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
Vvi5g449 . . . . . Bpe14g01314 . . . Cmo17g00251 . . . . . . . . . . . . . . Cla06g00552 Cam06g0595 Cec06g0593 Cco06g0600 Clacu06g0581 Cmu06g0576 Cre06g1342 Cone14ag0830 . Cone7ag0224 Cone4ag0215 . . . . . . . . . . Bma02g00689 . . . . . Cma17g00263 . Car17g00237 Cpe12g00219 . Bhi12g01814 . . . . . . . . . . . . . Lsi09g01347 . . Cme11g01927
Vvi5g450 . . . . . Bpe14g01313 . . . . Cma06g01426 . Car06g01230 . . . . . . . . . . . . . . . . . . . . Cone7ag0225 . . . . . . . . . . . Bma02g00688 . . Cmo06g01430 . . . . . . . . . . . . . . . . . . . . . . Csa03g01356 . .
Vvi5g451 . . . . . Bpe14g01312 . . . Cmo17g00248 . Cma14g01686 . Car14g01520 Sed02g1259 . Cpe03g01421 Bhi01g00844 Tan10g0872 Cmetu11g1384 Lac12g2316 Hepe05g1531 . Lcy11g1518 Cla06g00553 Cam06g0596 Cec06g0594 . Clacu06g0582 Cmu06g0577 Cre06g1343 . . Cone7ag0226 . Lsi05g01444 . . Cme06g00631 . . . . . . Bma02g00687 . . . Cmo14g01731 . Cma17g00261 . Car17g00235 Cpe12g00217 . Bhi12g01815 . . . . . . Cla05g00567 Cam05g0623 Cec05g0633 Cco05g0628 Clacu05g0619 Cmu05g0587 Cre05g0655 Lsi09g01345 . Chy06g00601 Cme11g01925
Vvi5g452 . . . . . Bpe14g01311 . . . Cmo17g00247 . . . . . . . . . . . . . . Cla06g00556 Cam06g0597 Cec06g0595 Cco06g0602 Clacu06g0583 Cmu06g0578 Cre06g1344 . . Cone7ag0227 Cone4ag0217 . . . . . . . . . . . . . . . . Cma17g00260 Car08g01040 Car17g00234 Cpe12g00216 Cpe17g00133 Bhi12g01817 . . . . . . . . . . . . . Lsi09g01343 . . .
Vvi5g453 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g454 . . . . . . Bma04g01199 . . Cmo17g00246 . . . . . . . . . . . . . . Cla06g00557 Cam06g0598 Cec06g0596 Cco06g0603 Clacu06g0584 Cmu06g0579 Cre06g1345 Cone14ag0831 . . . . . . . . . . . . . . . . . . . Cma17g00259 . Car17g00233 Cpe12g00215 . Bhi12g01818 . . . . . . . . . . . . . Lsi09g01342 . . .
Vvi5g455 . . . . . . . . . Cmo17g00245 . . . . . . . . . . . . . . Cla06g00558 . . . . . . . . Cone7ag0228 Cone4ag0218 . . . . . . . . . . . . . . . . Cma17g00258 . Car17g00232 Cpe12g00214 . Bhi12g01819 . . . . . . . . . . . . . Lsi09g01341 . . .
Vvi5g456 . . . . . Bpe14g01172 . . Cmo08g01134 Cmo17g00243 . Cma14g01688 Car06g01229 Car14g01521 . Cpe08g00248 Cpe03g01422 . . . . . . . Cla06g00560 Cam06g0600 Cec06g0600 Cco06g0605 Clacu06g0586 Cmu06g0581 Cre06g1347 . . Cone7ag0229 Cone4ag0219 Lsi05g01442 . . Cme06g00629 Blo02g00554 Blo07g00210 Bda11g00566 . . . . Bma06g01545 . Cmo06g01429 Cmo14g01732 Cma08g01162 Cma17g00257 Car08g01039 Car17g00231 Cpe12g00213 Cpe17g00134 Bhi12g01820 . . . . . . Cla05g00565 Cam05g0621 Cec05g0631 Cco05g0626 Clacu05g0617 Cmu05g0585 Cre05g0653 Lsi09g01340 Csa03g01354 Chy06g00599 .
