 4991187 - Vvi3g516 Vvi3g516 516
3 4994798 5003359 - Vvi3g517 Vvi3g517 517
3 5003383 5004868 + Vvi3g518 Vvi3g518 518
3 5006519 5008252 + Vvi3g519 Vvi3g519 519
3 5017308 5018886 + Vvi3g520 Vvi3g520 520
3 5021075 5026440 + Vvi3g521 Vvi3g521 521
3 5037282 5039660 + Vvi3g522 Vvi3g522 522
3 5052306 5052789 + Vvi3g523 Vvi3g523 523
3 5052864 5063441 - Vvi3g524 Vvi3g524 524
3 5071223 5110910 + Vvi3g525 Vvi3g525 525
       

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