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
Vvi3g206 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda15g01023 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g207 . . Bda06g00472 . . . . Bma12g00914 . . Cma02g00274 . . . . . . . . . . . . . . . . . . . . . . . . . . Chy11g00238 . . . . . . . . . . Cmo02g00271 . . . . . . Cpe05g01358 . . . . . . . Cla02g01186 Cam02g1264 Cec02g1275 Cco02g1312 Clacu02g1247 Cmu02g1213 Cre02g1528 . Csa02g01410 . Cme11g00360
Vvi3g208 . . . . . Bpe12g00131 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo13g00495 Bda15g01022 . . . . Bma08g00609 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g209 . . . . . . . . . . Cma02g00277 . Car02g00160 . . . . . . . . . . . . . . . . . . . . . . Lsi10g00807 . . . . . . . . . . . . Cmo02g00273 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g210 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g211 . . . . . Bpe12g00132 . . Cmo19g00768 . . . . Car20g00636 . . Cpe15g00610 Bhi05g01676 Tan02g0650 . . Hepe02g0405 . . Cla02g00405 Cam02g0410 Cec02g0410 Cco02g0427 Clacu02g0413 Cmu02g0409 Cre02g0744 Cone12ag1249 . . . . Csa07g00124 . Cme01g01232 Blo04g00585 Blo13g00494 Bda15g01021 Bda14g00627 Bpe15g00800 . . . . . . . Cma19g00755 . Car19g00589 Cpe16g00333 Cpe05g01357 . . . . . . . Cla02g01087 Cam02g1163 Cec02g1162 Cco02g1210 Clacu02g1155 Cmu02g1117 Cre02g1420 Lsi11g01219 . Chy01g00659 .
Vvi3g212 . Blo15g00392 Bda06g00470 . Bpe07g00706 . . . Cmo19g00770 . . . . . Sed04g3828 . Cpe15g00612 Bhi05g01673 Tan02g0645 Cmetu01g0918 . Hepe02g0403 . . . . . . . . . . . Cone3ag0974 . . Csa07g00126 . Cme01g01222 . . . . . . . . . . . . Cma19g00757 . Car19g00591 . . . . . . . . . . . . . . . . Lsi11g01221 . Chy01g00657 .
Vvi3g213 . . . . . . . . . Cmo11g01756 . . . . . . . Bhi05g01672 . . . Hepe02g0402 . . Cla02g00403 . . . . . . . Cone8ag1304 . . . Csa07g00127 . . . . . . Bpe15g00799 . Bma03g00618 . . . . Cma11g01362 . Car11g01386 . . . . . . . . . . . . . . . . . Lsi11g01222 . Chy01g00656 .
Vvi3g214 . Blo15g00393 Bda06g00469 . Bpe07g00705 . . Bma12g00911 . . . Cma20g00733 . Car20g00635 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo20g00731 . . . . Cpe16g00334 . . . . . . . . . . . . . . . . . . .
Vvi3g215 . . . . . Bpe12g00133 . . . . . . . . Sed04g3826 Cpe04g00609 . Bhi05g01671 Tan02g0643 Cmetu01g0717 . Hepe02g0401 . . Cla02g00402 Cam02g0407 Cec02g0407 Cco02g0423 Clacu02g0410 Cmu02g0406 Cre02g0741 . . . . . Csa07g00128 . Cme01g01220 . Blo13g00493 . . . . . Bma08g00743 . . . Cma11g01361 . Car11g01387 . . . . . . . . . . . . . . . . . Lsi11g01223 . Chy01g00655 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 6729358 6730961 - Bda033760 Bda06g00469 469
6 6732201 6737362 + Bda023715.1 Bda06g00470 470
6 6746718 6748473 + Bda023717.1 Bda06g00472 472
14 4703263 4706735 + Bda027382.1 Bda14g00627 627
15 19181314 19186163 - Bda013003.1 Bda15g01021 1021
15 19188871 19191070 + Bda013004.1 Bda15g01022 1022
15 19192771 19194195 + Bda013005.1 Bda15g01023 1023
5 54778478 54815535 + XM_039031287.1 Bhi05g01671 1671
5 54840366 54842819 + XM_039031018.1 Bhi05g01672 1672
5 54847418 54854114 + XM_039032059.1 Bhi05g01673 1673
