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
Vvi3g16 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag1222 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g17 . . . . . . . . . . . . . . . Cpe04g00108 . . . . . . . . . . . . . . . Cone12ag1179 . . . . . . . Blo04g00531 . . . Bpe15g00850 . Bma03g00568 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g18 . . Bda06g00954 Bda08g00955 . . . Bma12g00543 . . . Cma20g00817 . Car20g00702 . Cpe04g00107 Cpe15g00559 . . . . . . . Cla02g00492 Cam02g0502 Cec02g0502 Cco02g0508 Clacu02g0505 Cmu02g0501 Cre02g0833 . . Cone3ag1218 Cone10ag1103 Lsi10g00408 Csa07g00027 Chy11g00343 Cme01g01353 Blo04g00532 . . Bda14g00574 Bpe15g00849 Bpe05g00323 . . Sed05g3539 . Cmo20g00825 . Cma19g00687 . . Cpe16g00269 . Bhi10g01956 Tan05g1250 Cmetu11g0516 . Hepe08g0983 . . . . . . . . . . Csa02g01300 . Cme11g00162
Vvi3g19 . . . . . Bpe12g00090 . . Cmo19g00700 . Cma02g00369 Cma20g00816 Car02g00236 Car20g00701 . Cpe04g00106 Cpe15g00560 . . . . . . . Cla02g00491 Cam02g0500 Cec02g0501 Cco02g0507 Clacu02g0504 Cmu02g0500 Cre02g0832 . Cone8ag1224 Cone3ag1217 Cone10ag1102 Lsi10g00409 Csa07g00028 Chy11g00342 Cme01g01352 Blo04g00533 Blo13g00539 Bda15g01073 Bda14g00575 Bpe15g00848 . . Bma08g00784 . Cmo02g00375 Cmo20g00824 . Cma19g00690 . Car19g00532 Cpe16g00270 Cpe05g01286 Bhi10g01955 . . . . . . . . . . . . . . Csa02g01301 Chy01g00750 Cme11g00163
Vvi3g20 . Blo15g00671 Bda06g00960 . . . . . . . . Cma20g00815 . Car20g00699 . . . . . . . . . . . . . . . . . . . . Cone10ag1101 Lsi10g00411 . Chy11g00341 . . . . . . . . . . . Cmo20g00823 . . . . Cpe16g00271 . Bhi10g01950 . . . Hepe08g0981 . . . . . . . . . . Csa02g01302 . Cme11g00164
Vvi3g21 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1180 Cone8ag1225 . . . . . . Blo04g00534 . . . Bpe15g00847 . Bma03g00569 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g22 . . . . . . . . . . . . . . . Cpe04g00105 . . . . . . . . Cla02g00490 Cam02g0499 Cec02g0500 Cco02g0506 Clacu02g0503 Cmu02g0499 Cre02g0831 . Cone8ag1226 . . . Csa07g00029 . Cme01g01351 . . Bda15g01072 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi11g01134 . Chy01g00749 .
Vvi3g23 . Blo15g00670 . . . . . Bma12g00542 . . Cma02g00367 Cma20g00814 Car02g00235 Car20g00698 . . . . . . . . . . . . . . . . . . . Cone3ag1216 Cone10ag1100 . . Chy11g00340 . . . . . Bpe15g00846 . . . Sed01g0267 Cmo02g00372 Cmo20g00822 . . . . . . Bhi10g01948 Tan05g1245 . . Hepe08g0980 . . . . . . . . . . Csa02g01303 . .