Vvi5g457 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g458 Blo01g00131 Blo12g00317 Bda03g00897 Bda08g00230 Bpe04g00842 . Bma04g00794 . Cmo08g01133 Cmo17g00242 . . . . . . . . . . . . . . Cla06g00561 Cam06g0601 Cec06g0601 Cco06g0606 Clacu06g0587 Cmu06g0582 Cre06g1348 . . Cone7ag0231 Cone4ag0220 . . . . . . . . Bpe05g00909 . . . . . . Cma08g01161 Cma17g00256 Car08g01038 Car17g00230 Cpe12g00212 Cpe17g00135 Bhi12g01821 . . . . . . . . . . . . . Lsi09g01339 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 7832645 7838235 - Bda016892.1 Bda03g00897 897
8 2296955 2303410 + Bda024645.2 Bda08g00230 230
11 5859205 5860137 + Bda005304.1 Bda11g00566 566
1 16012496 16017284 + XM_039036566.1 Bhi01g00844 844
12 57990310 57994182 - XM_039050647.1 Bhi12g01814 1814
12 58000390 58009960 - XM_039019593.1 Bhi12g01815 1815
12 58019922 58021973 + XM_039019460.1 Bhi12g01817 1817
12 58023333 58026773 - XM_039020214.1 Bhi12g01818 1818
12 58033278 58042215 + XM_039050803.1 Bhi12g01819 1819
12 58078467 58079457 - XM_039019277.1 Bhi12g01820 1820
12 58131783 58138062 + XM_039020334.1 Bhi12g01821 1821
1 1790226 1801105 - BLOR00131 Blo01g00131 131
2 9856763 9857659 - BLOR10284 Blo02g00554 554
7 2679741 2680670 + BLOR18142 Blo07g00210 210
12 18627616 18635391 + BLOR04336 Blo12g00317 317
2 25286290 25289510 + Bma030895 Bma02g00687 687
2 25289260 25294239 - Bma015326.2 Bma02g00688 688
2 25313384 25315457 + Bma015328.1 Bma02g00689 689
4 9035602 9041273 - Bma019319.1 Bma04g00794 794
4 33054733 33057608 + Bma019954.1 Bma04g01199 1199
6 51805308 51806231 + Bma024662.1 Bma06g01545 1545
4 5542024 5547861 - Bpe015502.1 Bpe04g00842 842
5 22108113 22114408 - Bpe018320.1 Bpe05g00909 909
14 8760156 8761070 + Bpe014546.1 Bpe14g01172 1172
14 10110773 10112482 - Bpe014667.1 Bpe14g01311 1311
14 10127954 10131170 + Bpe014668.1 Bpe14g01312 1312
14 10132274 10135878 - Bpe025554 Bpe14g01313 1313
14 10146664 10148742 + Bpe014669.1 Bpe14g01314 1314
5 5401044 5402030 - CaPI482276_05g006210.1 Cam05g0621 621
5 5428641 5432854 + CaPI482276_05g006230.1 Cam05g0623 623
6 8097245 8100317 - CaPI482276_06g005950.1 Cam06g0595 595
6 8104802 8113064 - CaPI482276_06g005960.1 Cam06g0596 596
6 8119980 8122015 + CaPI482276_06g005970.1 Cam06g0597 597
6 8123641 8126608 - CaPI482276_06g005980.1 Cam06g0598 598
6 8143900 8144682 - CaPI482276_06g006000.1 Cam06g0600 600
6 8164321 8170372 + CaPI482276_06g006010.1 Cam06g0601 601
6 8896609 8897583 - Carg17406-RA Car06g01229 1229
6 8902832 8911458 - Carg17405-RA Car06g01230 1230
8 7100785 7106124 - Carg15917-RA Car08g01038 1038
8 7108374 7109087 + Carg15918-RA Car08g01039 1039