5 54862136 54880244 - XM_039031059.1 Bhi05g01676 1676
4 5044421 5047170 + BLOR13497 Blo04g00585 585
13 26157602 26172845 + BLOR05774 Blo13g00493 493
13 26172997 26181090 - BLOR05775 Blo13g00494 494
13 26193250 26195661 + BLOR05776 Blo13g00495 495
15 5492854 5498835 - BLOR06786 Blo15g00392 392
15 5503577 5505177 + BLOR06787 Blo15g00393 393
3 5108235 5109995 - Bma016909.1 Bma03g00618 618
8 38506790 38509102 + Bma027914.1 Bma08g00609 609
8 43730906 43748605 + Bma028114.2 Bma08g00743 743
12 40548584 40550191 - Bma030516 Bma12g00911 911
12 40579416 40581104 + Bma008244.1 Bma12g00914 914
7 13650137 13651741 - Bpe026075 Bpe07g00705 705
7 13652201 13656213 + Bpe021551.1 Bpe07g00706 706
12 939616 941814 - Bpe005371.1 Bpe12g00131 131
12 943580 947102 + Bpe005372.1 Bpe12g00132 132
12 950063 971194 - Bpe005373.1 Bpe12g00133 133
15 18206584 18208344 + Bpe024581 Bpe15g00799 799
15 18215366 18217556 - Bpe001726.1 Bpe15g00800 800
2 4804093 4818189 + CaPI482276_02g004070.1 Cam02g0407 407
2 4843775 4856210 - CaPI482276_02g004100.1 Cam02g0410 410
2 22799506 22803177 + CaPI482276_02g011630.1 Cam02g1163 1163
2 24909184 24912508 - CaPI482276_02g012640.1 Cam02g1264 1264
2 944634 946816 + Carg19749-RA Car02g00160 160
11 11333029 11336935 - Carg26375-RA Car11g01386 1386
11 11339920 11352778 - Carg26374-RA Car11g01387 1387
19 7287377 7294998 + Carg25756-RA Car19g00589 589
19 7300406 7307587 - Carg25754-RA Car19g00591 591
20 3557088 3558923 - Carg16155-RA Car20g00635 635
20 3561224 3563998 - Carg16156-RA Car20g00636 636
2 3811259 3825315 + CcPI632755_02g004230.1 Cco02g0423 423
2 3851050 3863876 - CcPI632755_02g004270.1 Cco02g0427 427
2 22532240 22535920 + CcPI632755_02g012100.1 Cco02g1210 1210
2 24897184 24900549 - CcPI632755_02g013120.1 Cco02g1312 1312
2 3837935 3852025 + CePI673135_02g004070.1 Cec02g0407 407
2 3876371 3889891 - CePI673135_02g004100.1 Cec02g0410 410
2 27184466 27188151 + CePI673135_02g011620.1 Cec02g1162 1162
2 29416653 29419957 - CePI673135_02g012750.1 Cec02g1275 1275
1 4665913 4679343 + Chy1G006550.1 Chy01g00655 655
1 4684178 4686202 + Chy1G006560.1 Chy01g00656 656
1 4689989 4702856 + Chy1G006570.1 Chy01g00657 657
1 4714323 4723685 - Chy1G006590.1 Chy01g00659 659
11 2245817 2246896 + Chy11G188180.1 Chy11g00238 238
2 3679961 3694059 + ClG42_02g0041000.10 Clacu02g0410 410
2 3718418 3732028 - ClG42_02g0041300.10 Clacu02g0413 413
2 22905831 22909499 + ClG42_02g0115500.10 Clacu02g1155 1155
2 25074842 25075909 - ClG42_02g0124700.10 Clacu02g1247 1247
2 3914672 3928181 + ClCG02G003850.1 Cla02g00402 402
2 3932167 3942493 + ClCG02G003860.2 Cla02g00403 403
2 3953219 3970065 - ClCG02G003890.1 Cla02g00405 405
2 23045211 23048408 + ClCG02G011130.2 Cla02g01087 1087
2 25378829 25384467 - ClCG02G012100.2 Cla02g01186 1186
2 1258470 1260963 - CmaCh02G002740.1 Cma02g00274 274
2 1273709 1278027 + CmaCh02G002770.1 Cma02g00277 277
11 9012553 9027521 + CmaCh11G013610.1 Cma11g01361 1361
11 9028796 9034133 + CmaCh11G013620.1 Cma11g01362 1362
19 7499544 7505890 + CmaCh19G007550.1 Cma19g00755 755
19 7510639 7517338 - CmaCh19G007570.1 Cma19g00757 757
20 3410373 3421746 - CmaCh20G007330.1 Cma20g00733 733