Vvi3g24 . . Bda06g00961 . . . . Bma12g00541 . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi10g00412 . . . Blo04g00535 . . Bda14g00576 . . Bma03g00570 . Sed01g0265 Cmo02g00371 . . . . . Cpe16g00272 Cpe05g01288 Bhi10g01946 Tan05g1243 Cmetu11g1869 . Hepe08g0979 . . . . . . . . . . Csa02g01304 . Cme11g00165
Vvi3g25 . . . Bda08g00956 . Bpe12g00091 Bma05g00429 . . . Cma02g00366 Cma20g00812 Car02g00234 Car20g00697 . . . . . . . . . . . . . . . . . . . Cone3ag1214 . Lsi10g00413 . Chy11g00339 . Blo04g00536 Blo13g00537 Bda15g01071 Bda14g00577 Bpe15g00845 Bpe05g00322 Bma03g00571 Bma08g00783 Sed01g0264 Cmo02g00370 Cmo20g00820 . . . . Cpe16g00273 Cpe05g01289 Bhi10g01944 Tan05g1241 Cmetu11g1041 . Hepe08g0978 . . . . . . . . . . Csa02g01305 . Cme11g00166
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 26410287 26410992 + Bda022590.1 Bda06g00954 954
6 26607410 26610204 + Bda022600.1 Bda06g00960 960
6 26775171 26779762 - Bda022602.1 Bda06g00961 961
8 18590465 18591150 + Bda029619.1 Bda08g00955 955
8 18672017 18678112 + Bda029621.1 Bda08g00956 956
14 4384124 4384827 + Bda027325.1 Bda14g00574 574
14 4386081 4394439 - Bda027326.1 Bda14g00575 575
14 4408926 4411689 - Bda027328.1 Bda14g00576 576
14 4415583 4420096 + Bda027329.1 Bda14g00577 577
15 19942100 19946491 - Bda013066.1 Bda15g01071 1071
15 19954108 19955764 - Bda013067.1 Bda15g01072 1072
15 19967430 19975881 + Bda013068.1 Bda15g01073 1073
10 48442101 48453316 - XM_039046199.1 Bhi10g01944 1944
10 48531326 48537759 + XM_039046872.1 Bhi10g01946 1946
10 48531327 48537759 + XM_039046871.1 Bhi10g01948 1948
10 48595731 48600411 - XM_039046318.1 Bhi10g01950 1950
10 48693842 48705515 + XM_039045511.1 Bhi10g01955 1955
10 48774845 48775459 - XM_039046544.1 Bhi10g01956 1956
4 4576745 4581560 - BLOR13443 Blo04g00531 531
4 4583064 4584273 + BLOR13444 Blo04g00532 532
4 4585298 4593742 - BLOR13445 Blo04g00533 533
4 4595995 4597624 + BLOR13446 Blo04g00534 534
4 4604177 4609251 - BLOR13447 Blo04g00535 535
4 4613791 4618474 + BLOR13448 Blo04g00536 536
13 27206484 27215581 - BLOR05818 Blo13g00537 537
13 27246059 27254627 + BLOR05820 Blo13g00539 539
15 20218232 20228089 + BLOR07064 Blo15g00670 670
15 20228812 20232913 - BLOR07065 Blo15g00671 671
3 4717951 4735629 - Bma016856.2 Bma03g00568 568
3 4737625 4738954 + Bma016857.1 Bma03g00569 569
3 4742342 4746624 - Bma016858.1 Bma03g00570 570
3 4770695 4776273 + Bma016859.1 Bma03g00571 571
5 13752137 13758003 - Bma021270.1 Bma05g00429 429
8 45152238 45156399 - Bma028164.1 Bma08g00783 783
8 45211148 45228371 + Bma028165.1 Bma08g00784 784
12 21663111 21667713 + Bma007670.1 Bma12g00541 541
