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
Vvi3g406 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g407 . . . . . . . . Cmo19g00619 . . . . . . Cpe04g00282 Cpe15g00485 Bhi05g01066 . . . . . . Cla02g00603 Cam02g0632 Cec02g0632 Cco02g0651 Clacu02g0636 Cmu02g0632 Cre02g0956 . . . . . . . Cme01g00053 . . . . . . . . . . . Cma11g01747 Cma19g00601 . Car19g00454 . . . . . . . . . . . . . . . . . . Chy01g00057 .
Vvi3g408 Blo02g00831 Blo15g00748 Bda06g01072 Bda08g00885 . . Bma05g00514 . Cmo19g00620 . . . . . . . Cpe15g00486 Bhi05g01063 . . . . . . Cla02g00602 Cam02g0631 Cec02g0631 Cco02g0650 Clacu02g0635 Cmu02g0631 Cre02g0955 . . Cone3ag1179 Cone10ag0987 . Csa07g00757 . Cme01g00052 . . . . . . . . . . . . Cma19g00602 . Car19g00455 Cpe14g00294 Cpe01g00439 . . . . . . . . . . . . . . . . Chy01g00056 .
Vvi3g409 . Blo15g00744 Bda06g01068 . Bpe07g00380 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1177 Cone10ag0984 . . . . . . . . . . . . . . . . . . . Cpe14g00297 . . . . . . . . . . . . . . . . . . .
Vvi3g410 . Blo15g00743 . . Bpe07g00382 . . Bma12g00454 . Cmo11g01361 . . . . . Cpe04g00279 Cpe15g00489 Bhi05g01060 . . . . . . Cla02g00599 Cam02g0628 Cec02g0628 Cco02g0647 Clacu02g0632 Cmu02g0628 Cre02g0952 Cone12ag1091 Cone8ag1134 . . . Csa07g00762 . Cme01g00047 . . . . . . . . . . . Cma11g01752 . . Car19g00458 . . . . . . . . . . . . . . . . . . Chy01g00052 .
Vvi3g411 . Blo15g00742 Bda06g01067 Bda08g00869 Bpe07g00383 . Bma05g00516 . Cmo19g00623 Cmo11g01360 . . . . . Cpe04g00278 Cpe15g00490 Bhi05g01059 . . . . . . Cla02g00598 Cam02g0627 Cec02g0627 Cco02g0646 Clacu02g0631 Cmu02g0627 Cre02g0951 Cone12ag1092 Cone8ag1135 . . . Csa07g00763 . Cme01g00046 . . . . . . . . . . . Cma11g01753 Cma19g00605 . Car19g00459 . . . . . . . . . . . . . . . . . . Chy01g00051 .
Vvi3g412 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g413 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g414 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g415 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 37823196 37826344 - Bda033715 Bda06g01067 1067
6 37998473 37998874 - Bda022830.1 Bda06g01068 1068
6 38053311 38058866 + Bda022835.1 Bda06g01072 1072
8 15224789 15235283 + Bda034028 Bda08g00869 869
8 15959542 15963332 - Bda029492.1 Bda08g00885 885
5 38221189 38227479 - XM_039032627.1 Bhi05g01059 1059
5 38271627 38276449 - XM_039031405.1 Bhi05g01060 1060
5 38443637 38449708 - XM_039032081.1 Bhi05g01063 1063
5 38452125 38456309 - XM_039031075.1 Bhi05g01066 1066
2 29957294 29966879 - BLOR10561 Blo02g00831 831
15 25054935 25058008 - BLOR07136 Blo15g00742 742
15 25143596 25146171 - BLOR07137 Blo15g00743 743
15 25226594 25229032 - BLOR07138 Blo15g00744 744
15 25386504 25402101 + BLOR07142 Blo15g00748 748
5 25445802 25449550 - Bma021457.2 Bma05g00514 514
5 25762218 25765823 + Bma021460.1 Bma05g00516 516
12 11694491 11697110 + Bma007465.2 Bma12g00454 454
7 3307890 3310261 + Bpe021195.1 Bpe07g00380 380
7 3390754 3393315 + Bpe021197.1 Bpe07g00382 382
7 3439856 3443245 + Bpe021198.1 Bpe07g00383 383
2 7194533 7199686 - CaPI482276_02g006270.1 Cam02g0627 627
2 7212391 7216412 - CaPI482276_02g006280.1 Cam02g0628 628
2 7292746 7298232 - CaPI482276_02g006310.1 Cam02g0631 631
2 7308851 7314116 - CaPI482276_02g006320.1 Cam02g0632 632
19 6259133 6261816 + Carg22070-RA Car19g00454 454
19 6263774 6270012 + Carg22069-RA Car19g00455 455
19 6287688 6291530 + Carg22066-RA Car19g00458 458
19 6294712 6299971 + Carg22065-RA Car19g00459 459
2 6384420 6389483 - CcPI632755_02g006460.1 Cco02g0646 646
2 6402125 6406315 - CcPI632755_02g006470.1 Cco02g0647 647
2 6487056 6492533 - CcPI632755_02g006500.1 Cco02g0650 650
2 6503036 6508304 - CcPI632755_02g006510.1 Cco02g0651 651
2 6277109 6282145 - CePI673135_02g006270.1 Cec02g0627 627
