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
Vvi3g106 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g107 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g108 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g109 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g110 . . . Bda08g01041 . . Bma05g00412 . . . Cma02g00330 Cma20g00770 Car02g00210 Car20g00673 . . . . . . . . . . . . . . . . . . . . Cone10ag1184 Lsi10g00462 . Chy11g00296 . . . . . . . . . . Cmo02g00325 Cmo20g00770 . . . . Cpe16g00296 . Bhi10g01892 . . . Hepe08g0946 . . Cla02g01114 Cam02g1187 . . Clacu02g1177 Cmu02g1137 . . Csa02g01353 . Cme11g00418
Vvi3g111 . . Bda06g00968 . Bpe07g00490 . Bma05g00413 . . . Cma02g00329 . . . . . . . . . . . . . . . . . . . . Cone12ag1212 Cone8ag1264 . . Lsi10g00463 . Chy11g00295 . . . . . . . . . Sed01g0221 . . . . . . . Cpe05g01310 Bhi10g01891 Tan05g1191 Cmetu11g1417 . Hepe08g0945 . . Cla02g01113 Cam02g1185 . . Clacu02g1175 Cmu02g1136 . . Csa02g01354 . .
Vvi3g112 . Blo15g00654 Bda06g00967 . Bpe07g00488 . . . . . Cma02g00328 Cma20g00769 Car02g00209 Car20g00672 . . . . . . . . . . . . . . . . . . . . . . . Chy11g00294 . . . . . . . . . . Cmo02g00323 Cmo20g00769 . . . . Cpe16g00297 Cpe05g01311 Bhi10g01890 . . . Hepe08g0944 . . Cla02g01112 Cam02g1184 . . Clacu02g1174 Cmu02g1135 . . Csa02g01355 . Cme11g00416
Vvi3g113 . . . . Bpe07g00487 . Bma05g00414 . Cmo19g00733 . Cma02g00327 . Car02g00208 . Sed05g2236 Cpe04g00576 Cpe15g00579 Bhi05g01745 Tan02g0712 Cmetu01g0699 . Hepe02g0443 . . . . . . . . . Cone12ag1213 Cone8ag1265 . Cone10ag1183 Lsi10g00464 Csa07g00080 Chy11g00293 Cme01g01284 . . . . . . . . Sed01g0219 Cmo02g00322 Cmo20g00768 Cma11g01395 Cma19g00724 . Car19g00553 Cpe16g00298 Cpe05g01312 Bhi10g01888 Tan05g1184 Cmetu11g1977 . Hepe08g0943 . . Cla02g01111 Cam02g1183 . . Clacu02g1173 Cmu02g1133 . . Csa02g01356 Chy01g00697 Cme11g00415
Vvi3g114 . . Bda06g00966 . Bpe07g00486 . . . . Cmo11g01725 Cma02g00326 Cma20g00768 Car02g00207 Car20g00671 Sed05g2235 Cpe04g00577 . Bhi05g01744 Tan02g0711 Cmetu01g1502 . . . . Cla02g00445 Cam02g0454 Cec02g0452 Cco02g0471 Clacu02g0455 Cmu02g0450 Cre02g0783 . Cone8ag1266 . . . . Chy11g00292 Cme01g01283 Blo04g00553 . . Bda14g00602 . . Bma03g00593 . Sed05g3586 Cmo02g00321 Cmo20g00767 Cma11g01394 . . . . . Bhi10g01887 Tan05g1183 Cmetu11g2155 . Hepe08g0942 . . Cla02g01110 Cam02g1182 . . Clacu02g1172 Cmu02g1132 . Lsi11g01181 . Chy01g00696 Cme11g00414
Vvi3g115 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 27805492 27806944 - Bda022617.2 Bda06g00966 966
6 27930412 27936711 - Bda022619.1 Bda06g00967 967
