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
Vvi5g329 . Blo12g00020 . . Bpe04g01129 . . . Cmo08g01191 . . . . . . . . . . . . . . . Cla06g00491 . . . . . . . . . Cone4ag0156 . . Chy11g01486 . . . . . . . . . . . . Cma08g01218 . Car08g01091 . . Cpe17g00013 Bhi12g02081 . . . Hepe03g0114 . Lcy13g0186 . . . . . . . Lsi09g01416 . . Cme11g01993
Vvi5g330 . . . . . . . Bma05g01045 Cmo08g01190 Cmo17g00302 . . . . . . . . . . . . . . Cla06g00492 Cam06g0529 Cec06g0529 Cco06g0533 Clacu06g0513 Cmu06g0515 Cre06g1286 . . Cone7ag0159 Cone4ag0157 . . Chy11g01485 . . . . . . . . . Sed09g1215 . . Cma08g01217 Cma17g00314 Car08g01090 Car17g00288 Cpe12g00266 Cpe17g00012 Bhi12g02083 Tan06g0860 Cmetu01g0223 Lac12g2393 Hepe03g0115 . Lcy13g0188 . . . . . . . Lsi09g01415 . . Cme11g01992
Vvi5g331 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g332 . Blo12g00021 . Bda08g00284 Bpe04g01128 Bpe14g01135 . Bma05g01047 Cmo08g01189 . . . . . . . . . . . . . . . Cla06g00493 Cam06g0530 Cec06g0530 Cco06g0534 Clacu06g0514 Cmu06g0516 Cre06g1287 Cone14ag0773 Cone15ag0779 . . . . Chy11g01484 . Blo02g00514 . . Bda13g00180 Bpe05g00844 . . . Sed09g0226 . . Cma08g01216 . Car08g01087 Car17g00287 Cpe12g00265 Cpe17g00011 Bhi12g02085 Tan06g2644 Cmetu11g2330 . Hepe03g0116 . Lcy13g0190 . . . . . . . Lsi09g01414 . . Cme11g01991
Vvi5g333 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g334 . . . . Bpe04g01127 . . . . . . Cma14g01631 . Car14g01457 Sed02g1196 . Cpe03g01373 Bhi01g00978 Tan10g0983 Cmetu06g1761 . Hepe05g1461 . Lcy11g1429 . . . . . . . . Cone15ag0780 . . Lsi05g01525 . . Cme06g00715 . . . . . . . . . . Cmo14g01668 . . . . . . . . . . . . . Cla05g00635 Cam05g0696 Cec05g0709 Cco05g0705 Clacu05g0691 Cmu05g0658 Cre05g0730 . Csa03g01443 Chy06g00684 .
Vvi5g335 . . . . . Bpe14g01136 . . . . Cma06g01485 Cma14g01632 Car06g01277 Car14g01458 . Cpe08g00199 Cpe03g01374 Bhi01g00974 . . . Hepe05g1463 . . . . . . . . . . . Cone7ag0162 Cone4ag0158 Lsi05g01524 . . Cme06g00712 Blo02g00515 . Bda11g00533 Bda13g00178 . Bpe13g00656 . Bma06g01509 . Cmo06g01480 Cmo14g01669 . . . . . . . . . . . . . Cla05g00634 Cam05g0695 Cec05g0708 Cco05g0704 Clacu05g0690 Cmu05g0657 Cre05g0729 . Csa03g01442 Chy06g00683 .
Vvi5g336 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g337 . . . Bda08g00283 . Bpe14g01137 . Bma05g01055 Cmo08g01188 . Cma06g01484 Cma14g01633 . . . . . . . . . . . . Cla06g00494 Cam06g0531 Cec06g0531 Cco06g0535 Clacu06g0515 Cmu06g0517 Cre06g1288 Cone11ag0062 Cone18ag1417 . . Lsi05g01523 . . Cme06g00711 Blo02g00516 Blo07g00180 Bda11g00534 Bda13g00173 Bpe05g00845 Bpe13g00655 . Bma06g01511 Sed02g1207 . Cmo14g01671 Cma08g01215 . Car08g01086 . . . Bhi12g02086 Tan06g0862 Cmetu06g1898 . . . Lcy13g0191 Cla05g00633 Cam05g0694 Cec05g0705 Cco05g0701 Clacu05g0689 Cmu05g0656 Cre05g0727 Lsi09g01413 Csa03g01436 Chy06g00675 .
