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
Vvi5g419 . . . . . . . . . . Cma06g01440 . Car06g01242 . . Cpe08g00235 . Bhi01g00866 Tan10g0900 Cmetu09g0387 . Hepe05g1515 . Lcy11g1494 . . . . . . . Cone14ag0814 Cone15ag0812 . Cone4ag0199 Lsi05g01462 . . Cme06g00652 . . . . . . . . . Cmo06g01442 . . . . . . . . . . . . . . Cla05g00584 Cam05g0642 Cec05g0651 Cco05g0646 Clacu05g0636 Cmu05g0604 Cre05g0673 . Csa03g01379 Chy06g00621 .
Vvi5g420 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00556 . . Bpe13g00627 . Bma06g01535 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g421 . . . Bda08g00388 . . . Bma05g00941 Cmo08g01146 Cmo17g00264 . . . . . . . . . . . . . . Cla06g00539 Cam06g0580 Cec06g0577 Cco06g0585 Clacu06g0567 Cmu06g0561 Cre06g1329 Cone14ag0817 . . . . . Chy11g01437 . Blo02g00645 . . . Bpe05g00752 . . . . . . Cma08g01175 Cma17g00277 Car08g01052 Car17g00252 Cpe12g00230 Cpe17g00120 Bhi12g01790 . . . . . . . . . . . . . Lsi09g01363 . . Cme11g01942
Vvi5g422 . . . . Bpe04g01189 . . . . Cmo17g00263 . . . . . . . . . . . . . . Cla06g00540 . . . . . . . Cone15ag0813 . . . . Chy11g01436 . . . . . . . . . . . . . Cma17g00276 . Car17g00251 Cpe12g00229 . Bhi12g01792 . . . . . . . . . . . . . Lsi09g01362 . . .
Vvi5g423 . . . Bda08g00389 Bpe04g01190 . Bma04g01182 Bma05g00942 Cmo08g01145 Cmo17g00262 . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy11g01435 . . . . . Bpe05g00753 . . . . . . Cma08g01173 Cma17g00275 Car08g01050 Car17g00250 Cpe12g00228 Cpe17g00122 Bhi12g01794 . . . . . . . . . . . . . Lsi09g01361 . . Cme11g01941
Vvi5g424 . . . . . . . . . Cmo17g00261 . . . . . . . . . . . . . . Cla06g00542 Cam06g0584 Cec06g0581 Cco06g0589 Clacu06g0570 Cmu06g0564 Cre06g1332 . . Cone7ag0210 Cone4ag0200 . . Chy11g01434 . . Blo07g00203 Bda11g00557 . . Bpe13g00626 . Bma06g01536 . . . . Cma17g00274 . Car17g00249 Cpe12g00227 . Bhi12g01795 . . . . . . . . . . . . . . . . Cme11g01939
Vvi5g425 . . . Bda08g00390 Bpe04g01193 Bpe14g01325 Bma04g01184 Bma05g00943 Cmo08g01144 Cmo17g00260 . . . . . . . . . . . . . . Cla06g00543 Cam06g0586 Cec06g0583 Cco06g0591 Clacu06g0573 Cmu06g0567 Cre06g1333 Cone14ag0819 Cone15ag0815 . . . . Chy11g01433 . . . . . Bpe05g00754 . . . . . . Cma08g01171 Cma17g00273 Car08g01049 Car17g00248 Cpe12g00226 Cpe17g00123 Bhi12g01796 . . . . . . . . . . . . . Lsi09g01359 . . Cme11g01938
Vvi5g426 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g427 . . . . . Bpe14g01324 . . Cmo08g01143 Cmo17g00259 Cma06g01439 Cma14g01673 Car06g01241 Car14g01507 Sed02g1277 Cpe08g00236 Cpe03g01412 Bhi01g00864 Tan10g0896 Cmetu11g1902 Lac12g2331 . . Lcy11g1500 Cla06g00544 Cam06g0587 Cec06g0584 Cco06g0592 Clacu06g0574 Cmu06g0568 Cre06g1334 . . Cone7ag0211 Cone4ag0202 Lsi05g01461 . Chy11g01432 Cme06g00651 . Blo07g00204 . . . . . Bma06g01537 . Cmo06g01441 . Cma08g01170 Cma17g00272 Car08g01048 Car17g00247 Cpe12g00225 Cpe17g00124 Bhi12g01797 . . . . . . Cla05g00583 Cam05g0641 Cec05g0650 Cco05g0645 Clacu05g0635 Cmu05g0603 Cre05g0672 Lsi09g01358 Csa03g01377 Chy06g00620 Cme11g01937