8 7113591 7115400 - Carg15919-RA Car08g01040 1040
14 12502304 12506506 - Carg23812-RA Car14g01520 1520
14 12511296 12512261 + Carg23811-RA Car14g01521 1521
17 1416815 1423470 - Carg05436-RA Car17g00230 230
17 1431057 1431788 + Carg05437-RA Car17g00231 231
17 1433358 1439606 - Carg05438-RA Car17g00232 232
17 1440743 1444130 + Carg05439-RA Car17g00233 233
17 1444516 1446885 - Carg05440-RA Car17g00234 234
17 1447594 1457266 + Carg05441-RA Car17g00235 235
17 1459079 1463757 + Carg05443-RA Car17g00237 237
5 5095177 5096157 - CcPI632755_05g006260.1 Cco05g0626 626
5 5122879 5127069 + CcPI632755_05g006280.1 Cco05g0628 628
6 6535692 6538749 + CcPI632755_06g006000.1 Cco06g0600 600
6 6562379 6564372 + CcPI632755_06g006020.1 Cco06g0602 602
6 6566027 6568849 - CcPI632755_06g006030.1 Cco06g0603 603
6 6586314 6587096 - CcPI632755_06g006050.1 Cco06g0605 605
6 6607374 6613267 + CcPI632755_06g006060.1 Cco06g0606 606
5 5106823 5107809 - CePI673135_05g006310.1 Cec05g0631 631
5 5134606 5140699 + CePI673135_05g006330.1 Cec05g0633 633
6 6621811 6627193 - CePI673135_06g005930.1 Cec06g0593 593
6 6631599 6639884 - CePI673135_06g005940.1 Cec06g0594 594
6 6645800 6647787 + CePI673135_06g005950.1 Cec06g0595 595
6 6649439 6652271 - CePI673135_06g005960.1 Cec06g0596 596
6 6675932 6676702 - CePI673135_06g006000.1 Cec06g0600 600
6 6694845 6700873 + CePI673135_06g006010.1 Cec06g0601 601
6 4086024 4087034 - Chy6G111270.1 Chy06g00599 599
6 4110138 4114233 + Chy6G111290.1 Chy06g00601 601
5 5117068 5118069 - ClG42_05g0061700.10 Clacu05g0617 617
5 5144878 5149089 + ClG42_05g0061900.10 Clacu05g0619 619
6 6642908 6645985 - ClG42_06g0058100.10 Clacu06g0581 581
6 6650528 6658759 - ClG42_06g0058200.10 Clacu06g0582 582
6 6665508 6667532 + ClG42_06g0058300.10 Clacu06g0583 583
6 6669194 6672024 - ClG42_06g0058400.10 Clacu06g0584 584
6 6689213 6689995 - ClG42_06g0058600.10 Clacu06g0586 586
6 6711274 6717337 + ClG42_06g0058700.10 Clacu06g0587 587
5 5175719 5176720 - ClCG05G005305.1 Cla05g00565 565
5 5203994 5208205 + ClCG05G005320.1 Cla05g00567 567
6 6735276 6738831 - ClCG06G005890.1 Cla06g00552 552
6 6742908 6751717 - ClCG06G005900.2 Cla06g00553 553
6 6758042 6760271 + ClCG06G005930.2 Cla06g00556 556
6 6761749 6764976 - ClCG06G005940.1 Cla06g00557 557
6 6766067 6770174 + ClCG06G005950.2 Cla06g00558 558
6 6781908 6782690 - ClCG06G005960.1 Cla06g00560 560
6 6804192 6810938 + ClCG06G005970.2 Cla06g00561 561
6 9173121 9178585 - CmaCh06G014260.1 Cma06g01426 1426
8 7148868 7154733 - CmaCh08G011610.1 Cma08g01161 1161
8 7157637 7158350 + CmaCh08G011620.1 Cma08g01162 1162