6 28070388 28072976 - Bda022620.1 Bda06g00968 968
8 21865316 21868618 + Bda029735.1 Bda08g01041 1041
14 4553243 4554866 + Bda027356.1 Bda14g00602 602
5 56026685 56028991 - XM_039032637.1 Bhi05g01744 1744
5 56031528 56035461 - XM_039030920.1 Bhi05g01745 1745
10 47412822 47415493 - XM_039046332.1 Bhi10g01887 1887
10 47422793 47428862 - XM_039046599.1 Bhi10g01888 1888
10 47438225 47445611 - XM_039046852.1 Bhi10g01890 1890
10 47505098 47508860 + XM_039046607.1 Bhi10g01891 1891
10 47510652 47516139 + XM_039046705.1 Bhi10g01892 1892
4 4774231 4778809 + BLOR13465 Blo04g00553 553
15 18467517 18472712 + BLOR07048 Blo15g00654 654
3 4928546 4929715 + Bma016884.1 Bma03g00593 593
5 12956621 12961765 - Bma021247.1 Bma05g00412 412
5 12971497 12973778 - Bma021251.1 Bma05g00413 413
5 12989431 12992468 + Bma021252.1 Bma05g00414 414
7 8943556 8944998 - Bpe021325.2 Bpe07g00486 486
7 9087165 9090433 - Bpe021328.1 Bpe07g00487 487
7 9136507 9142953 - Bpe021329.1 Bpe07g00488 488
7 9238445 9239373 + Bpe021332.1 Bpe07g00490 490
2 5241390 5243549 - CaPI482276_02g004540.1 Cam02g0454 454
2 23515174 23518034 - CaPI482276_02g011820.1 Cam02g1182 1182
2 23525697 23531080 - CaPI482276_02g011830.1 Cam02g1183 1183
2 23584637 23587711 - CaPI482276_02g011840.1 Cam02g1184 1184
2 23593294 23595709 + CaPI482276_02g011850.1 Cam02g1185 1185
2 23599574 23604046 + CaPI482276_02g011870.1 Cam02g1187 1187
2 1264862 1266508 - Carg19797-RA Car02g00207 207
2 1269585 1274019 - Carg19798-RA Car02g00208 208
2 1274940 1278704 - Carg19799-RA Car02g00209 209
2 1283173 1287963 + Carg19800-RA Car02g00210 210
19 7084462 7088739 + Carg19366-RA Car19g00553 553
20 3773304 3775188 - Carg16191-RA Car20g00671 671
20 3783186 3787885 - Carg16193-RA Car20g00672 672
20 3791703 3795969 + Carg16194-RA Car20g00673 673
2 4253721 4255824 - CcPI632755_02g004710.1 Cco02g0471 471
2 4263679 4265779 - CePI673135_02g004520.1 Cec02g0452 452
1 5088003 5093351 - Chy1G006960.1 Chy01g00696 696
1 5096833 5100408 - Chy1G006970.1 Chy01g00697 697
11 2692573 2694878 - Chy11G188720.1 Chy11g00292 292
11 2703805 2712942 - Chy11G188730.1 Chy11g00293 293
11 2713417 2715864 - Chy11G188740.1 Chy11g00294 294
11 2718166 2720680 + Chy11G188750.1 Chy11g00295 295
11 2722978 2726950 + Chy11G188760.1 Chy11g00296 296
2 4124283 4126255 - ClG42_02g0045500.10 Clacu02g0455 455
2 23598363 23601418 - ClG42_02g0117200.10 Clacu02g1172 1172
2 23606586 23611983 - ClG42_02g0117300.10 Clacu02g1173 1173
2 23654229 23657274 - ClG42_02g0117400.10 Clacu02g1174 1174
2 23659796 23666550 + ClG42_02g0117500.10 Clacu02g1175 1175
2 23670267 23674569 + ClG42_02g0117700.10 Clacu02g1177 1177