Vvi5g428 . . . . . . . . . . Cma06g01438 Cma14g01674 Car06g01240 Car14g01508 Sed02g1276 Cpe08g00237 Cpe03g01413 Bhi01g00863 Tan10g0895 Cmetu06g0203 . Hepe05g1518 . Lcy11g1502 . . . . . . . . . Cone7ag0212 Cone4ag0203 Lsi05g01460 . . Cme06g00650 . Blo07g00205 Bda11g00558 . . Bpe13g00625 . . . Cmo06g01440 Cmo14g01719 . . . . . . . . . . . . . Cla05g00582 Cam05g0640 Cec05g0649 Cco05g0644 Clacu05g0634 Cmu05g0602 Cre05g0671 . Csa03g01376 Chy06g00619 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 4033259 4043788 + Bda024834.1 Bda08g00388 388
8 4050104 4050703 - Bda024835.1 Bda08g00389 389
8 4052612 4056789 - Bda024836.2 Bda08g00390 390
11 5776289 5778778 + Bda005293.1 Bda11g00556 556
11 5779397 5783781 - Bda005294.1 Bda11g00557 557
11 5799528 5803946 + Bda005295.1 Bda11g00558 558
1 16306103 16312069 - XM_039021782.1 Bhi01g00863 863
1 16337780 16339789 - XM_039043010.1 Bhi01g00864 864
1 16404939 16409129 + XM_039026366.1 Bhi01g00866 866
12 57415753 57427570 + XM_039020338.1 Bhi12g01790 1790
12 57427659 57429967 - XM_039020341.1 Bhi12g01792 1792
12 57434503 57438800 - XM_039020342.1 Bhi12g01794 1794
12 57441938 57447408 - XM_039050673.1 Bhi12g01795 1795
12 57478234 57483148 - XM_039019448.1 Bhi12g01796 1796
12 57596426 57599070 - XM_039019985.1 Bhi12g01797 1797
2 15195020 15198201 + BLOR10375 Blo02g00645 645
7 2527786 2530785 - BLOR18135 Blo07g00203 203
7 2583703 2584617 - BLOR18136 Blo07g00204 204
7 2599413 2603519 + BLOR18137 Blo07g00205 205
4 31505205 31505834 - Bma019924.1 Bma04g01182 1182
4 31673591 31679142 + Bma031135 Bma04g01184 1184
5 47436266 47443901 + Bma022077.1 Bma05g00941 941
5 47445954 47446553 - Bma022078.1 Bma05g00942 942
5 47454042 47464655 - Bma022079.1 Bma05g00943 943
6 51698405 51700731 + Bma024649.1 Bma06g01535 1535
6 51701097 51704086 - Bma024650.1 Bma06g01536 1536
6 51726041 51727024 - Bma024653.1 Bma06g01537 1537
4 14124143 14126236 - Bpe015887.1 Bpe04g01189 1189
4 14129524 14130153 - Bpe015888.1 Bpe04g01190 1190
4 14333948 14337790 - Bpe015891.1 Bpe04g01193 1193
5 20920877 20928538 + Bpe018166.1 Bpe05g00752 752
5 20930510 20931136 - Bpe025826 Bpe05g00753 753
5 20935978 20940053 - Bpe018167.1 Bpe05g00754 754
13 13198978 13202842 - Bpe010324.1 Bpe13g00625 625
13 13223294 13226263 + Bpe010325.1 Bpe13g00626 626
13 13226935 13229429 - Bpe010326.1 Bpe13g00627 627
14 10268861 10269841 + Bpe014679.1 Bpe14g01324 1324
14 10292789 10296525 + Bpe014680.1 Bpe14g01325 1325
5 5547015 5552890 - CaPI482276_05g006400.1 Cam05g0640 640
5 5563780 5564748 - CaPI482276_05g006410.1 Cam05g0641 641
5 5578229 5581621 + CaPI482276_05g006420.1 Cam05g0642 642
6 7867193 7879432 + CaPI482276_06g005800.1 Cam06g0580 580
6 7900190 7906191 - CaPI482276_06g005840.1 Cam06g0584 584
6 7926995 7931929 - CaPI482276_06g005860.1 Cam06g0586 586
6 7948733 7951536 - CaPI482276_06g005870.1 Cam06g0587 587
6 8956170 8961308 - Carg17395-RA Car06g01240 1240
6 8967022 8968067 + Carg17394-RA Car06g01241 1241
