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
Vvi3g646 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g647 . . . . . . . . Cmo19g00586 . . . . . . . Cpe15g00458 . . . . . . . Cla02g00651 Cam02g0684 Cec02g0698 Cco02g0718 Clacu02g0692 Cmu02g0687 Cre02g1006 . Cone8ag1100 . . Lsi03g00548 Csa07g00711 . . . . . . . . Bma03g01373 . . . . . Cma19g00572 . Car19g00431 . . . . . . . . . . . . . . . . . . Chy01g00104 .
Vvi3g648 . . . . . Bpe12g00300 . . Cmo19g00585 . . . . . . . Cpe15g00457 . . . . . . . Cla02g00654 Cam02g0688 Cec02g0700 Cco02g0721 Clacu02g0694 Cmu02g0690 Cre02g1007 . Cone8ag1099 . . Lsi03g00549 Csa07g00710 . Cme01g00096 . . Bda15g00841 . . . . . . . . . Cma19g00571 . Car19g00430 . . . . . . . . . . . . . . . . . . Chy01g00105 .
Vvi3g649 Blo02g00950 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag1098 . . . . . . . . . . . Bpe05g00493 . . . Cmo04g00500 . . . . . . Cpe01g00420 . . . . . . . . . . . . . . . . . .
Vvi3g650 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g651 Blo02g00947 . Bda06g01219 Bda08g00663 Bpe07g00259 . Bma05g00676 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone10ag1024 . . . . . . . . . Bpe05g00491 . . . Cmo04g00499 Cmo16g00358 . . . . Cpe14g00279 Cpe01g00419 . . . . . . . . . . . . . . . . . .
Vvi3g652 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe01g00418 . . . . . . . . . . . . . . . . . .
Vvi3g653 Blo02g00945 . Bda06g01217 Bda08g00665 . . . Bma12g00266 Cmo19g00582 . . . . . . . . . . . . . . . Cla02g00657 Cam02g0692 Cec02g0704 Cco02g0724 Clacu02g0698 Cmu02g0696 Cre02g1011 . . Cone3ag1008 Cone10ag1025 Lsi03g00552 . . Cme01g00099 . . . . . Bpe05g00489 . . . Cmo04g00497 . . Cma19g00568 . Car19g00428 . . . . . . . . . . . . . . . . . . . .
Vvi3g654 . . . . . . . . . Cmo11g01398 . . . . Sed05g2617 Cpe04g00308 . Bhi05g01058 Tan02g0993 Cmetu01g1914 Lac12g0196 Hepe02g0629 . . Cla02g00658 Cam02g0693 Cec02g0705 Cco02g0725 Clacu02g0699 Cmu02g0697 Cre02g1012 Cone12ag1062 Cone8ag1095 . . Lsi03g00553 Csa07g00706 . Cme01g00100 . . . Bda14g01466 . . Bma03g01376 . . . . Cma11g01717 . Car11g01124 . . . . . . . . . . . . . . . . . . . . .
Vvi3g655 . . . . . . . . Cmo19g00580 Cmo11g01399 . . . . . Cpe04g00309 Cpe15g00455 Bhi05g01057 Tan02g1772 . Lac12g0195 . . . Cla02g00659 Cam02g0694 Cec02g0707 Cco02g0726 Clacu02g0700 Cmu02g0698 Cre02g1013 . . . . Lsi03g00554 Csa07g00705 . Cme01g00101 . . . . . . . . . . . Cma11g01716 Cma19g00567 Car11g01125 Car19g00427 . . . . . . . . . . . . . . . . . . Chy01g00109 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 42109724 42110284 - Bda023039.2 Bda06g01217 1217
6 42117243 42127092 - Bda023041.1 Bda06g01219 1219
8 6934243 6938582 + Bda029125.1 Bda08g00663 663
8 6954335 6954904 + Bda029127.2 Bda08g00665 665
14 20516518 20527673 - Bda011220.1 Bda14g01466 1466
15 12886514 12888054 + Bda012712.1 Bda15g00841 841
5 38156413 38159981 + XM_039032642.1 Bhi05g01057 1057
5 38204381 38208595 + XM_039031453.1 Bhi05g01058 1058
2 36724178 36724735 - BLOR10675 Blo02g00945 945
2 36818217 36823006 - BLOR10677 Blo02g00947 947
2 36878603 36878815 + BLOR10680 Blo02g00950 950