14 12543542 12547828 - CmaCh14G016860.1 Cma14g01686 1686
14 12552548 12553519 + CmaCh14G016880.1 Cma14g01688 1688
17 1316673 1323211 - CmaCh17G002560.1 Cma17g00256 256
17 1330175 1330894 + CmaCh17G002570.1 Cma17g00257 257
17 1332965 1338652 - CmaCh17G002580.1 Cma17g00258 258
17 1340140 1343430 + CmaCh17G002590.1 Cma17g00259 259
17 1343979 1346407 - CmaCh17G002600.1 Cma17g00260 260
17 1347187 1349277 + CmaCh17G002610.1 Cma17g00261 261
17 1350939 1361581 + CmaCh17G002630.1 Cma17g00263 263
6 4035171 4036396 - MELO3C006550.2.1 Cme06g00629 629
6 4056021 4060859 + MELO3C006552.2.1 Cme06g00631 631
11 27325283 27332251 + MELO3C021412.2.1 Cme11g01925 1925
11 27334695 27338062 + MELO3C021411.2.1 Cme11g01927 1927
11 4854312 4862126 - PI0022221.1 Cmetu11g1384 1384
6 10365482 10366456 - CmoCh06G014290.1 Cmo06g01429 1429
6 10371701 10380875 - CmoCh06G014300.1 Cmo06g01430 1430
8 7240122 7245540 - CmoCh08G011330.1 Cmo08g01133 1133
8 7248523 7249254 + CmoCh08G011340.1 Cmo08g01134 1134
14 13509303 13513531 - CmoCh14G017310.1 Cmo14g01731 1731
14 13518860 13519825 + CmoCh14G017320.1 Cmo14g01732 1732
17 1429561 1437554 - CmoCh17G002420.1 Cmo17g00242 242
17 1445982 1446701 + CmoCh17G002430.1 Cmo17g00243 243
17 1450940 1454640 - CmoCh17G002450.1 Cmo17g00245 245
17 1455714 1459367 + CmoCh17G002460.1 Cmo17g00246 246
17 1459807 1462267 - CmoCh17G002470.1 Cmo17g00247 247
17 1463283 1464253 + CmoCh17G002480.1 Cmo17g00248 248
17 1474781 1478194 + CmoCh17G002510.1 Cmo17g00251 251
5 4960736 4961746 - CmPI595203_05g005850.1 Cmu05g0585 585
5 4988628 4992839 + CmPI595203_05g005870.1 Cmu05g0587 587
6 6449508 6452582 - CmPI595203_06g005760.1 Cmu06g0576 576
6 6457123 6465383 - CmPI595203_06g005770.1 Cmu06g0577 577
6 6472137 6474160 + CmPI595203_06g005780.1 Cmu06g0578 578
6 6475839 6478669 - CmPI595203_06g005790.1 Cmu06g0579 579
6 6495882 6496664 - CmPI595203_06g005810.1 Cmu06g0581 581
6 6517946 6524007 + CmPI595203_06g005820.1 Cmu06g0582 582
4 987989 990539 - Conep04aG0022400.1 Cone4ag0215 215
4 997040 999064 + Conep04aG0022600.1 Cone4ag0217 217
4 999361 1003333 + Conep04aG0022700.1 Cone4ag0218 218
4 1008492 1009853 + Conep04aG0022800.1 Cone4ag0219 219
4 1013385 1016338 + Conep04aG0022900.1 Cone4ag0220 220
7 954446 956994 - Conep07aG0022900.1 Cone7ag0224 224
7 957170 959566 + Conep07aG0023000.1 Cone7ag0225 225
7 959738 964135 - Conep07aG0023100.1 Cone7ag0226 226
7 964623 966511 + Conep07aG0023200.1 Cone7ag0227 227
7 966856 970762 + Conep07aG0023300.1 Cone7ag0228 228
7 976350 977390 + Conep07aG0023400.1 Cone7ag0229 229
7 984882 985703 + Conep07aG0023600.1 Cone7ag0231 231
14 5063129 5066167 - Conep14aG0084700.1 Cone14ag0830 830