12 21825061 21829738 + Bma007674.1 Bma12g00542 542
12 21913214 21913915 - Bma007676.1 Bma12g00543 543
5 16846128 16851652 - Bpe017736.1 Bpe05g00322 322
5 16885232 16885917 - Bpe017737.1 Bpe05g00323 323
12 648633 657095 - Bpe005329.1 Bpe12g00090 90
12 665052 669305 + Bpe005331.1 Bpe12g00091 91
15 18468475 18473005 - Bpe001769.1 Bpe15g00845 845
15 18477638 18482146 + Bpe001770.1 Bpe15g00846 846
15 18483902 18484598 - Bpe001771.1 Bpe15g00847 847
15 18487635 18495954 + Bpe001772.1 Bpe15g00848 848
15 18497243 18498000 - Bpe001773.1 Bpe15g00849 849
15 18502183 18509040 + Bpe001774.4 Bpe15g00850 850
2 5651047 5653053 - CaPI482276_02g004990.1 Cam02g0499 499
2 5665003 5675157 + CaPI482276_02g005000.1 Cam02g0500 500
2 5679070 5679896 - CaPI482276_02g005020.1 Cam02g0502 502
2 1565398 1571266 - Carg24137-RA Car02g00234 234
2 1574580 1587295 + Carg24138-RA Car02g00235 235
2 1595297 1606076 + Carg24140-RA Car02g00236 236
19 6898336 6908373 - Carg19388-RA Car19g00532 532
20 3986654 3992882 - Carg25948-RA Car20g00697 697
20 3995356 4000839 + Carg25947-RA Car20g00698 698
20 3999633 4006124 - Carg25946-RA Car20g00699 699
20 4016625 4019059 + Carg25944-RA Car20g00701 701
20 4019655 4020302 - Carg25943-RA Car20g00702 702
2 4696117 4698127 - CcPI632755_02g005060.1 Cco02g0506 506
2 4706611 4720063 + CcPI632755_02g005070.1 Cco02g0507 507
2 4723704 4724800 - CcPI632755_02g005080.1 Cco02g0508 508
2 4661525 4663528 - CePI673135_02g005000.1 Cec02g0500 500
2 4676010 4686371 + CePI673135_02g005010.1 Cec02g0501 501
2 4689833 4690929 - CePI673135_02g005020.1 Cec02g0502 502
1 5542959 5545698 - Chy1G007490.1 Chy01g00749 749
1 5556542 5566241 + Chy1G007500.1 Chy01g00750 750
11 3053872 3058505 - Chy11G189190.1 Chy11g00339 339
11 3069601 3084280 + Chy11G189200.1 Chy11g00340 340
11 3085159 3089575 - Chy11G189210.1 Chy11g00341 341
11 3098371 3107206 + Chy11G189220.1 Chy11g00342 342
11 3109953 3112860 - Chy11G189230.1 Chy11g00343 343
2 4601803 4603809 - ClG42_02g0050300.10 Clacu02g0503 503
2 4625683 4636981 + ClG42_02g0050400.10 Clacu02g0504 504
2 4639427 4640522 - ClG42_02g0050500.10 Clacu02g0505 505
2 4813331 4815586 - ClCG02G004640.1 Cla02g00490 490
2 4841435 4852210 + ClCG02G004660.1 Cla02g00491 491
2 4855440 4856716 - ClCG02G004670.1 Cla02g00492 492
2 1813921 1819736 - CmaCh02G003660.1 Cma02g00366 366
2 1824000 1836595 + CmaCh02G003670.1 Cma02g00367 367
2 1845006 1855722 + CmaCh02G003690.1 Cma02g00369 369
19 7115841 7117491 + CmaCh19G006870.1 Cma19g00687 687
19 7121604 7142840 - CmaCh19G006900.1 Cma19g00690 690
20 3824283 3834913 - CmaCh20G008120.1 Cma20g00812 812