6 8971246 8974303 + Carg17393-RA Car06g01242 1242
8 7163957 7164931 + Carg15927-RA Car08g01048 1048
8 7166086 7171075 + Carg15928-RA Car08g01049 1049
8 7177685 7182596 + Carg15929-RA Car08g01050 1050
8 7184454 7198038 - Carg15931-RA Car08g01052 1052
14 12450051 12451016 + Carg23826-RA Car14g01507 1507
14 12453530 12457236 + Carg23825-RA Car14g01508 1508
17 1514445 1515419 + Carg05453-RA Car17g00247 247
17 1519662 1524566 + Carg05454-RA Car17g00248 248
17 1532472 1537673 + Carg05455-RA Car17g00249 249
17 1538950 1542832 + Carg05456-RA Car17g00250 250
17 1543949 1546057 + Carg05457-RA Car17g00251 251
17 1546472 1557483 - Carg05458-RA Car17g00252 252
5 5243580 5249710 - CcPI632755_05g006440.1 Cco05g0644 644
5 5260558 5261526 - CcPI632755_05g006450.1 Cco05g0645 645
5 5274714 5278103 + CcPI632755_05g006460.1 Cco05g0646 646
6 6305615 6317843 + CcPI632755_06g005850.1 Cco06g0585 585
6 6344067 6349977 - CcPI632755_06g005890.1 Cco06g0589 589
6 6370877 6375824 - CcPI632755_06g005910.1 Cco06g0591 591
6 6393073 6394053 - CcPI632755_06g005920.1 Cco06g0592 592
5 5253257 5259391 - CePI673135_05g006490.1 Cec05g0649 649
5 5270483 5271451 - CePI673135_05g006500.1 Cec05g0650 650
5 5285210 5288625 + CePI673135_05g006510.1 Cec05g0651 651
6 6404654 6416928 + CePI673135_06g005770.1 Cec06g0577 577
6 6438027 6443947 - CePI673135_06g005810.1 Cec06g0581 581
6 6463289 6468109 - CePI673135_06g005830.1 Cec06g0583 583
6 6481867 6482847 - CePI673135_06g005840.1 Cec06g0584 584
6 4204178 4208483 - Chy6G111470.1 Chy06g00619 619
6 4215619 4216587 - Chy6G111480.1 Chy06g00620 620
6 4234313 4237486 + Chy6G111490.1 Chy06g00621 621
11 21097821 21098801 + Chy11G200120.1 Chy11g01432 1432
11 21106992 21111232 + Chy11G200130.1 Chy11g01433 1433
11 21119935 21125219 + Chy11G200140.1 Chy11g01434 1434
11 21127626 21131351 + Chy11G200150.1 Chy11g01435 1435
11 21134773 21136884 + Chy11G200160.1 Chy11g01436 1436
11 21137671 21159252 - Chy11G200170.1 Chy11g01437 1437
5 5264805 5270693 - ClG42_05g0063400.10 Clacu05g0634 634
5 5281412 5282380 - ClG42_05g0063500.10 Clacu05g0635 635
5 5296068 5299450 + ClG42_05g0063600.10 Clacu05g0636 636
6 6413063 6425256 + ClG42_06g0056700.10 Clacu06g0567 567
6 6446258 6452208 - ClG42_06g0057000.10 Clacu06g0570 570
6 6473230 6478088 - ClG42_06g0057300.10 Clacu06g0573 573
6 6495357 6498182 - ClG42_06g0057400.10 Clacu06g0574 574
5 5325436 5331726 - ClCG05G005460.2 Cla05g00582 582
5 5341795 5344319 - ClCG05G005465.1 Cla05g00583 583
5 5357068 5360450 + ClCG05G005470.2 Cla05g00584 584
6 6486928 6500971 + ClCG06G005740.1 Cla06g00539 539
6 6501393 6503486 - ClCG06G005750.1 Cla06g00540 540
6 6518331 6529350 - ClCG06G005765.1 Cla06g00542 542
6 6550062 6555244 - ClCG06G005790.1 Cla06g00543 543
6 6572407 6573387 - ClCG06G005800.1 Cla06g00544 544
6 9226752 9232049 - CmaCh06G014380.1 Cma06g01438 1438
6 9238950 9239927 + CmaCh06G014390.1 Cma06g01439 1439
6 9243226 9246851 + CmaCh06G014400.1 Cma06g01440 1440
8 7206886 7207860 + CmaCh08G011700.1 Cma08g01170 1170
