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
Vvi3g806 . . . . . . . . . . . . . . . . . . . . . . . . Cla10g00948 Cam10g0971 . Cco10g0965 Clacu10g0993 Cmu10g1776 Cre10g1150 . . . . . . . . . . . . . . . . Sed07g1156 Cmo04g00452 . . . . . . Cpe01g00379 Bhi11g01090 Tan01g0593 Cmetu07g0703 . . Mch10g0398 . . . . . . . . Lsi03g00996 . . Cme07g02222
Vvi3g807 . . . . . . Bma05g00633 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe05g00456 . . . . Cmo16g00314 . . . . Cpe14g00245 . . . . . . . . . . . . . . . . . . .
Vvi3g808 . . . . . Bpe12g00729 . . Cmo19g00531 Cmo11g01435 . . . . Sed14g0958 Cpe04g00340 Cpe15g00414 Bhi05g00998 Tan02g1073 Cmetu10g0686 Lac12g0133 Hepe02g0670 . . Cla02g00720 Cam02g0766 Cec02g0764 Cco02g0793 Clacu02g0762 Cmu02g0755 Cre02g1069 Cone12ag1020 Cone8ag1050 . . Lsi03g00637 Csa07g00655 . Cme01g00148 . . Bda15g00472 . . . . Bma08g00021 Sed07g1157 Cmo04g00451 . Cma11g01687 Cma19g00518 Car11g01153 Car19g00393 . Cpe01g00378 Bhi11g01089 Tan01g0592 Cmetu07g2246 . . Mch10g0397 . . . . . . . . . . Chy01g00157 Cme07g02223
Vvi3g809 . . . . . Bpe12g00728 . . Cmo19g00530 Cmo11g01436 . . . . Sed06g0826 Cpe04g00341 Cpe15g00413 Bhi05g00995 Tan02g1077 Cmetu01g2263 Lac12g0132 Hepe02g0671 . . Cla02g00721 Cam02g0768 Cec02g0765 Cco02g0796 Clacu02g0763 Cmu02g0756 Cre02g1070 . Cone8ag1049 . . Lsi03g00638 Csa07g00654 . Cme01g00149 . Blo13g00274 Bda15g00473 . . . . Bma08g00022 . . . Cma11g01686 Cma19g00517 Car11g01154 Car19g00392 . . . . . . . . . . . . . . . . . . Chy01g00158 .
Vvi3g810 Blo02g00911 . . . . . Bma05g00632 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo16g00313 . . . . Cpe14g00244 . . . . . . . . . . . . . . . . . . .
Vvi3g811 . Blo03g00048 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed07g1158 . Cmo16g00312 . . . . . . Bhi11g01088 Tan01g0587 Cmetu07g0545 . . . . . . . . . . . . . . .
Vvi3g812 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g813 . . . . . . Bma05g00631 . . . . . . . . . . . . . . . . . Cla10g00945 Cam10g0968 Cec10g1002 Cco10g0963 Clacu10g0990 Cmu10g1773 Cre10g1147 Cone12ag1018 Cone8ag1048 . . . . . . . Blo13g00238 . . . Bpe05g00455 . . . Cmo04g00449 . . . . . Cpe14g00243 Cpe01g00377 Bhi11g01087 . . . Hepe07g0382 Mch10g0394 . . . . . . . . Lsi03g00994 . . Cme07g02224
Vvi3g814 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g815 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1055 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
15 7899887 7903061 - Bda012302.1 Bda15g00472 472
15 7908185 7915827 + Bda033300 Bda15g00473 473
5 35049814 35055275 - XM_039031770.1 Bhi05g00995 995
5 35267688 35274555 + XM_039032768.1 Bhi05g00998 998
11 31945334 31953352 - XM_039049018.1 Bhi11g01087 1087
11 31945360 31953352 - XM_039049017.1 Bhi11g01088 1088
11 32026762 32030476 + XM_039049964.1 Bhi11g01089 1089
11 32035500 32039943 + XM_039050410.1 Bhi11g01090 1090
2 35187054 35196335 + BLOR10641 Blo02g00911 911
3 1812038 1820179 - BLOR11229 Blo03g00048 48
13 10486996 10492903 + BLOR05519 Blo13g00238 238
13 13747496 13757970 + BLOR05555 Blo13g00274 274