3 32304174 32319398 + Bma017933.2 Bma03g01373 1373
3 32495742 32505966 + Bma017936.1 Bma03g01376 1376
5 39426522 39430828 - Bma021729.1 Bma05g00676 676
12 3514435 3514995 + Bma007160.1 Bma12g00266 266
5 19122893 19123462 - Bpe017909.1 Bpe05g00489 489
5 19137256 19141588 - Bpe017911.1 Bpe05g00491 491
5 19150376 19150782 + Bpe017913.1 Bpe05g00493 493
7 1866276 1870208 + Bpe021071.2 Bpe07g00259 259
12 4408219 4409725 - Bpe005546.1 Bpe12g00300 300
2 8088383 8099948 + CaPI482276_02g006840.1 Cam02g0684 684
2 8130816 8132391 - CaPI482276_02g006880.1 Cam02g0688 688
2 8163490 8164113 + CaPI482276_02g006920.1 Cam02g0692 692
2 8171053 8177035 - CaPI482276_02g006930.1 Cam02g0693 693
2 8189765 8192909 - CaPI482276_02g006940.1 Cam02g0694 694
11 8988729 8992127 - Carg26989-RA Car11g01124 1124
11 8994451 8997546 - Carg26990-RA Car11g01125 1125
19 6071411 6075259 + Carg16349-RA Car19g00427 427
19 6077023 6083575 - Carg16350-RA Car19g00428 428
19 6091901 6092853 + Carg16352-RA Car19g00430 430
19 6095798 6108270 - Carg16353-RA Car19g00431 431
2 7377724 7389327 + CcPI632755_02g007180.1 Cco02g0718 718
2 7420618 7422182 - CcPI632755_02g007210.1 Cco02g0721 721
2 7453370 7453990 + CcPI632755_02g007240.1 Cco02g0724 724
2 7465516 7473586 - CcPI632755_02g007250.1 Cco02g0725 725
2 7477161 7480317 - CcPI632755_02g007260.1 Cco02g0726 726
2 7301713 7315124 + CePI673135_02g006980.1 Cec02g0698 698
2 7355477 7356651 - CePI673135_02g007000.1 Cec02g0700 700
2 7385046 7385669 + CePI673135_02g007040.1 Cec02g0704 704
2 7390054 7396069 - CePI673135_02g007050.1 Cec02g0705 705
2 7403638 7407131 - CePI673135_02g007070.1 Cec02g0707 707
1 678801 694129 + Chy1G001040.1 Chy01g00104 104
1 696755 700160 - Chy1G001050.1 Chy01g00105 105
1 706935 725648 - Chy1G001090.1 Chy01g00109 109
2 7112605 7124221 + ClG42_02g0069200.10 Clacu02g0692 692
2 7154410 7155596 - ClG42_02g0069400.10 Clacu02g0694 694
2 7189370 7189993 + ClG42_02g0069800.10 Clacu02g0698 698
2 7194348 7200236 - ClG42_02g0069900.10 Clacu02g0699 699
2 7212989 7216175 - ClG42_02g0070000.10 Clacu02g0700 700
2 7446767 7458630 + ClCG02G006490.2 Cla02g00651 651
2 7491248 7492434 - ClCG02G006520.2 Cla02g00654 654
2 7528849 7529472 + ClCG02G006550.1 Cla02g00657 657
2 7533827 7539715 - ClCG02G006560.2 Cla02g00658 658
2 7554924 7562001 - ClCG02G006570.2 Cla02g00659 659
11 11366810 11370193 + CmaCh11G017160.1 Cma11g01716 1716
11 11372001 11376626 + CmaCh11G017170.1 Cma11g01717 1717
19 6402662 6406814 + CmaCh19G005670.1 Cma19g00567 567
19 6407804 6408466 - CmaCh19G005680.1 Cma19g00568 568
19 6420766 6421957 + CmaCh19G005710.1 Cma19g00571 571
19 6422989 6435857 - CmaCh19G005720.1 Cma19g00572 572
1 681451 683438 - MELO3C018496.2.1 Cme01g00096 96
1 696518 697190 + MELO3C018499.2.1 Cme01g00099 99
1 700201 704287 - MELO3C018500.2.1 Cme01g00100 100
1 705414 708702 - MELO3C018501.2.1 Cme01g00101 101
1 838083 842266 - PI0012307.1 Cmetu01g1914 1914
4 2489709 2490284 - CmoCh04G004970.1 Cmo04g00497 497
4 2499610 2504534 - CmoCh04G004990.1 Cmo04g00499 499
4 2505932 2506601 + CmoCh04G005000.1 Cmo04g00500 500
11 9831661 9835685 - CmoCh11G013980.1 Cmo11g01398 1398