1 15422168 15448297 + MELO3C013324.2.1 Cme01g01220 1220
1 15464393 15471111 + MELO3C013326.2.1 Cme01g01222 1222
1 15703103 15713279 - MELO3C013331.2.1 Cme01g01232 1232
11 3679460 3681344 + MELO3C020837.2.1 Cme11g00360 360
1 4999417 5022141 + PI0021938.1 Cmetu01g0717 717
1 5031783 5040201 + PI0015362.1 Cmetu01g0918 918
2 1314715 1315884 - CmoCh02G002710.1 Cmo02g00271 271
2 1327367 1329547 + CmoCh02G002730.1 Cmo02g00273 273
11 12370123 12372276 - CmoCh11G017560.1 Cmo11g01756 1756
19 7764196 7771236 + CmoCh19G007680.1 Cmo19g00768 768
19 7777696 7783119 - CmoCh19G007700.1 Cmo19g00770 770
20 3623481 3630422 - CmoCh20G007310.1 Cmo20g00731 731
2 3675934 3690032 + CmPI595203_02g004060.1 Cmu02g0406 406
2 3714433 3728064 - CmPI595203_02g004090.1 Cmu02g0409 409
2 22769716 22773384 + CmPI595203_02g011170.1 Cmu02g1117 1117
2 24941382 24942449 - CmPI595203_02g012130.1 Cmu02g1213 1213
3 28363689 28365160 - Conep03aG0146900.1 Cone3ag0974 974
8 10639320 10641032 - Conep08aG0134200.1 Cone8ag1304 1304
12 9632580 9636268 + Conep12aG0128900.1 Cone12ag1249 1249
4 6344103 6358830 - Cp4.1LG04g04750.1 Cpe04g00609 609
5 9548825 9553909 - Cp4.1LG05g13560.1 Cpe05g01357 1357
5 9555923 9558505 + Cp4.1LG05g13460.1 Cpe05g01358 1358
15 6797626 6805192 + Cp4.1LG15g06060.1 Cpe15g00610 610
15 6810584 6817523 - Cp4.1LG15g06120.1 Cpe15g00612 612
16 5146556 5150168 + Cp4.1LG16g03370.1 Cpe16g00333 333
16 5151727 5157233 + Cp4.1LG16g03300.1 Cpe16g00334 334
2 4247265 4261435 + CrPI670011_02g007410.1 Cre02g0741 741
2 4286039 4299786 - CrPI670011_02g007440.1 Cre02g0744 744
2 24770622 24774336 + CrPI670011_02g014200.1 Cre02g1420 1420
2 27577512 27580751 - CrPI670011_02g015280.1 Cre02g1528 1528
2 13474343 13476352 - CsaV3_2G016260.1 Csa02g01410 1410
7 1090953 1101853 + CsaV3_7G001240.1 Csa07g00124 124
7 1110579 1119324 - CsaV3_7G001260.1 Csa07g00126 126
7 1123383 1126614 - CsaV3_7G001270.1 Csa07g00127 127
7 1127537 1141655 + CsaV3_7G001280.1 Csa07g00128 128
2 3836438 3847228 + Hsped.02g04010.1 Hepe02g0401 401
2 3847853 3850234 + Hsped.02g04020.1 Hepe02g0402 402
2 3852977 3858116 + Hsped.02g04030.1 Hepe02g0403 403
2 3864064 3875978 - Hsped.02g04050.1 Hepe02g0405 405
10 11015688 11017477 - Lsi10G008070.1 Lsi10g00807 807
11 20777835 20790633 + Lsi11G012190.1 Lsi11g01219 1219
11 20800263 20807055 - Lsi11G012210.1 Lsi11g01221 1221
11 20810925 20812955 - Lsi11G012220.1 Lsi11g01222 1222
11 20816695 20833864 - Lsi11G012230.1 Lsi11g01223 1223
4 46718089 46732024 + Sed0017558.1 Sed04g3826 3826
4 46737176 46741951 + Sed0000019.1 Sed04g3828 3828
2 5919060 5936302 + Tan0020286.1 Tan02g0643 643
2 5947781 5952975 + Tan0022388.1 Tan02g0645 645
2 5982312 5994782 - Tan0012072.3 Tan02g0650 650
3 2018525 2021184 - Vvi3g206 Vvi3g206 206
3 2022218 2031739 - Vvi3g207 Vvi3g207 207
3 2034766 2037175 - Vvi3g208 Vvi3g208 208
3 2042273 2050248 - Vvi3g209 Vvi3g209 209
3 2054487 2055821 - Vvi3g210 Vvi3g210 210
3 2060586 2066331 + Vvi3g211 Vvi3g211 211
3 2066433 2081541 - Vvi3g212 Vvi3g212 212
3 2084982 2086497 - Vvi3g213 Vvi3g213 213
3 2088699 2090248 + Vvi3g214 Vvi3g214 214
3 2090778 2108596 - Vvi3g215 Vvi3g215 215
       

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