20 3837919 3844114 + CmaCh20G008140.1 Cma20g00814 814
20 3843590 3848558 - CmaCh20G008150.1 Cma20g00815 815
20 3850753 3863924 + CmaCh20G008160.1 Cma20g00816 816
20 3862961 3863605 - CmaCh20G008170.1 Cma20g00817 817
1 16879355 16882387 - MELO3C013428.2.1 Cme01g01351 1351
1 16892381 16909596 + MELO3C013429.2.1 Cme01g01352 1352
1 16917918 16919435 - MELO3C013430.2.1 Cme01g01353 1353
11 1739205 1739758 + MELO3C023341.2.1 Cme11g00162 162
11 1744215 1753644 - MELO3C023342.2.1 Cme11g00163 163
11 1764455 1768846 + MELO3C023343.2.1 Cme11g00164 164
11 1769624 1776261 - MELO3C023344.2.1 Cme11g00165 165
11 1796496 1801936 + MELO3C023346.2.1 Cme11g00166 166
11 27843886 27844434 + PI0024730.1 Cmetu11g0516 516
11 27899010 27904548 + PI0007795.1 Cmetu11g1041 1041
11 27881970 27889277 - PI0020060.3 Cmetu11g1869 1869
2 1874006 1879707 - CmoCh02G003700.1 Cmo02g00370 370
2 1884655 1891663 + CmoCh02G003710.1 Cmo02g00371 371
2 1892468 1898091 + CmoCh02G003720.1 Cmo02g00372 372
2 1910956 1917490 + CmoCh02G003750.1 Cmo02g00375 375
19 7385691 7396389 - CmoCh19G007000.1 Cmo19g00700 700
20 4057005 4066628 - CmoCh20G008200.1 Cmo20g00820 820
20 4069564 4075784 + CmoCh20G008220.1 Cmo20g00822 822
20 4075644 4081331 - CmoCh20G008230.1 Cmo20g00823 823
20 4083837 4094710 + CmoCh20G008240.1 Cmo20g00824 824
20 4095081 4095728 - CmoCh20G008250.1 Cmo20g00825 825
2 4540193 4542199 - CmPI595203_02g004990.1 Cmu02g0499 499
2 4564199 4574329 + CmPI595203_02g005000.1 Cmu02g0500 500
2 4577916 4579011 - CmPI595203_02g005010.1 Cmu02g0501 501
3 30867107 30871531 + Conep03aG0172100.1 Cone3ag1214 1214
3 30895345 30905403 + Conep03aG0172300.1 Cone3ag1216 1216
3 30911045 30921971 + Conep03aG0172400.1 Cone3ag1217 1217
3 30922973 30923893 - Conep03aG0172500.1 Cone3ag1218 1218
8 10333267 10334202 - Conep08aG0125900.1 Cone8ag1222 1222
8 10345782 10353661 - Conep08aG0126100.1 Cone8ag1224 1224
8 10354882 10356186 + Conep08aG0126200.1 Cone8ag1225 1225
8 10357270 10359413 + Conep08aG0126400.1 Cone8ag1226 1226
10 7730077 7737409 + Conep10aG0112900.1 Cone10ag1100 1100
10 7743293 7746963 - Conep10aG0113000.1 Cone10ag1101 1101
10 7768536 7784565 + Conep10aG0113100.1 Cone10ag1102 1102
10 7787512 7788680 - Conep10aG0113200.1 Cone10ag1103 1103
12 9318641 9329530 - Conep12aG0121800.1 Cone12ag1179 1179
12 9332686 9333000 + Conep12aG0121900.1 Cone12ag1180 1180
4 944707 948358 - Cp4.1LG04g01020.1 Cpe04g00105 105
4 952506 964879 + Cp4.1LG04g01100.1 Cpe04g00106 106
4 966757 968544 - Cp4.1LG04g01010.1 Cpe04g00107 107
4 972040 979161 + Cp4.1LG04g01080.1 Cpe04g00108 108
5 8966598 8977449 - Cp4.1LG05g12940.1 Cpe05g01286 1286
