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
Vvi3g196 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g197 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g198 . . . . . Bpe12g00130 . . Cmo19g00765 Cmo11g01753 . . . . Sed05g2251 Cpe04g00605 Cpe15g00607 Bhi05g01684 Tan02g0657 Cmetu10g1323 . . . . Cla02g00408 Cam02g0414 Cec02g0413 Cco02g0431 Clacu02g0417 Cmu02g0413 Cre02g0748 Cone12ag1245 . . . . Csa07g00121 . Cme01g01238 Blo04g00583 Blo13g00496 Bda15g01024 Bda14g00625 Bpe15g00802 . Bma03g00617 Bma08g00610 . . . Cma11g01365 Cma19g00752 . Car19g00587 . . . . . . . . . . . . . . . . Lsi11g01217 . Chy01g00662 .
Vvi3g199 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed01g0634 . . . . . . . . Bhi10g01252 Tan05g1059 Cmetu11g1933 . . . . . . . . . . . . . . .
Vvi3g200 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g201 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g202 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g203 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g204 . . . . . . . . . Cmo11g01754 . . . . . Cpe04g00606 . . . . . . . . . . . . . . . . . . . . . . . Blo04g00584 . . Bda14g00626 Bpe15g00801 . . . . . . Cma11g01363 . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g205 . Blo15g00387 Bda06g00473 Bda08g00980 Bpe07g00709 . . . . . Cma02g00273 Cma20g00736 . Car20g00638 . . . . . . . . . . . . . . . . . . . Cone3ag0971 Cone10ag1175 Lsi10g00510 . Chy11g00239 . . . . . . Bpe05g00300 . . . Cmo02g00270 Cmo20g00733 . . . . Cpe16g00330 Cpe05g01359 Bhi10g01809 . . . . . . Cla02g01185 Cam02g1263 Cec02g1274 Cco02g1311 Clacu02g1246 Cmu02g1212 Cre02g1527 . Csa02g01409 . Cme11g00361
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 6749376 6760990 - Bda023718.1 Bda06g00473 473
8 19515635 19521266 - Bda029649.1 Bda08g00980 980
14 4693528 4696863 + Bda027380.1 Bda14g00625 625
14 4697816 4700139 - Bda027381.1 Bda14g00626 626
15 19195465 19199077 - Bda013006.1 Bda15g01024 1024
5 54939079 54944617 - XM_039032209.1 Bhi05g01684 1684
10 29142527 29146523 - XM_039044484.1 Bhi10g01252 1252
10 45456281 45472867 + XM_039044947.1 Bhi10g01809 1809
4 5022477 5029808 + BLOR13495 Blo04g00583 583
4 5030859 5033295 - BLOR13496 Blo04g00584 584
13 26200860 26206939 - BLOR05777 Blo13g00496 496
15 5442123 5451204 + BLOR06781 Blo15g00387 387
3 5093699 5097037 + Bma016908.2 Bma03g00617 617
8 38513192 38514942 - Bma027915.1 Bma08g00610 610
5 16323894 16342997 + Bpe025807 Bpe05g00300 300
7 13666020 13677343 - Bpe021554.2 Bpe07g00709 709
12 931133 934700 + Bpe005370.1 Bpe12g00130 130
15 18220010 18222444 + Bpe001727.1 Bpe15g00801 801
15 18223397 18226734 - Bpe001728.1 Bpe15g00802 802
2 4880163 4884732 - CaPI482276_02g004140.1 Cam02g0414 414
2 24891297 24907221 + CaPI482276_02g012630.1 Cam02g1263 1263
19 7271788 7276588 + Carg25758-RA Car19g00587 587
20 3577102 3586044 - Carg16158-RA Car20g00638 638