Vvi5g338 . Blo12g00022 . . . . . . . . Cma06g01483 Cma14g01634 Car06g01276 Car14g01459 Sed02g1209 Cpe08g00200 Cpe03g01375 Bhi01g00972 Tan10g0977 Cmetu06g2468 . Hepe05g1466 . Lcy11g1433 . . . . . . . Cone14ag0775 Cone15ag0782 . . Lsi05g01521 . . Cme06g00709 . Blo07g00181 . . . Bpe13g00654 . Bma06g01512 . Cmo06g01479 Cmo14g01672 . . . . . . . . . . . . . Cla05g00632 Cam05g0692 Cec05g0702 Cco05g0698 Clacu05g0686 Cmu05g0654 Cre05g0725 . Csa03g01433 Chy06g00673 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 2941588 2947318 + Bda024716.1 Bda08g00283 283
8 2949382 2956083 - Bda024717.1 Bda08g00284 284
11 5600529 5610701 - Bda005268.1 Bda11g00533 533
11 5612669 5613811 - Bda005269.1 Bda11g00534 534
13 2210017 2211159 + Bda001035.1 Bda13g00173 173
13 2256554 2258069 + Bda001042.1 Bda13g00178 178
13 2307056 2313755 - Bda001047.2 Bda13g00180 180
1 17827598 17832099 - XM_039048328.1 Bhi01g00972 972
1 17970766 17989929 + XM_039034918.1 Bhi01g00974 974
1 17990118 17991549 - XM_039034927.1 Bhi01g00978 978
12 64539467 64541117 + XM_039019392.1 Bhi12g02081 2081
12 64543100 64550985 - XM_039018681.1 Bhi12g02083 2083
12 64614209 64621662 + XM_039018500.1 Bhi12g02085 2085
12 64624575 64625978 - XM_039050698.1 Bhi12g02086 2086
2 8335322 8342239 + BLOR10244 Blo02g00514 514
2 8342666 8355270 - BLOR10245 Blo02g00515 515
2 8392191 8399085 - BLOR10246 Blo02g00516 516
7 2262853 2263995 - BLOR18112 Blo07g00180 180
7 2281253 2290216 + BLOR18113 Blo07g00181 181
12 1248441 1250000 + BLOR04039 Blo12g00020 20
12 1390914 1399049 + BLOR04040 Blo12g00021 21
12 1544529 1546406 - BLOR04041 Blo12g00022 22
5 49043832 49051706 - Bma022203.2 Bma05g01045 1045
5 49133925 49135575 - Bma022207.1 Bma05g01047 1047
5 49222676 49223833 - Bma022218.1 Bma05g01055 1055
6 51535529 51544315 - Bma024622.1 Bma06g01509 1509
6 51571777 51572919 - Bma024624.1 Bma06g01511 1511
6 51579673 51582023 + Bma024625.1 Bma06g01512 1512
4 9817066 9818726 - Bpe015807.1 Bpe04g01127 1127
4 9821057 9828796 - Bpe015808.2 Bpe04g01128 1128
4 9882151 9883971 + Bpe015809.1 Bpe04g01129 1129
5 21650674 21657426 + Bpe018257.3 Bpe05g00844 844
5 21659771 21660928 - Bpe018258.1 Bpe05g00845 845
13 13357877 13360238 - Bpe010355.2 Bpe13g00654 654
13 13369862 13371010 + Bpe010356.2 Bpe13g00655 655
13 13377612 13386367 + Bpe010357.1 Bpe13g00656 656
14 8448799 8453391 + Bpe014511.1 Bpe14g01135 1135
14 8454179 8462555 - Bpe014512.1 Bpe14g01136 1136
14 8473448 8474623 - Bpe014513.3 Bpe14g01137 1137
5 6050852 6055552 - CaPI482276_05g006920.1 Cam05g0692 692
