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
Vvi3g36 . . . . . Bpe12g00093 . . . . Cma02g00363 Cma20g00810 Car02g00230 Car20g00694 . . . . . . . . . . . . . . . . . Cone12ag1183 Cone8ag1229 . Cone10ag1097 Lsi10g00417 . Chy11g00334 . Blo04g00537 Blo13g00535 Bda15g01067 Bda14g00578 Bpe15g00844 . Bma03g00572 . . Cmo02g00366 Cmo20g00818 . . . . Cpe16g00277 Cpe05g01293 Bhi10g01937 Tan05g1234 . . Hepe08g0973 . . . . . . . . . . Csa02g01310 . Cme11g00171
Vvi3g37 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g38 . . . . . . . . Cmo19g00701 . . . . . Sed05g2290 Cpe04g00103 Cpe15g00561 Bhi05g01262 Tan02g0757 Cmetu01g2730 . . . . Cla02g00488 Cam02g0497 Cec02g0498 Cco02g0503 Clacu02g0501 Cmu02g0496 Cre02g0829 Cone12ag1185 Cone8ag1230 . . . Csa07g00034 . Cme01g01347 Blo04g00538 . . . Bpe15g00843 . . . . . . . . . Car19g00533 . . . . . . . . . Cla02g01127 Cam02g1202 Cec02g1205 Cco02g1255 Clacu02g1191 Cmu02g1153 Cre02g1463 . . Chy01g00747 .
Vvi3g39 . . . . . Bpe12g00094 . . Cmo19g00702 . . . . . . Cpe04g00102 Cpe15g00562 Bhi05g01259 . . . . . . Cla02g00487 Cam02g0496 Cec02g0497 Cco02g0502 Clacu02g0500 Cmu02g0495 Cre02g0828 . . . . . Csa07g00035 . Cme01g01346 Blo04g00539 Blo13g00534 Bda15g01066 Bda14g00579 Bpe15g00842 . Bma03g00573 Bma08g00782 . . . . Cma19g00691 . . . . . . . . . . . . . . . . . . . . Chy01g00746 .
Vvi3g40 Blo02g00647 . . Bda08g00960 Bpe07g00496 . Bma05g00425 . . . . Cma20g00808 . Car20g00693 . . . . . . . . . . . . . . . . . . Cone8ag1232 Cone3ag1210 . Lsi10g00418 . Chy11g00333 . . . . . . Bpe05g00318 . . Sed01g3719 . Cmo20g00816 . . . . . . Bhi10g01935 Tan05g1233 Cmetu09g0145 . Hepe08g0972 . . . . . . . . . . Csa02g01311 . Cme11g00172
Vvi3g41 Blo02g00648 . . Bda08g00961 . . Bma05g00420 . . . . . . . . Cpe04g00101 . Bhi05g01257 . . . . . . Cla02g00486 Cam02g0495 Cec02g0495 Cco02g0501 Clacu02g0499 Cmu02g0494 Cre02g0827 . . . . . Csa07g00036 . . . . . . . Bpe05g00315 . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy01g00745 .
Vvi3g42 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g43 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g44 . Blo15g00665 Bda06g00513 . Bpe07g00495 . . Bma12g00539 . . Cma02g00362 Cma20g00807 Car02g00229 Car20g00692 . . . . . . . . . . . . . . . . . . . . . Lsi10g00419 . Chy11g00332 . . . . . . . . . Sed01g0256 Cmo02g00365 Cmo20g00815 . . . . Cpe16g00278 Cpe05g01294 Bhi10g01934 Tan05g1232 Cmetu09g0265 . Hepe08g0970 . . . . . . . . . . Csa02g01312 . Cme11g00173
Vvi3g45 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag1235 . . Lsi10g00420 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 7367811 7370063 + Bda033762 Bda06g00513 513
8 18790075 18792319 + Bda029625.1 Bda08g00960 960
8 18851645 18852370 + Bda029626.1 Bda08g00961 961
14 4421770 4432752 - Bda027330.2 Bda14g00578 578
14 4435624 4438044 - Bda027331.1 Bda14g00579 579
15 19840773 19843289 + Bda013059.1 Bda15g01066 1066
15 19845790 19848942 + Bda013060.1 Bda15g01067 1067
5 45516703 45517401 - XM_039031239.1 Bhi05g01257 1257
5 45532228 45537370 + XM_039031952.1 Bhi05g01259 1259
5 45539736 45553679 + XM_039032229.1 Bhi05g01262 1262
10 48279807 48282540 - XM_039045463.1 Bhi10g01934 1934
10 48301735 48306162 - XM_039044480.1 Bhi10g01935 1935
10 48377348 48381402 + XM_039044529.1 Bhi10g01937 1937
2 15484628 15487138 + BLOR10377 Blo02g00647 647
2 15626772 15631417 + BLOR10378 Blo02g00648 648