5 8985296 8998012 - Cp4.1LG05g12960.1 Cpe05g01288 1288
5 9002368 9007620 + Cp4.1LG05g12870.1 Cpe05g01289 1289
15 6419234 6420921 + Cp4.1LG15g05520.1 Cpe15g00559 559
15 6422357 6434324 - Cp4.1LG15g05640.1 Cpe15g00560 560
16 4700975 4701619 + Cp4.1LG16g02630.1 Cpe16g00269 269
16 4702600 4714357 - Cp4.1LG16g02680.1 Cpe16g00270 270
16 4718286 4729326 + Cp4.1LG16g02760.1 Cpe16g00271 271
16 4729113 4735381 - Cp4.1LG16g02810.1 Cpe16g00272 272
16 4738336 4744361 + Cp4.1LG16g02730.1 Cpe16g00273 273
2 5089632 5091844 - CrPI670011_02g008310.1 Cre02g0831 831
2 5103926 5113403 + CrPI670011_02g008320.1 Cre02g0832 832
2 5117104 5118198 - CrPI670011_02g008330.1 Cre02g0833 833
2 12644521 12645374 + CsaV3_2G015160.1 Csa02g01300 1300
2 12650213 12660646 - CsaV3_2G015170.1 Csa02g01301 1301
2 12669123 12674407 + CsaV3_2G015180.1 Csa02g01302 1302
2 12674408 12681961 - CsaV3_2G015190.1 Csa02g01303 1303
2 12682159 12689244 - CsaV3_2G015200.1 Csa02g01304 1304
2 12698177 12703772 + CsaV3_2G015210.1 Csa02g01305 1305
7 395757 397689 + CsaV3_7G000270.1 Csa07g00027 27
7 401392 411300 - CsaV3_7G000280.1 Csa07g00028 28
7 419448 423435 + CsaV3_7G000290.1 Csa07g00029 29
8 9204251 9210136 - Hsped.08g09780.1 Hepe08g0978 978
8 9219225 9229110 + Hsped.08g09790.1 Hepe08g0979 979
8 9232207 9237815 + Hsped.08g09800.1 Hepe08g0980 980
8 9239617 9245423 - Hsped.08g09810.1 Hepe08g0981 981
8 9285986 9286630 - Hsped.08g09830.1 Hepe08g0983 983
10 6209617 6210219 + Lsi10G004080.1 Lsi10g00408 408
10 6214377 6226423 - Lsi10G004090.1 Lsi10g00409 409
10 6236464 6242819 + Lsi10G004110.1 Lsi10g00411 411
10 6242937 6264090 - Lsi10G004120.1 Lsi10g00412 412
10 6270730 6277329 + Lsi10G004130.1 Lsi10g00413 413
11 19803691 19806585 - Lsi11G011340.1 Lsi11g01134 1134
1 2038096 2045186 - Sed0017571.2 Sed01g0264 264
1 2050070 2059648 + Sed0027400.1 Sed01g0265 265
1 2060330 2077314 + Sed0018473.2 Sed01g0267 267
5 44017457 44018017 + Sed0010735.1 Sed05g3539 3539
5 12939991 12945788 - Tan0019870.1 Tan05g1241 1241
5 13020100 13038035 + Tan0021700.1 Tan05g1243 1243
5 13056215 13061608 + Tan0005469.1 Tan05g1245 1245
5 13163052 13164186 - Tan0009666.1 Tan05g1250 1250
3 288652 289862 - Vvi3g16 Vvi3g16 16
3 291231 302906 - Vvi3g17 Vvi3g17 17
3 310968 312061 + Vvi3g18 Vvi3g18 18
3 341581 357538 - Vvi3g19 Vvi3g19 19
3 362661 370801 + Vvi3g20 Vvi3g20 20
3 373305 374140 + Vvi3g21 Vvi3g21 21
3 376742 380317 + Vvi3g22 Vvi3g22 22
3 380764 396708 - Vvi3g23 Vvi3g23 23
3 398626 406803 - Vvi3g24 Vvi3g24 24
3 415126 427415 + Vvi3g25 Vvi3g25 25
       

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