2 3887427 3892070 - CcPI632755_02g004310.1 Cco02g0431 431
2 24879407 24895164 + CcPI632755_02g013110.1 Cco02g1311 1311
2 3913712 3918293 - CePI673135_02g004130.1 Cec02g0413 413
2 29398874 29414705 + CePI673135_02g012740.1 Cec02g1274 1274
1 4756116 4761736 - Chy1G006620.1 Chy01g00662 662
11 2249413 2264768 - Chy11G188190.1 Chy11g00239 239
2 3755720 3760284 - ClG42_02g0041700.10 Clacu02g0417 417
2 25054663 25072844 + ClG42_02g0124600.10 Clacu02g1246 1246
2 3993271 3998850 - ClCG02G003920.1 Cla02g00408 408
2 25360426 25379775 + ClCG02G012090.2 Cla02g01185 1185
2 1245631 1258855 + CmaCh02G002730.1 Cma02g00273 273
11 9035952 9039597 + CmaCh11G013630.1 Cma11g01363 1363
11 9040663 9045436 - CmaCh11G013650.1 Cma11g01365 1365
19 7482281 7487337 + CmaCh19G007520.1 Cma19g00752 752
20 3437365 3448557 - CmaCh20G007360.1 Cma20g00736 736
1 15746545 15753046 - MELO3C013334.2.1 Cme01g01238 1238
11 3682281 3699745 - MELO3C020836.2.1 Cme11g00361 361
10 10822453 10823833 - PI0022850.1 Cmetu10g1323 1323
11 16855620 16863901 - PI0012360.1 Cmetu11g1933 1933
2 1300145 1313173 + CmoCh02G002700.1 Cmo02g00270 270
11 12355259 12361036 + CmoCh11G017530.1 Cmo11g01753 1753
11 12361720 12365173 - CmoCh11G017540.1 Cmo11g01754 1754
19 7744068 7748734 + CmoCh19G007650.1 Cmo19g00765 765
20 3645146 3661687 - CmoCh20G007330.1 Cmo20g00733 733
2 3751636 3756200 - CmPI595203_02g004130.1 Cmu02g0413 413
2 24922098 24939383 + CmPI595203_02g012120.1 Cmu02g1212 1212
3 28068993 28133280 - Conep03aG0146600.1 Cone3ag0971 971
10 8552019 8572245 - Conep10aG0121000.1 Cone10ag1175 1175
12 9617835 9621752 + Conep12aG0128500.1 Cone12ag1245 1245
4 6326037 6331251 + Cp4.1LG04g04880.1 Cpe04g00605 605
4 6332209 6336080 - Cp4.1LG04g04800.1 Cpe04g00606 606
5 9558996 9571235 - Cp4.1LG05g13680.1 Cpe05g01359 1359
15 6781831 6786379 + Cp4.1LG15g06070.1 Cpe15g00607 607
16 5120999 5132298 + Cp4.1LG16g03290.1 Cpe16g00330 330
2 4323333 4327907 - CrPI670011_02g007480.1 Cre02g0748 748
2 27559549 27575489 + CrPI670011_02g015270.1 Cre02g1527 1527
2 13456976 13473630 + CsaV3_2G016250.1 Csa02g01409 1409
7 1064569 1071345 + CsaV3_7G001210.1 Csa07g00121 121
10 7271485 7287975 + Lsi10G005100.1 Lsi10g00510 510
11 20747670 20753340 + Lsi11G012170.1 Lsi11g01217 1217
1 4569761 4573202 + Sed0023624.1 Sed01g0634 634
5 35199328 35205468 + Sed0017188.2 Sed05g2251 2251
2 6041062 6047178 - Tan0020840.2 Tan02g0657 657
5 8950805 8954471 + Tan0020231.1 Tan05g1059 1059
3 1917759 1921426 + Vvi3g196 Vvi3g196 196
3 1929875 1930536 + Vvi3g197 Vvi3g197 197
3 1933535 1941032 + Vvi3g198 Vvi3g198 198
3 1941770 1946893 - Vvi3g199 Vvi3g199 199
3 1949394 1949676 + Vvi3g200 Vvi3g200 200
3 1949694 1949805 + Vvi3g201 Vvi3g201 201
3 1950824 1954840 - Vvi3g202 Vvi3g202 202
3 1964775 1967268 - Vvi3g203 Vvi3g203 203
3 1967317 1978417 + Vvi3g204 Vvi3g204 204
3 1980617 2018018 + Vvi3g205 Vvi3g205 205
       

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