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
Vvi3g416 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g417 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g418 . . . . . Bpe12g00058 . . Cmo19g00624 Cmo11g01359 . . . . Sed04g1638 . . Bhi05g01124 Tan02g0906 Cmetu06g0968 . Hepe02g0583 . . Cla02g00597 Cam02g0626 Cec02g0626 Cco02g0641 Clacu02g0630 Cmu02g0626 Cre02g0950 Cone6ag1392 . . . . Csa07g00764 . . Blo04g00488 Blo13g00573 . Bda14g00518 Bpe15g00897 . Bma03g00518 Bma08g00799 . . . Cma11g01754 Cma19g00606 . Car19g00460 . . . . . . . . . . . . . . . . . . Chy01g00050 .
Vvi3g419 Blo02g00833 Blo15g00741 Bda06g01066 Bda08g00855 Bpe07g00384 . Bma05g00517 Bma12g00456 . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1094 Cone8ag1136 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g420 . . Bda06g01065 . Bpe07g00385 . . Bma12g00457 . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1095 Cone8ag1137 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g421 . . . . . . . . Cmo19g00625 . . . . . Sed05g2434 . Cpe15g00491 Bhi05g01125 Tan02g0904 Cmetu01g2340 . Hepe02g0582 . . Cla02g00596 Cam02g0625 Cec02g0625 Cco02g0640 Clacu02g0629 Cmu02g0625 Cre02g0949 Cone12ag1096 . . . . Csa07g00765 . Cme01g00044 Blo04g00489 . . Bda14g00519 . . Bma03g00519 . . . . . Cma19g00607 . Car19g00461 . . . . . . . . . . . . . . . . . . . .
Vvi3g422 . Blo15g00740 Bda06g01063 . Bpe07g00387 . . Bma12g00458 . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1097 . . . . . . . . . . . . . . . . . . . . . . . Cpe01g00441 . . . . . . . . . . . . . . . . . .
Vvi3g423 . . . . . . . . Cmo19g00627 Cmo11g01358 . . . . Sed05g3402 Cpe04g00276 Cpe15g00493 Bhi05g01126 Tan02g0902 Cmetu11g1775 . Hepe02g0581 . . Cla02g00595 Cam02g0624 Cec02g0624 Cco02g0639 Clacu02g0628 Cmu02g0624 Cre02g0948 Cone11ag0284 . . . . Csa07g00766 . Cme01g00043 . . . . . . . . . Cmo02g00564 . . Cma19g00609 Car11g01088 . . . . . . . . . . . . . . . . . . . Chy01g00049 Cme11g00303
Vvi3g424 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g425 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag1140 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 37761422 37762645 - Bda033713 Bda06g01063 1063
6 37815373 37817552 + Bda033714 Bda06g01065 1065
6 37818958 37821247 + Bda022827.1 Bda06g01066 1066
8 14387251 14388729 - Bda029429.1 Bda08g00855 855
14 3751311 3752090 + Bda027263.1 Bda14g00518 518
14 3753467 3755313 + Bda027264.1 Bda14g00519 519
5 40565766 40566839 + XM_039032475.1 Bhi05g01124 1124
5 40599184 40603352 + XM_039030880.1 Bhi05g01125 1125
5 40624523 40625409 + XM_039032253.1 Bhi05g01126 1126
2 30198768 30201321 - BLOR10563 Blo02g00833 833
4 4042314 4043081 + BLOR13400 Blo04g00488 488
4 4045386 4047636 + BLOR13401 Blo04g00489 489
13 27859579 27860196 - BLOR19625 Blo13g00573 573
15 25000620 25001990 - BLOR07134 Blo15g00740 740
15 25050900 25053198 + BLOR07135 Blo15g00741 741
3 4016799 4017557 + Bma016800.1 Bma03g00518 518
3 4022371 4024211 + Bma016801.1 Bma03g00519 519
5 25767572 25769707 - Bma021461.1 Bma05g00517 517
8 45611279 45611977 - Bma028187.1 Bma08g00799 799
12 11769934 11772239 - Bma007467.1 Bma12g00456 456
12 11775008 11777206 - Bma007468.1 Bma12g00457 457
12 11808912 11810116 + Bma030501 Bma12g00458 458
7 3444841 3447163 - Bpe021199.1 Bpe07g00384 384
7 3448575 3450781 - Bpe021200.1 Bpe07g00385 385
7 3460199 3461690 + Bpe021202.1 Bpe07g00387 387
12 436846 437583 + Bpe005297.1 Bpe12g00058 58
15 18866172 18866927 - Bpe001818.1 Bpe15g00897 897
2 7165827 7166384 - CaPI482276_02g006240.1 Cam02g0624 624
2 7171986 7175601 - CaPI482276_02g006250.1 Cam02g0625 625
2 7181809 7182507 - CaPI482276_02g006260.1 Cam02g0626 626
11 8504415 8510548 - Carg26414-RA Car11g01088 1088
19 6303101 6303778 + Carg22064-RA Car19g00460 460
19 6304986 6309140 + Carg22063-RA Car19g00461 461