2 4377667 4381722 - ClCG02G004300.1 Cla02g00445 445
2 23828370 23831232 - ClCG02G011360.1 Cla02g01110 1110
2 23836841 23845203 - ClCG02G011370.1 Cla02g01111 1111
2 23889304 23892769 - ClCG02G011380.2 Cla02g01112 1112
2 23899468 23902878 + ClCG02G011390.2 Cla02g01113 1113
2 23905549 23910711 + ClCG02G011400.2 Cla02g01114 1114
2 1595670 1598026 - CmaCh02G003260.1 Cma02g00326 326
2 1600581 1605134 - CmaCh02G003270.1 Cma02g00327 327
2 1612441 1615914 - CmaCh02G003280.1 Cma02g00328 328
2 1617043 1620855 + CmaCh02G003290.1 Cma02g00329 329
2 1622263 1629480 + CmaCh02G003300.1 Cma02g00330 330
11 9184837 9186165 - CmaCh11G013940.1 Cma11g01394 1394
11 9188254 9191769 - CmaCh11G013950.1 Cma11g01395 1395
19 7317818 7321480 + CmaCh19G007240.1 Cma19g00724 724
20 3624920 3626990 - CmaCh20G007680.1 Cma20g00768 768
20 3631085 3641104 - CmaCh20G007690.1 Cma20g00769 769
20 3644974 3651783 + CmaCh20G007700.1 Cma20g00770 770
1 16186555 16188766 - MELO3C013376.2.1 Cme01g01283 1283
1 16190681 16194912 - MELO3C013377.2.1 Cme01g01284 1284
11 4170472 4172799 - MELO3C020785.2.1 Cme11g00414 414
11 4181330 4187377 - MELO3C020784.2.1 Cme11g00415 415
11 4195342 4199171 - MELO3C020783.2.1 Cme11g00416 416
11 4217604 4222147 + MELO3C020780.2.1 Cme11g00418 418
1 5412617 5416875 - PI0011537.1 Cmetu01g0699 699
1 5408775 5410573 - PI0025510.1 Cmetu01g1502 1502
11 28240320 28242916 - PI0004209.1 Cmetu11g1417 1417
11 28251460 28257510 + PI0010490.1 Cmetu11g1977 1977
11 28268951 28272346 + PI0006267.1 Cmetu11g2155 2155
2 1661008 1663158 - CmoCh02G003210.1 Cmo02g00321 321
2 1666151 1670547 - CmoCh02G003220.1 Cmo02g00322 322
2 1671507 1675157 - CmoCh02G003230.1 Cmo02g00323 323
2 1679683 1682437 + CmoCh02G003250.1 Cmo02g00325 325
11 12208598 12215000 + CmoCh11G017250.1 Cmo11g01725 1725
19 7573592 7576901 + CmoCh19G007330.1 Cmo19g00733 733
20 3844358 3846514 - CmoCh20G007670.1 Cmo20g00767 767
20 3848129 3853146 - CmoCh20G007680.1 Cmo20g00768 768
20 3855174 3859841 - CmoCh20G007690.1 Cmo20g00769 769
20 3863703 3867895 + CmoCh20G007700.1 Cmo20g00770 770
2 4120327 4122307 - CmPI595203_02g004500.1 Cmu02g0450 450
2 23459220 23462076 - CmPI595203_02g011320.1 Cmu02g1132 1132
2 23467225 23474426 - CmPI595203_02g011330.1 Cmu02g1133 1133
2 23518660 23521705 - CmPI595203_02g011350.1 Cmu02g1135 1135
2 23524227 23530980 + CmPI595203_02g011360.1 Cmu02g1136 1136
2 23534697 23539009 + CmPI595203_02g011370.1 Cmu02g1137 1137
8 10483506 10485355 - Conep08aG0130200.1 Cone8ag1264 1264
8 10485503 10488432 + Conep08aG0130300.1 Cone8ag1265 1265
8 10490141 10492323 + Conep08aG0130400.1 Cone8ag1266 1266