5 6088475 6088810 - CaPI482276_05g006940.1 Cam05g0694 694
5 6088871 6110727 + CaPI482276_05g006950.1 Cam05g0695 695
5 6111461 6112460 - CaPI482276_05g006960.1 Cam05g0696 696
6 7366436 7373220 - CaPI482276_06g005290.1 Cam06g0529 529
6 7386510 7392372 + CaPI482276_06g005300.1 Cam06g0530 530
6 7396263 7397414 - CaPI482276_06g005310.1 Cam06g0531 531
6 9156655 9159840 - Carg17357-RA Car06g01276 1276
6 9170309 9182584 + Carg17356-RA Car06g01277 1277
8 7408822 7409982 + Carg15965-RA Car08g01086 1086
8 7411713 7417471 - Carg15966-RA Car08g01087 1087
8 7430158 7432924 + Carg18831-RA Car08g01090 1090
8 7433934 7435724 - Carg18832-RA Car08g01091 1091
14 12158679 12160370 + Carg20121-RA Car14g01457 1457
14 12159916 12174656 - Carg20122-RA Car14g01458 1458
14 12187897 12190522 + Carg20123-RA Car14g01459 1459
17 1777052 1783574 - Carg05493-RA Car17g00287 287
17 1785417 1792954 + Carg05494-RA Car17g00288 288
5 5750258 5754979 - CcPI632755_05g006980.1 Cco05g0698 698
5 5793620 5794717 - CcPI632755_05g007010.1 Cco05g0701 701
5 5802456 5819375 + CcPI632755_05g007040.1 Cco05g0704 704
5 5820109 5821079 - CcPI632755_05g007050.1 Cco05g0705 705
6 5792217 5798988 - CcPI632755_06g005330.1 Cco06g0533 533
6 5812398 5818246 + CcPI632755_06g005340.1 Cco06g0534 534
6 5819879 5823288 - CcPI632755_06g005350.1 Cco06g0535 535
5 5774244 5778951 - CePI673135_05g007020.1 Cec05g0702 702
5 5811225 5812322 - CePI673135_05g007050.1 Cec05g0705 705
5 5820426 5836940 + CePI673135_05g007080.1 Cec05g0708 708
5 5837674 5838662 - CePI673135_05g007090.1 Cec05g0709 709
6 5899916 5906677 - CePI673135_06g005290.1 Cec06g0529 529
6 5918795 5926401 + CePI673135_06g005300.1 Cec06g0530 530
6 5933829 5934980 - CePI673135_06g005310.1 Cec06g0531 531
6 4622284 4625628 - Chy6G112010.1 Chy06g00673 673
6 4637622 4638734 - Chy6G112030.1 Chy06g00675 675
6 4663204 4675420 + Chy6G112110.1 Chy06g00683 683
6 4676111 4677025 - Chy6G112120.1 Chy06g00684 684
11 21569853 21575919 - Chy11G200640.1 Chy11g01484 1484
11 21584590 21591360 + Chy11G200650.1 Chy11g01485 1485
11 21592246 21594057 - Chy11G200660.1 Chy11g01486 1486
5 5782483 5785934 - ClG42_05g0068600.10 Clacu05g0686 686
5 5818508 5819329 - ClG42_05g0068900.10 Clacu05g0689 689
5 5824711 5841311 + ClG42_05g0069000.10 Clacu05g0690 690
5 5842041 5843041 - ClG42_05g0069100.10 Clacu05g0691 691
6 5905957 5912740 - ClG42_06g0051300.10 Clacu06g0513 513
6 5924862 5930693 + ClG42_06g0051400.10 Clacu06g0514 514
6 5934602 5935753 - ClG42_06g0051500.10 Clacu06g0515 515
5 5863747 5867936 - ClCG05G005940.1 Cla05g00632 632
5 5893824 5904157 - ClCG05G005950.2 Cla05g00633 633