8 7209028 7215039 + CmaCh08G011710.1 Cma08g01171 1171
8 7217771 7219895 + CmaCh08G011730.1 Cma08g01173 1173
8 7224699 7238859 - CmaCh08G011750.1 Cma08g01175 1175
14 12492822 12493787 + CmaCh14G016730.1 Cma14g01673 1673
14 12495417 12499056 + CmaCh14G016740.1 Cma14g01674 1674
17 1413745 1414719 + CmaCh17G002720.1 Cma17g00272 272
17 1418758 1424052 + CmaCh17G002730.1 Cma17g00273 273
17 1431967 1436900 + CmaCh17G002740.1 Cma17g00274 274
17 1437929 1442201 + CmaCh17G002750.1 Cma17g00275 275
17 1442955 1445063 + CmaCh17G002760.1 Cma17g00276 276
17 1445210 1457043 - CmaCh17G002770.1 Cma17g00277 277
6 4182770 4187810 - MELO3C006570.2.1 Cme06g00650 650
6 4194184 4195347 - MELO3C006571.2.1 Cme06g00651 651
6 4213121 4216658 + MELO3C031613.2.1 Cme06g00652 652
11 27417060 27418046 + MELO3C021401.2.1 Cme11g01937 1937
11 27428704 27432334 + MELO3C021400.2.1 Cme11g01938 1938
11 27443667 27449111 + MELO3C021398.2.1 Cme11g01939 1939
11 27451007 27455813 + MELO3C021397.2.1 Cme11g01941 1941
11 27460592 27473546 - MELO3C021395.2.1 Cme11g01942 1942
6 4421988 4427246 - PI0027935.1 Cmetu06g0203 203
9 21816833 21819802 + PI0026882.1 Cmetu09g0387 387
11 4750987 4753222 - PI0019164.1 Cmetu11g1902 1902
6 10423144 10431169 - CmoCh06G014400.1 Cmo06g01440 1440
6 10436722 10438448 + CmoCh06G014410.1 Cmo06g01441 1441
6 10446198 10449360 + CmoCh06G014420.1 Cmo06g01442 1442
8 7303649 7304623 + CmoCh08G011430.1 Cmo08g01143 1143
8 7305776 7310539 + CmoCh08G011440.1 Cmo08g01144 1144
8 7310622 7315973 + CmoCh08G011450.1 Cmo08g01145 1145
8 7321806 7335308 - CmoCh08G011460.1 Cmo08g01146 1146
14 13453804 13457896 + CmoCh14G017190.1 Cmo14g01719 1719
17 1532508 1533482 + CmoCh17G002590.1 Cmo17g00259 259
17 1537741 1542869 + CmoCh17G002600.1 Cmo17g00260 260
17 1550367 1555575 + CmoCh17G002610.1 Cmo17g00261 261
17 1556628 1561077 + CmoCh17G002620.1 Cmo17g00262 262
17 1561792 1563900 + CmoCh17G002630.1 Cmo17g00263 263
17 1564099 1575935 - CmoCh17G002640.1 Cmo17g00264 264
5 5108365 5114253 - CmPI595203_05g006020.1 Cmu05g0602 602
5 5124964 5125932 - CmPI595203_05g006030.1 Cmu05g0603 603
5 5139602 5142985 + CmPI595203_05g006040.1 Cmu05g0604 604
6 6219987 6232177 + CmPI595203_06g005610.1 Cmu06g0561 561
6 6252849 6258800 - CmPI595203_06g005640.1 Cmu06g0564 564
6 6279822 6284680 - CmPI595203_06g005670.1 Cmu06g0567 567
6 6301912 6302892 - CmPI595203_06g005680.1 Cmu06g0568 568
4 925969 928693 - Conep04aG0020800.1 Cone4ag0199 199
4 929749 930159 - Conep04aG0020900.1 Cone4ag0200 200
4 937582 938493 - Conep04aG0021100.1 Cone4ag0202 202
4 941810 944986 + Conep04aG0021200.1 Cone4ag0203 203
7 894048 896363 - Conep07aG0021500.1 Cone7ag0210 210
7 902172 903107 - Conep07aG0021600.1 Cone7ag0211 211
7 908462 911674 + Conep07aG0021700.1 Cone7ag0212 212
14 4855304 4857398 - Conep14aG0083100.1 Cone14ag0814 814
14 4871168 4879744 + Conep14aG0083400.1 Cone14ag0817 817
14 4891444 4895732 - Conep14aG0083600.1 Cone14ag0819 819
15 5047525 5051826 - Conep15aG0082700.1 Cone15ag0812 812