2 6294729 6298841 - CePI673135_02g006280.1 Cec02g0628 628
2 6376433 6381921 - CePI673135_02g006310.1 Cec02g0631 631
2 6393918 6398877 - CePI673135_02g006320.1 Cec02g0632 632
1 372644 376955 - Chy1G000510.1 Chy01g00051 51
1 381119 383584 - Chy1G000520.1 Chy01g00052 52
1 419901 425005 - Chy1G000560.1 Chy01g00056 56
1 427155 430294 - Chy1G000570.1 Chy01g00057 57
2 6202859 6207932 - ClG42_02g0063100.10 Clacu02g0631 631
2 6219695 6227225 - ClG42_02g0063200.10 Clacu02g0632 632
2 6303238 6308850 - ClG42_02g0063500.10 Clacu02g0635 635
2 6318254 6323544 - ClG42_02g0063600.10 Clacu02g0636 636
2 6490561 6496754 - ClCG02G005920.1 Cla02g00598 598
2 6511683 6515882 - ClCG02G005930.1 Cla02g00599 599
2 6592714 6598799 - ClCG02G005960.1 Cla02g00602 602
2 6607168 6614995 - ClCG02G005970.1 Cla02g00603 603
11 11591856 11595623 + CmaCh11G017470.1 Cma11g01747 1747
11 11648636 11651168 + CmaCh11G017520.1 Cma11g01752 1752
11 11674198 11680306 + CmaCh11G017530.1 Cma11g01753 1753
19 6595273 6598692 + CmaCh19G006010.1 Cma19g00601 601
19 6599899 6605384 + CmaCh19G006020.1 Cma19g00602 602
19 6623302 6635276 + CmaCh19G006050.1 Cma19g00605 605
1 366355 371286 - MELO3C018448.2.1 Cme01g00046 46
1 374836 377730 - MELO3C018449.2.1 Cme01g00047 47
1 410903 416478 - MELO3C018453.2.1 Cme01g00052 52
1 418396 422426 - MELO3C018454.2.1 Cme01g00053 53
11 9461604 9467868 - CmoCh11G013600.1 Cmo11g01360 1360
11 9491145 9493567 - CmoCh11G013610.1 Cmo11g01361 1361
19 6793342 6796662 + CmoCh19G006190.1 Cmo19g00619 619
19 6797917 6803816 + CmoCh19G006200.1 Cmo19g00620 620
19 6822808 6838390 + CmoCh19G006230.1 Cmo19g00623 623
2 6109690 6114768 - CmPI595203_02g006270.1 Cmu02g0627 627
2 6130004 6134060 - CmPI595203_02g006280.1 Cmu02g0628 628
2 6210092 6215708 - CmPI595203_02g006310.1 Cmu02g0631 631
2 6225114 6230411 - CmPI595203_02g006320.1 Cmu02g0632 632
3 30447805 30450806 - Conep03aG0168300.1 Cone3ag1177 1177
3 30459668 30463807 + Conep03aG0168600.1 Cone3ag1179 1179
8 9977254 9979415 + Conep08aG0116500.1 Cone8ag1134 1134
8 9980238 9983854 + Conep08aG0116600.1 Cone8ag1135 1135
10 6648995 6650855 - Conep10aG0101000.1 Cone10ag0984 984
10 6682381 6686028 + Conep10aG0101300.1 Cone10ag0987 987
12 8915820 8918484 + Conep12aG0112600.1 Cone12ag1091 1091
12 8918612 8923267 + Conep12aG0112700.1 Cone12ag1092 1092
1 2526392 2530972 - Cp4.1LG01g02170.1 Cpe01g00439 439
4 3444723 3451154 - Cp4.1LG04g08090.1 Cpe04g00278 278
4 3474111 3476373 - Cp4.1LG04g08030.1 Cpe04g00279 279
4 3543550 3547993 - Cp4.1LG04g08000.1 Cpe04g00282 282
14 1726751 1730515 - Cp4.1LG14g04240.1 Cpe14g00294 294
14 1740110 1744310 - Cp4.1LG14g04230.1 Cpe14g00297 297
15 5839491 5842958 + Cp4.1LG15g04790.1 Cpe15g00485 485
15 5844027 5850343 + Cp4.1LG15g04780.1 Cpe15g00486 486
15 5867774 5871791 + Cp4.1LG15g04810.1 Cpe15g00489 489
15 5877225 5880367 + Cp4.1LG15g04950.1 Cpe15g00490 490
2 6726245 6731311 - CrPI670011_02g009510.1 Cre02g0951 951
2 6742332 6748261 - CrPI670011_02g009520.1 Cre02g0952 952
2 6828406 6833898 - CrPI670011_02g009550.1 Cre02g0955 955
2 6844624 6849645 - CrPI670011_02g009560.1 Cre02g0956 956
7 5313624 5319190 + CsaV3_7G008560.1 Csa07g00757 757
7 5351643 5354773 + CsaV3_7G008610.1 Csa07g00762 762
7 5358371 5363655 + CsaV3_7G008620.1 Csa07g00763 763
3 3900265 3903031 + Vvi3g406 Vvi3g406 406
3 3907432 3915967 + Vvi3g407 Vvi3g407 407
3 3918249 3929199 + Vvi3g408 Vvi3g408 408
3 3930216 3943910 + Vvi3g409 Vvi3g409 409
3 3944461 3947232 + Vvi3g410 Vvi3g410 410
3 3947670 3979555 + Vvi3g411 Vvi3g411 411
3 3980931 3983684 + Vvi3g412 Vvi3g412 412
3 3984148 3989228 + Vvi3g413 Vvi3g413 413
3 3989797 3991292 + Vvi3g414 Vvi3g414 414
3 3991829 3999550 + Vvi3g415 Vvi3g415 415
       

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