2 6348925 6349482 - CcPI632755_02g006390.1 Cco02g0639 639
2 6354961 6358524 - CcPI632755_02g006400.1 Cco02g0640 640
2 6362607 6363308 - CcPI632755_02g006410.1 Cco02g0641 641
2 6242352 6242909 - CePI673135_02g006240.1 Cec02g0624 624
2 6248136 6252089 - CePI673135_02g006250.1 Cec02g0625 625
2 6256031 6256729 - CePI673135_02g006260.1 Cec02g0626 626
1 355459 361770 - Chy1G000490.1 Chy01g00049 49
1 366046 366837 - Chy1G000500.1 Chy01g00050 50
2 6168285 6168842 - ClG42_02g0062800.10 Clacu02g0628 628
2 6174035 6177961 - ClG42_02g0062900.10 Clacu02g0629 629
2 6183549 6184250 - ClG42_02g0063000.10 Clacu02g0630 630
2 6456275 6456832 - ClCG02G005880.1 Cla02g00595 595
2 6462337 6465975 - ClCG02G005890.2 Cla02g00596 596
2 6471824 6472525 - ClCG02G005910.1 Cla02g00597 597
11 11688280 11689047 + CmaCh11G017540.1 Cma11g01754 1754
19 6638726 6639424 + CmaCh19G006060.1 Cma19g00606 606
19 6641186 6645401 + CmaCh19G006070.1 Cma19g00607 607
19 6647034 6648209 + CmaCh19G006090.1 Cma19g00609 609
1 349055 349916 - MELO3C018445.2.1 Cme01g00043 43
1 352181 356614 - MELO3C018446.2.1 Cme01g00044 44
11 3252806 3253537 + MELO3C020884.2.1 Cme11g00303 303
1 28926265 28932333 - PI0024412.1 Cmetu01g2340 2340
6 9853247 9854080 + PI0018483.1 Cmetu06g0968 968
11 29338411 29339981 + PI0021588.1 Cmetu11g1775 1775
2 3257479 3258595 - CmoCh02G005640.1 Cmo02g00564 564
11 9443657 9444211 - CmoCh11G013580.1 Cmo11g01358 1358
11 9453240 9454022 - CmoCh11G013590.1 Cmo11g01359 1359
19 6842440 6843108 + CmoCh19G006240.1 Cmo19g00624 624
19 6844134 6848314 + CmoCh19G006250.1 Cmo19g00625 625
19 6850031 6851172 + CmoCh19G006270.1 Cmo19g00627 627
2 6075126 6075683 - CmPI595203_02g006240.1 Cmu02g0624 624
2 6080883 6084833 - CmPI595203_02g006250.1 Cmu02g0625 625
2 6090393 6091094 - CmPI595203_02g006260.1 Cmu02g0626 626
6 11213338 11213901 - Conep06aG0145100.1 Cone6ag1392 1392
8 9986988 9990244 - Conep08aG0116700.1 Cone8ag1136 1136
8 9990712 9992816 - Conep08aG0116800.1 Cone8ag1137 1137
8 9996456 9997233 - Conep08aG0117200.1 Cone8ag1140 1140
11 1380156 1382469 - Conep11aG0029100.1 Cone11ag0284 284
12 8931326 8934515 - Conep12aG0112900.1 Cone12ag1094 1094
12 8935116 8935749 - Conep12aG0113000.1 Cone12ag1095 1095
12 8937190 8939561 + Conep12aG0113200.1 Cone12ag1096 1096
12 8940100 8941431 + Conep12aG0113300.1 Cone12ag1097 1097
1 2542115 2546004 + Cp4.1LG01g02250.1 Cpe01g00441 441
4 3425690 3426244 - Cp4.1LG04g08070.1 Cpe04g00276 276
15 5885705 5890024 + Cp4.1LG15g04940.1 Cpe15g00491 491
15 5891517 5892071 + Cp4.1LG15g04910.1 Cpe15g00493 493
2 6698155 6698712 - CrPI670011_02g009480.1 Cre02g0948 948
2 6704026 6707918 - CrPI670011_02g009490.1 Cre02g0949 949
2 6713247 6713948 - CrPI670011_02g009500.1 Cre02g0950 950
7 5367835 5369430 + CsaV3_7G008630.1 Csa07g00764 764
7 5372466 5376536 + CsaV3_7G008640.1 Csa07g00765 765
7 5377697 5378591 + CsaV3_7G008650.1 Csa07g00766 766
2 5897400 5898171 - Hsped.02g05810.1 Hepe02g0581 581
2 5900123 5903535 - Hsped.02g05820.1 Hepe02g0582 582
2 5908045 5909151 - Hsped.02g05830.1 Hepe02g0583 583
4 31088982 31089949 + Sed0018799.1 Sed04g1638 1638
5 36644941 36651500 + Sed0023207.2 Sed05g2434 2434
5 43135205 43136344 + Sed0008130.1 Sed05g3402 3402
2 10276838 10278097 - Tan0001816.1 Tan02g0902 902
2 10286240 10290212 - Tan0002694.2 Tan02g0904 904
2 10300919 10302667 - Tan0014474.1 Tan02g0906 906
3 4000149 4010034 + Vvi3g416 Vvi3g416 416
3 4012516 4015118 + Vvi3g417 Vvi3g417 417
3 4015609 4023622 + Vvi3g418 Vvi3g418 418
3 4027213 4030627 + Vvi3g419 Vvi3g419 419
3 4031292 4040609 - Vvi3g420 Vvi3g420 420
3 4041064 4046927 + Vvi3g421 Vvi3g421 421
3 4047421 4053894 + Vvi3g422 Vvi3g422 422
3 4054283 4059659 + Vvi3g423 Vvi3g423 423
3 4060721 4066802 - Vvi3g424 Vvi3g424 424
3 4067223 4070468 - Vvi3g425 Vvi3g425 425
       

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