4 4619440 4622638 - BLOR13449 Blo04g00537 537
4 4629142 4638321 - BLOR13450 Blo04g00538 538
4 4639718 4642364 - BLOR13451 Blo04g00539 539
13 27120045 27126973 + BLOR05815 Blo13g00534 534
13 27165842 27175365 + BLOR05816 Blo13g00535 535
15 19468070 19469835 - BLOR07059 Blo15g00665 665
3 4783012 4785758 - Bma016861.1 Bma03g00572 572
3 4786331 4799592 - Bma016862.1 Bma03g00573 573
5 13366586 13367305 - Bma021262.1 Bma05g00420 420
5 13622504 13624639 - Bma021267.1 Bma05g00425 425
8 45138090 45144805 + Bma028163.1 Bma08g00782 782
12 21360145 21361872 - Bma007664.1 Bma12g00539 539
5 16748234 16748953 - Bpe017729.1 Bpe05g00315 315
5 16795243 16797340 - Bpe017732.1 Bpe05g00318 318
7 9654058 9655774 - Bpe026060 Bpe07g00495 495
7 9665190 9667120 - Bpe021339.1 Bpe07g00496 496
12 675434 678619 - Bpe005333.1 Bpe12g00093 93
12 682010 684452 - Bpe005334.1 Bpe12g00094 94
15 18449805 18452426 + Bpe001766.1 Bpe15g00842 842
15 18455048 18464181 + Bpe001767.1 Bpe15g00843 843
15 18464757 18467488 + Bpe001768.1 Bpe15g00844 844
2 5614200 5617083 - CaPI482276_02g004950.1 Cam02g0495 495
2 5622715 5626104 + CaPI482276_02g004960.1 Cam02g0496 496
2 5630338 5643906 + CaPI482276_02g004970.1 Cam02g0497 497
2 23950154 23955906 + CaPI482276_02g012020.1 Cam02g1202 1202
2 1493635 1496149 - Carg27198-RA Car02g00229 229
2 1497897 1502567 + Carg27197-RA Car02g00230 230
19 6912942 6921266 - Carg19387-RA Car19g00533 533
20 3955265 3957440 - Carg25954-RA Car20g00692 692
20 3959109 3962194 - Carg25953-RA Car20g00693 693
20 3971393 3975855 + Carg25952-RA Car20g00694 694
2 4658830 4661752 - CcPI632755_02g005010.1 Cco02g0501 501
2 4667347 4669411 + CcPI632755_02g005020.1 Cco02g0502 502
2 4675321 4689100 + CcPI632755_02g005030.1 Cco02g0503 503
2 23903929 23909913 + CcPI632755_02g012550.1 Cco02g1255 1255
2 4625444 4628379 - CePI673135_02g004950.1 Cec02g0495 495
2 4631764 4637306 + CePI673135_02g004970.1 Cec02g0497 497
2 4640923 4654553 + CePI673135_02g004980.1 Cec02g0498 498
2 28339687 28345099 + CePI673135_02g012050.1 Cec02g1205 1205
1 5477728 5479836 - Chy1G007450.1 Chy01g00745 745
1 5499784 5505932 + Chy1G007460.1 Chy01g00746 746
1 5514003 5527703 + Chy1G007470.1 Chy01g00747 747
11 2984108 2986496 - Chy11G189120.1 Chy11g00332 332
11 2991499 2994426 - Chy11G189130.1 Chy11g00333 333
11 3005283 3020692 + Chy11G189140.1 Chy11g00334 334
2 4564812 4567644 - ClG42_02g0049900.10 Clacu02g0499 499
2 4573241 4576617 + ClG42_02g0050000.10 Clacu02g0500 500
2 4581189 4594771 + ClG42_02g0050100.10 Clacu02g0501 501
2 24120539 24125897 + ClG42_02g0119100.10 Clacu02g1191 1191
2 4774523 4780872 - ClCG02G004590.2 Cla02g00486 486
2 4780794 4785307 + ClCG02G004610.1 Cla02g00487 487
2 4790731 4806726 + ClCG02G004620.2 Cla02g00488 488
2 24380291 24385505 + ClCG02G011530.2 Cla02g01127 1127
2 1786100 1788347 - CmaCh02G003620.1 Cma02g00362 362
2 1790417 1795693 + CmaCh02G003630.1 Cma02g00363 363
19 7144349 7147355 - CmaCh19G006910.1 Cma19g00691 691
20 3796753 3799549 - CmaCh20G008070.1 Cma20g00807 807
20 3801054 3804504 - CmaCh20G008080.1 Cma20g00808 808
20 3812638 3816980 + CmaCh20G008100.1 Cma20g00810 810
1 16824184 16829462 + MELO3C013423.2.1 Cme01g01346 1346
1 16830649 16844337 + MELO3C013424.2.1 Cme01g01347 1347
11 1829732 1838792 - MELO3C023351.2.1 Cme11g00171 171
11 1874052 1877412 + MELO3C023353.2.1 Cme11g00172 172
11 1884391 1886822 + MELO3C023354.2.1 Cme11g00173 173
1 5763078 5775592 + PI0020747.1 Cmetu01g2730 2730