5 37263759 37274898 - Bma021661.2 Bma05g00631 631
5 37281524 37282771 + Bma021662.1 Bma05g00632 632
5 37283882 37286949 + Bma021663.1 Bma05g00633 633
8 393153 397963 - Bma027013.1 Bma08g00021 21
8 403065 411375 + Bma027014.1 Bma08g00022 22
5 18907434 18912968 - Bpe017874.2 Bpe05g00455 455
5 18920076 18923118 + Bpe017875.1 Bpe05g00456 456
12 12789496 12794247 - Bpe005989.1 Bpe12g00728 728
12 12797646 12801220 + Bpe005990.1 Bpe12g00729 729
2 9280934 9287263 - CaPI482276_02g007660.1 Cam02g0766 766
2 9356365 9360996 + CaPI482276_02g007680.1 Cam02g0768 768
10 21758737 21765029 - CaPI482276_10g009680.1 Cam10g0968 968
10 21803790 21809256 + CaPI482276_10g009710.1 Cam10g0971 971
11 9263665 9269127 - Carg23047-RA Car11g01153 1153
11 9270980 9276504 + Carg23048-RA Car11g01154 1154
19 5728339 5734322 - Carg16313-RA Car19g00392 392
19 5744974 5748124 + Carg16314-RA Car19g00393 393
2 8617498 8621959 - CcPI632755_02g007930.1 Cco02g0793 793
2 8720654 8725293 + CcPI632755_02g007960.1 Cco02g0796 796
10 20931265 20942584 - CcPI632755_10g009630.1 Cco10g0963 963
10 20976336 20981651 + CcPI632755_10g009650.1 Cco10g0965 965
2 8516637 8521216 - CePI673135_02g007640.1 Cec02g0764 764
2 8593147 8597747 + CePI673135_02g007650.1 Cec02g0765 765
10 22646058 22652341 - CePI673135_10g010020.1 Cec10g1002 1002
1 1066218 1069711 - Chy1G001570.1 Chy01g00157 157
1 1081069 1085404 + Chy1G001580.1 Chy01g00158 158
2 8202003 8206543 - ClG42_02g0076200.10 Clacu02g0762 762
2 8282594 8287387 + ClG42_02g0076300.10 Clacu02g0763 763
10 21374491 21380788 - ClG42_10g0099000.10 Clacu10g0990 990
10 21438258 21443622 + ClG42_10g0099300.10 Clacu10g0993 993
2 8583138 8589268 - ClCG02G007360.1 Cla02g00720 720
2 8667795 8673330 + ClCG02G007370.1 Cla02g00721 721
10 22345680 22352700 - ClCG10G009860.1 Cla10g00945 945
10 22419328 22425551 + ClCG10G009880.2 Cla10g00948 948
11 11120800 11126884 - CmaCh11G016860.1 Cma11g01686 1686
11 11131659 11137821 + CmaCh11G016870.1 Cma11g01687 1687
19 6055358 6060919 - CmaCh19G005170.1 Cma19g00517 517
19 6069872 6085649 + CmaCh19G005180.1 Cma19g00518 518
1 1056003 1060570 - MELO3C018548.2.1 Cme01g00148 148
1 1072111 1077494 + MELO3C018549.2.1 Cme01g00149 149
7 26389969 26394471 - MELO3C018035.2.1 Cme07g02222 2222
7 26396244 26399716 - MELO3C018036.2.1 Cme07g02223 2223
7 26400998 26407952 + MELO3C018037.2.1 Cme07g02224 2224
1 1224395 1229728 + PI0028023.1 Cmetu01g2263 2263
7 182518 188172 - PI0023088.1 Cmetu07g0545 545
7 196770 200853 + PI0028680.1 Cmetu07g0703 703
7 191858 193125 + PI0021410.1 Cmetu07g2246 2246
10 12573809 12580452 - PI0026465.1 Cmetu10g0686 686
4 2232114 2242231 - CmoCh04G004490.1 Cmo04g00449 449
4 2245982 2247692 + CmoCh04G004510.1 Cmo04g00451 451
4 2249195 2254459 + CmoCh04G004520.1 Cmo04g00452 452
11 10104764 10110218 - CmoCh11G014350.1 Cmo11g01435 1435
11 10112274 10118042 + CmoCh11G014360.1 Cmo11g01436 1436
16 1429347 1436135 - CmoCh16G003120.1 Cmo16g00312 312
16 1438496 1440171 + CmoCh16G003130.1 Cmo16g00313 313
16 1440956 1444862 + CmoCh16G003140.1 Cmo16g00314 314
19 6184932 6190282 - CmoCh19G005300.1 Cmo19g00530 530