10 8707639 8713187 + Conep10aG0121800.1 Cone10ag1183 1183
10 8730528 8739045 + Conep10aG0121900.1 Cone10ag1184 1184
12 9455206 9457085 - Conep12aG0125200.1 Cone12ag1212 1212
12 9457242 9460141 + Conep12aG0125300.1 Cone12ag1213 1213
4 6177845 6181800 + Cp4.1LG04g05020.1 Cpe04g00576 576
4 6182973 6184895 + Cp4.1LG04g04950.1 Cpe04g00577 577
5 9192641 9205287 - Cp4.1LG05g13170.1 Cpe05g01310 1310
5 9206063 9209484 + Cp4.1LG05g13090.1 Cpe05g01311 1311
5 9210441 9214943 + Cp4.1LG05g13080.1 Cpe05g01312 1312
15 6614616 6618445 + Cp4.1LG15g05750.1 Cpe15g00579 579
16 4919574 4923774 - Cp4.1LG16g03110.1 Cpe16g00296 296
16 4928195 4933019 + Cp4.1LG16g03010.1 Cpe16g00297 297
16 4933922 4937878 + Cp4.1LG16g03000.1 Cpe16g00298 298
2 4684445 4686385 - CrPI670011_02g007830.1 Cre02g0783 783
2 13012940 13017083 - CsaV3_2G015690.1 Csa02g01353 1353
2 13017831 13023291 - CsaV3_2G015700.1 Csa02g01354 1354
2 13025252 13029711 + CsaV3_2G015710.1 Csa02g01355 1355
2 13031414 13036664 + CsaV3_2G015720.1 Csa02g01356 1356
7 773131 778233 + CsaV3_7G000800.1 Csa07g00080 80
2 4267935 4275787 - Hsped.02g04430.1 Hepe02g0443 443
8 8730783 8733453 - Hsped.08g09420.1 Hepe08g0942 942
8 8737970 8743670 - Hsped.08g09430.1 Hepe08g0943 943
8 8746291 8749862 - Hsped.08g09440.1 Hepe08g0944 944
8 8751741 8755540 + Hsped.08g09450.1 Hepe08g0945 945
8 8758261 8761686 + Hsped.08g09460.1 Hepe08g0946 946
10 6704726 6710168 - Lsi10G004620.1 Lsi10g00462 462
10 6712227 6715789 - Lsi10G004630.1 Lsi10g00463 463
10 6718804 6731088 + Lsi10G004640.1 Lsi10g00464 464
11 20293345 20302048 + Lsi11G011810.1 Lsi11g01181 1181
1 1756221 1760271 - Sed0009057.1 Sed01g0219 219
1 1761469 1766515 + Sed0015022.2 Sed01g0221 221
5 35067513 35069568 - Sed0022693.1 Sed05g2235 2235
5 35071868 35077506 - Sed0028085.1 Sed05g2236 2236
5 44338540 44341826 + Sed0012527.1 Sed05g3586 3586
2 6634881 6636425 - Tan0005396.1 Tan02g0711 711
2 6638004 6642056 - Tan0014653.1 Tan02g0712 712
5 11632965 11635065 - Tan0001122.1 Tan05g1183 1183
5 11677268 11683186 - Tan0016745.1 Tan05g1184 1184
5 11789296 11797171 - Tan0014788.1 Tan05g1191 1191
3 1215575 1222056 - Vvi3g106 Vvi3g106 106
3 1222323 1226936 - Vvi3g107 Vvi3g107 107
3 1231024 1235642 - Vvi3g108 Vvi3g108 108
3 1235712 1237448 + Vvi3g109 Vvi3g109 109
3 1237993 1248575 - Vvi3g110 Vvi3g110 110
3 1252096 1255340 - Vvi3g111 Vvi3g111 111
3 1263033 1274247 + Vvi3g112 Vvi3g112 112
3 1274978 1279253 + Vvi3g113 Vvi3g113 113
3 1283244 1285209 + Vvi3g114 Vvi3g114 114
3 1286454 1288521 + Vvi3g115 Vvi3g115 115
       

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