9 3637980 3642893 + PI0021127.1 Cmetu09g0145 145
9 4861909 4866040 + PI0023233.1 Cmetu09g0265 265
2 1845443 1847851 - CmoCh02G003650.1 Cmo02g00365 365
2 1849994 1854722 + CmoCh02G003660.1 Cmo02g00366 366
19 7399900 7408891 - CmoCh19G007010.1 Cmo19g00701 701
19 7410137 7412180 - CmoCh19G007020.1 Cmo19g00702 702
20 4029095 4031492 - CmoCh20G008150.1 Cmo20g00815 815
20 4033180 4036399 - CmoCh20G008160.1 Cmo20g00816 816
20 4045330 4049660 + CmoCh20G008180.1 Cmo20g00818 818
2 4503190 4506022 - CmPI595203_02g004940.1 Cmu02g0494 494
2 4511619 4514997 + CmPI595203_02g004950.1 Cmu02g0495 495
2 4519569 4533152 + CmPI595203_02g004960.1 Cmu02g0496 496
2 23989617 23994973 + CmPI595203_02g011530.1 Cmu02g1153 1153
3 30821376 30824621 - Conep03aG0171700.1 Cone3ag1210 1210
8 10368125 10369844 - Conep08aG0126700.1 Cone8ag1229 1229
8 10370478 10379397 - Conep08aG0126800.1 Cone8ag1230 1230
8 10383986 10386373 + Conep08aG0127000.1 Cone8ag1232 1232
8 10391492 10393090 - Conep08aG0127300.1 Cone8ag1235 1235
10 7706376 7709837 + Conep10aG0112600.1 Cone10ag1097 1097
12 9343970 9346339 - Conep12aG0122300.1 Cone12ag1183 1183
12 9349563 9358555 - Conep12aG0122500.1 Cone12ag1185 1185
4 915573 918846 - Cp4.1LG04g01000.1 Cpe04g00101 101
4 919182 923287 + Cp4.1LG04g01040.1 Cpe04g00102 102
4 924782 935958 + Cp4.1LG04g01060.1 Cpe04g00103 103
5 9025603 9030240 - Cp4.1LG05g12950.1 Cpe05g01293 1293
5 9032485 9035518 + Cp4.1LG05g12880.1 Cpe05g01294 1294
15 6436404 6445088 - Cp4.1LG15g05590.1 Cpe15g00561 561
15 6446392 6449584 - Cp4.1LG15g05600.1 Cpe15g00562 562
16 4756294 4761910 - Cp4.1LG16g02800.1 Cpe16g00277 277
16 4775316 4778301 + Cp4.1LG16g02770.1 Cpe16g00278 278
2 5052758 5055609 - CrPI670011_02g008270.1 Cre02g0827 827
2 5061257 5066097 + CrPI670011_02g008280.1 Cre02g0828 828
2 5069192 5082810 + CrPI670011_02g008290.1 Cre02g0829 829
2 26473865 26479274 + CrPI670011_02g014630.1 Cre02g1463 1463
2 12727707 12736033 - CsaV3_2G015260.1 Csa02g01310 1310
2 12747279 12750908 + CsaV3_2G015270.1 Csa02g01311 1311
2 12755055 12758372 + CsaV3_2G015280.1 Csa02g01312 1312
7 441994 456106 - CsaV3_7G000340.1 Csa07g00034 34
7 456998 462681 - CsaV3_7G000350.1 Csa07g00035 35
7 462871 465357 + CsaV3_7G000360.1 Csa07g00036 36
8 9099266 9101714 - Hsped.08g09700.1 Hepe08g0970 970
8 9119265 9124315 - Hsped.08g09720.1 Hepe08g0972 972
8 9145314 9151137 + Hsped.08g09730.1 Hepe08g0973 973
10 6316969 6321398 - Lsi10G004170.1 Lsi10g00417 417
10 6350186 6354212 + Lsi10G004180.1 Lsi10g00418 418
10 6364131 6365639 + Lsi10G004190.1 Lsi10g00419 419
10 6364840 6368982 - Lsi10G004200.1 Lsi10g00420 420
1 2002147 2005285 - Sed0002284.1 Sed01g0256 256
1 66275263 66284067 - Sed0000234.1 Sed01g3719 3719
5 35448557 35459214 + Sed0010772.1 Sed05g2290 2290
2 7152912 7164258 + Tan0001963.1 Tan02g0757 757
5 12740968 12743455 - Tan0021141.1 Tan05g1232 1232
5 12785553 12790467 - Tan0020121.1 Tan05g1233 1233
5 12825617 12830303 + Tan0021279.1 Tan05g1234 1234
3 524610 530365 - Vvi3g36 Vvi3g36 36
3 531691 533479 + Vvi3g37 Vvi3g37 37
3 533513 544910 - Vvi3g38 Vvi3g38 38
3 547344 562468 - Vvi3g39 Vvi3g39 39
3 565596 568081 + Vvi3g40 Vvi3g40 40
3 574480 578938 + Vvi3g41 Vvi3g41 41
3 579356 583313 - Vvi3g42 Vvi3g42 42
3 584366 587948 - Vvi3g43 Vvi3g43 43
3 593087 594606 + Vvi3g44 Vvi3g44 44
3 594822 598576 - Vvi3g45 Vvi3g45 45
       

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