11 9837969 9841249 - CmoCh11G013990.1 Cmo11g01399 1399
16 1653937 1656203 - CmoCh16G003580.1 Cmo16g00358 358
19 6571314 6583578 + CmoCh19G005800.1 Cmo19g00580 580
19 6585661 6586323 - CmoCh19G005820.1 Cmo19g00582 582
19 6601614 6602565 + CmoCh19G005850.1 Cmo19g00585 585
19 6605185 6617959 - CmoCh19G005860.1 Cmo19g00586 586
2 7017701 7029309 + CmPI595203_02g006870.1 Cmu02g0687 687
2 7059493 7061060 - CmPI595203_02g006900.1 Cmu02g0690 690
2 7094463 7095086 + CmPI595203_02g006960.1 Cmu02g0696 696
2 7099441 7105330 - CmPI595203_02g006970.1 Cmu02g0697 697
2 7118126 7121300 - CmPI595203_02g006980.1 Cmu02g0698 698
3 28885661 28886086 + Conep03aG0150700.1 Cone3ag1008 1008
8 9818693 9821295 + Conep08aG0112600.1 Cone8ag1095 1095
8 9828004 9828709 + Conep08aG0112900.1 Cone8ag1098 1098
8 9829962 9831230 + Conep08aG0113000.1 Cone8ag1099 1099
8 9834072 9841621 - Conep08aG0113100.1 Cone8ag1100 1100
10 7107954 7113296 + Conep10aG0105100.1 Cone10ag1024 1024
10 7136676 7137560 + Conep10aG0105200.1 Cone10ag1025 1025
12 8782521 8785095 + Conep12aG0109600.1 Cone12ag1062 1062
1 2424751 2431914 - Cp4.1LG01g02370.1 Cpe01g00418 418
1 2432652 2437567 - Cp4.1LG01g02360.1 Cpe01g00419 419
1 2438760 2439642 + Cp4.1LG01g02460.1 Cpe01g00420 420
4 3869105 3872620 - Cp4.1LG04g07770.1 Cpe04g00308 308
4 3874502 3877931 - Cp4.1LG04g07790.1 Cpe04g00309 309
14 1619470 1632204 - Cp4.1LG14g04380.1 Cpe14g00279 279
15 5624271 5628547 + Cp4.1LG15g04470.1 Cpe15g00455 455
15 5643517 5645189 + Cp4.1LG15g04460.1 Cpe15g00457 457
15 5648880 5661200 - Cp4.1LG15g04560.1 Cpe15g00458 458
2 7640594 7653884 + CrPI670011_02g010060.1 Cre02g1006 1006
2 7686133 7687703 - CrPI670011_02g010070.1 Cre02g1007 1007
2 7723620 7724243 + CrPI670011_02g010110.1 Cre02g1011 1011
2 7728533 7734475 - CrPI670011_02g010120.1 Cre02g1012 1012
2 7741902 7745061 - CrPI670011_02g010130.1 Cre02g1013 1013
7 5032351 5035656 + CsaV3_7G008040.1 Csa07g00705 705
7 5036799 5041299 + CsaV3_7G008050.1 Csa07g00706 706
7 5057906 5059973 + CsaV3_7G008090.1 Csa07g00710 710
7 5065494 5077859 - CsaV3_7G008100.1 Csa07g00711 711
2 6593438 6597044 - Hsped.02g06290.1 Hepe02g0629 629
12 2145644 2149430 + Lag0014567.1 Lac12g0195 195
12 2152007 2155430 + Lag0014568.1 Lac12g0196 196
3 6629735 6640451 + Lsi03G005480.1 Lsi03g00548 548
3 6659554 6660781 - Lsi03G005490.1 Lsi03g00549 549
3 6693062 6694189 + Lsi03G005520.1 Lsi03g00552 552
3 6701192 6706715 - Lsi03G005530.1 Lsi03g00553 553
3 6711122 6714750 - Lsi03G005540.1 Lsi03g00554 554
5 37769516 37773518 - Sed0018810.2 Sed05g2617 2617
2 13880441 13885066 - Tan0008742.1 Tan02g0993 993
2 82199619 82201937 + Tan0005706.2 Tan02g1772 1772
3 6447320 6451553 + Vvi3g646 Vvi3g646 646
3 6479124 6503918 - Vvi3g647 Vvi3g647 647
3 6507404 6509263 - Vvi3g648 Vvi3g648 648
3 6511004 6511621 - Vvi3g649 Vvi3g649 649
3 6512778 6514995 - Vvi3g650 Vvi3g650 650
3 6521842 6537917 + Vvi3g651 Vvi3g651 651
3 6538901 6539957 + Vvi3g652 Vvi3g652 652
3 6548596 6549754 + Vvi3g653 Vvi3g653 653
3 6551728 6559920 - Vvi3g654 Vvi3g654 654
3 6566135 6569256 - Vvi3g655 Vvi3g655 655
       

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