15 5061480 5063864 - Conep15aG0082800.1 Cone15ag0813 813
15 5114902 5119168 - Conep15aG0083000.1 Cone15ag0815 815
3 11369422 11370393 + Cp4.1LG03g11030.1 Cpe03g01412 1412
3 11372280 11375814 + Cp4.1LG03g11090.1 Cpe03g01413 1413
8 1542073 1547499 - Cp4.1LG08g04430.1 Cpe08g00235 235
8 1550592 1551569 - Cp4.1LG08g04350.1 Cpe08g00236 236
8 1557051 1562343 + Cp4.1LG08g04490.1 Cpe08g00237 237
12 1488237 1489211 + Cp4.1LG12g02120.1 Cpe12g00225 225
12 1493734 1499338 + Cp4.1LG12g02280.1 Cpe12g00226 226
12 1507784 1512979 + Cp4.1LG12g02270.1 Cpe12g00227 227
12 1513989 1517928 + Cp4.1LG12g02300.1 Cpe12g00228 228
12 1521226 1524754 + Cp4.1LG12g02310.1 Cpe12g00229 229
12 1521997 1535689 - Cp4.1LG12g02320.1 Cpe12g00230 230
17 749034 761440 + Cp4.1LG17g01210.1 Cpe17g00120 120
17 762971 771854 - Cp4.1LG17g01280.1 Cpe17g00122 122
17 772333 777377 - Cp4.1LG17g01260.1 Cpe17g00123 123
17 778507 779481 - Cp4.1LG17g01230.1 Cpe17g00124 124
5 5901363 5907497 - CrPI670011_05g006710.1 Cre05g0671 671
5 5918586 5919554 - CrPI670011_05g006720.1 Cre05g0672 672
5 5933308 5936693 + CrPI670011_05g006730.1 Cre05g0673 673
6 7271054 7283281 + CrPI670011_06g013290.1 Cre06g1329 1329
6 7305669 7311586 - CrPI670011_06g013320.1 Cre06g1332 1332
6 7330738 7335681 - CrPI670011_06g013330.1 Cre06g1333 1333
6 7353021 7354001 - CrPI670011_06g013340.1 Cre06g1334 1334
3 10331694 10337125 - CsaV3_3G013760.1 Csa03g01376 1376
3 10342248 10344529 - CsaV3_3G013770.1 Csa03g01377 1377
3 10358931 10362756 + CsaV3_3G013790.1 Csa03g01379 1379
5 64647857 64652538 - Hsped.05g15150.1 Hepe05g1515 1515
5 64691239 64696128 + Hsped.05g15180.1 Hepe05g1518 1518
12 40444664 40445638 + Lag0016703.1 Lac12g2331 2331
11 38833019 38842955 - Maker00031657 Lcy11g1494 1494
11 38888511 38889485 - Maker00031794 Lcy11g1500 1500
11 38914409 38919423 + Maker00031816 Lcy11g1502 1502
5 22450742 22456586 - Lsi05G014600.1 Lsi05g01460 1460
5 22468453 22470748 - Lsi05G014610.1 Lsi05g01461 1461
5 22484177 22487243 + Lsi05G014620.1 Lsi05g01462 1462
9 21592791 21593771 + Lsi09G013580.1 Lsi09g01358 1358
9 21610109 21615433 + Lsi09G013590.1 Lsi09g01359 1359
9 21627422 21639636 + Lsi09G013610.1 Lsi09g01361 1361
9 21643705 21645798 + Lsi09G013620.1 Lsi09g01362 1362
9 21646307 21657944 - Lsi09G013630.1 Lsi09g01363 1363
2 49434416 49440689 - Sed0000368.1 Sed02g1276 1276
2 49462285 49464362 + Sed0005172.1 Sed02g1277 1277
10 7484565 7490019 - Tan0006650.2 Tan10g0895 895
10 7519216 7521237 + Tan0002275.1 Tan10g0896 896
10 7536284 7540328 + Tan0017302.1 Tan10g0900 900
5 4226907 4231360 - Vvi5g419 Vvi5g419 419
5 4233885 4240321 + Vvi5g420 Vvi5g420 420
5 4243859 4260802 + Vvi5g421 Vvi5g421 421
5 4262619 4264704 - Vvi5g422 Vvi5g422 422
5 4266467 4282546 - Vvi5g423 Vvi5g423 423
5 4284969 4290269 - Vvi5g424 Vvi5g424 424
5 4296749 4305393 - Vvi5g425 Vvi5g425 425
5 4309880 4311482 - Vvi5g426 Vvi5g426 426
5 4315655 4317278 - Vvi5g427 Vvi5g427 427
5 4334242 4347479 + Vvi5g428 Vvi5g428 428
       

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