19 6203064 6210357 + CmoCh19G005310.1 Cmo19g00531 531
2 8110468 8115011 - CmPI595203_02g007550.1 Cmu02g0755 755
2 8191116 8195909 + CmPI595203_02g007560.1 Cmu02g0756 756
10 21982456 21988753 - CmPI595203_10g017730.1 Cmu10g1773 1773
10 22046255 22051622 + CmPI595203_10g017760.1 Cmu10g1776 1776
3 29283979 29287115 - Conep03aG0155600.1 Cone3ag1055 1055
8 9612075 9617448 - Conep08aG0107700.1 Cone8ag1048 1048
8 9618596 9622404 - Conep08aG0107800.1 Cone8ag1049 1049
8 9623717 9626729 + Conep08aG0107900.1 Cone8ag1050 1050
12 8572136 8575281 - Conep12aG0104700.1 Cone12ag1018 1018
12 8587309 8590263 + Conep12aG0104900.1 Cone12ag1020 1020
1 2177571 2183064 - Cp4.1LG01g02900.1 Cpe01g00377 377
1 2185955 2188127 + Cp4.1LG01g02980.1 Cpe01g00378 378
1 2189750 2193768 + Cp4.1LG01g02960.1 Cpe01g00379 379
4 4119368 4125029 - Cp4.1LG04g07440.1 Cpe04g00340 340
4 4126980 4133126 + Cp4.1LG04g07500.1 Cpe04g00341 341
14 1414224 1419873 - Cp4.1LG14g04730.1 Cpe14g00243 243
14 1422035 1424102 + Cp4.1LG14g04790.1 Cpe14g00244 244
14 1424841 1428422 + Cp4.1LG14g04800.1 Cpe14g00245 245
15 5279125 5284491 - Cp4.1LG15g04180.1 Cpe15g00413 413
15 5293125 5301010 + Cp4.1LG15g04050.1 Cpe15g00414 414
2 8753128 8757649 - CrPI670011_02g010690.1 Cre02g1069 1069
2 8824350 8828958 + CrPI670011_02g010700.1 Cre02g1070 1070
10 23680027 23686335 - CrPI670011_10g011470.1 Cre10g1147 1147
10 23723337 23728778 + CrPI670011_10g011500.1 Cre10g1150 1150
7 4693674 4699625 - CsaV3_7G007530.1 Csa07g00654 654
7 4707030 4712112 + CsaV3_7G007540.1 Csa07g00655 655
2 7349951 7356286 - Hsped.02g06700.1 Hepe02g0670 670
2 7377139 7382234 + Hsped.02g06710.1 Hepe02g0671 671
7 3866341 3871328 - Hsped.07g03820.1 Hepe07g0382 382
12 1458779 1463543 - Lag0014504.1 Lac12g0132 132
12 1488798 1493881 + Lag0014505.1 Lac12g0133 133
3 7885274 7892264 - Lsi03G006370.1 Lsi03g00637 637
3 7933581 7938911 + Lsi03G006380.1 Lsi03g00638 638
3 19164308 19173121 - Lsi03G009940.1 Lsi03g00994 994
3 19218273 19229016 + Lsi03G009960.1 Lsi03g00996 996
10 2619576 2625040 - MC10g0323 Mch10g0394 394
10 2631473 2634319 + MC10g0325 Mch10g0397 397
10 2635491 2640301 + MC10g0326 Mch10g0398 398
6 8935973 8942118 - Sed0019101.2 Sed06g0826 826
7 8660672 8666265 - Sed0019918.1 Sed07g1156 1156
7 8667725 8669224 - Sed0001844.1 Sed07g1157 1157
7 8675461 8681272 + Sed0028232.1 Sed07g1158 1158
14 18641948 18653428 + Sed0013685.6 Sed14g0958 958
1 5415311 5420774 - Tan0013458.1 Tan01g0587 587
1 5451234 5452658 + Tan0019849.1 Tan01g0592 592
1 5453632 5458692 + Tan0022846.1 Tan01g0593 593
2 17770489 17776967 - Tan0016368.1 Tan02g1073 1073
2 18122890 18128587 + Tan0009668.1 Tan02g1077 1077
3 9153203 9160193 - Vvi3g806 Vvi3g806 806
3 9160684 9162450 - Vvi3g807 Vvi3g807 807
3 9168262 9182594 - Vvi3g808 Vvi3g808 808
3 9215899 9223451 + Vvi3g809 Vvi3g809 809
3 9223729 9231652 - Vvi3g810 Vvi3g810 810
3 9274592 9285508 + Vvi3g811 Vvi3g811 811
3 9286347 9295982 - Vvi3g812 Vvi3g812 812
3 9296797 9310939 + Vvi3g813 Vvi3g813 813
3 9311014 9314129 - Vvi3g814 Vvi3g814 814
3 9341915 9347312 + Vvi3g815 Vvi3g815 815
       

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