14 5076770 5081196 - Conep14aG0084800.1 Cone14ag0831 831
3 11416708 11424651 - Cp4.1LG03g10860.1 Cpe03g01421 1421
3 11429676 11430644 + Cp4.1LG03g10870.1 Cpe03g01422 1422
8 1631997 1632977 + Cp4.1LG08g04290.1 Cpe08g00248 248
12 1384868 1391676 - Cp4.1LG12g02220.1 Cpe12g00212 212
12 1400495 1401214 + Cp4.1LG12g02130.1 Cpe12g00213 213
12 1402800 1408922 - Cp4.1LG12g02240.1 Cpe12g00214 214
12 1410083 1413552 + Cp4.1LG12g02140.1 Cpe12g00215 215
12 1414085 1416683 - Cp4.1LG12g02170.1 Cpe12g00216 216
12 1418531 1427709 + Cp4.1LG12g02160.1 Cpe12g00217 217
12 1430556 1434308 + Cp4.1LG12g02150.1 Cpe12g00219 219
17 828738 831689 + Cp4.1LG17g01350.1 Cpe17g00133 133
17 835415 836128 - Cp4.1LG17g01390.1 Cpe17g00134 134
17 841158 845833 + Cp4.1LG17g01360.1 Cpe17g00135 135
5 5751307 5752284 - CrPI670011_05g006530.1 Cre05g0653 653
5 5780596 5784802 + CrPI670011_05g006550.1 Cre05g0655 655
6 7508006 7511058 - CrPI670011_06g013420.1 Cre06g1342 1342
6 7515628 7523905 - CrPI670011_06g013430.1 Cre06g1343 1343
6 7530726 7532759 + CrPI670011_06g013440.1 Cre06g1344 1344
6 7534421 7537252 - CrPI670011_06g013450.1 Cre06g1345 1345
6 7554484 7555254 - CrPI670011_06g013470.1 Cre06g1347 1347
6 7573370 7579427 + CrPI670011_06g013480.1 Cre06g1348 1348
3 10216791 10218560 - CsaV3_3G013540.1 Csa03g01354 1354
3 10232396 10236702 - CsaV3_3G013560.1 Csa03g01356 1356
5 64859144 64863908 - Hsped.05g15310.1 Hepe05g1531 1531
12 40286206 40290793 + Lag0016688.1 Lac12g2316 2316
11 39067221 39072429 - Maker00031670 Lcy11g1518 1518
5 22302551 22303543 - Lsi05G014420.1 Lsi05g01442 1442
5 22330567 22335284 + Lsi05G014440.1 Lsi05g01444 1444
9 21336948 21342865 - Lsi09G013390.1 Lsi09g01339 1339
9 21365592 21366368 + Lsi09G013400.1 Lsi09g01340 1340
9 21376951 21381234 - Lsi09G013410.1 Lsi09g01341 1341
9 21385459 21388232 + Lsi09G013420.1 Lsi09g01342 1342
9 21389014 21391722 - Lsi09G013430.1 Lsi09g01343 1343
9 21410127 21419793 + Lsi09G013450.1 Lsi09g01345 1345
9 21426924 21430716 + Lsi09G013470.1 Lsi09g01347 1347
2 49331965 49342501 + Sed0023380.2 Sed02g1259 1259
10 7305156 7309647 + Tan0018701.1 Tan10g0872 872
5 4549692 4553760 - Vvi5g449 Vvi5g449 449
5 4554256 4559694 + Vvi5g450 Vvi5g450 450
5 4559701 4563672 - Vvi5g451 Vvi5g451 451
5 4600908 4604073 + Vvi5g452 Vvi5g452 452
5 4607326 4607404 + Vvi5g453 Vvi5g453 453
5 4607596 4617180 - Vvi5g454 Vvi5g454 454
5 4619228 4633132 + Vvi5g455 Vvi5g455 455
5 4640934 4642204 - Vvi5g456 Vvi5g456 456
5 4651063 4670328 + Vvi5g457 Vvi5g457 457
5 4673536 4694663 + Vvi5g458 Vvi5g458 458
       

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