5 5909115 5926171 + ClCG05G005970.2 Cla05g00634 634
5 5926361 5927701 - ClCG05G005980.1 Cla05g00635 635
6 5950469 5964365 + ClCG06G005250.2 Cla06g00491 491
6 5964823 5973092 - ClCG06G005270.2 Cla06g00492 492
6 5984768 5990599 + ClCG06G005280.2 Cla06g00493 493
6 5993828 5995969 - ClCG06G005290.2 Cla06g00494 494
6 9429815 9436573 - CmaCh06G014830.1 Cma06g01483 1483
6 9442857 9443948 + CmaCh06G014840.1 Cma06g01484 1484
6 9446426 9458475 + CmaCh06G014850.1 Cma06g01485 1485
8 7447937 7449088 + CmaCh08G012150.1 Cma08g01215 1215
8 7450884 7457472 - CmaCh08G012160.1 Cma08g01216 1216
8 7457386 7466507 + CmaCh08G012170.1 Cma08g01217 1217
8 7467054 7475965 - CmaCh08G012180.1 Cma08g01218 1218
14 12205016 12207212 + CmaCh14G016310.1 Cma14g01631 1631
14 12206350 12220806 - CmaCh14G016320.1 Cma14g01632 1632
14 12221174 12225070 + CmaCh14G016330.1 Cma14g01633 1633
14 12230592 12234782 + CmaCh14G016340.1 Cma14g01634 1634
17 1687631 1694084 + CmaCh17G003140.1 Cma17g00314 314
6 4618750 4622973 - MELO3C006627.2.1 Cme06g00709 709
6 4646332 4684470 - MELO3C006649.2.1 Cme06g00711 711
6 4660090 4662071 + MELO3C031729.2.1 Cme06g00712 712
6 4704012 4704900 - MELO3C006643.2.1 Cme06g00715 715
11 27855224 27862071 - MELO3C021347.2.1 Cme11g01991 1991
11 27873923 27880582 + MELO3C021346.2.1 Cme11g01992 1992
11 27881457 27883390 - MELO3C035186.2.1 Cme11g01993 1993
1 24629961 24638878 + PI0003322.1 Cmetu01g0223 223
6 4923908 4925591 - PI0027666.1 Cmetu06g1761 1761
6 4901414 4902889 + PI0028421.1 Cmetu06g1898 1898
6 4870108 4874369 - PI0027956.1 Cmetu06g2468 2468
11 4333502 4341055 + PI0002003.1 Cmetu11g2330 2330
6 10642781 10646918 - CmoCh06G014790.1 Cmo06g01479 1479
6 10656281 10671382 + CmoCh06G014800.1 Cmo06g01480 1480
8 7550584 7556567 + CmoCh08G011880.1 Cmo08g01188 1188
8 7556638 7562955 - CmoCh08G011890.1 Cmo08g01189 1189
8 7563782 7572170 + CmoCh08G011900.1 Cmo08g01190 1190
8 7573090 7574880 - CmoCh08G011910.1 Cmo08g01191 1191
14 13147245 13148631 + CmoCh14G016680.1 Cmo14g01668 1668
14 13148757 13164471 - CmoCh14G016690.1 Cmo14g01669 1669
14 13167290 13170779 + CmoCh14G016710.1 Cmo14g01671 1671
14 13175212 13181593 + CmoCh14G016720.1 Cmo14g01672 1672
17 1826846 1833294 + CmoCh17G003020.1 Cmo17g00302 302
5 5625746 5629196 - CmPI595203_05g006540.1 Cmu05g0654 654
5 5652700 5659970 - CmPI595203_05g006560.1 Cmu05g0656 656
5 5662680 5679835 + CmPI595203_05g006570.1 Cmu05g0657 657
5 5685303 5686297 - CmPI595203_05g006580.1 Cmu05g0658 658
6 5707793 5714577 - CmPI595203_06g005150.1 Cmu06g0515 515
6 5732579 5738412 + CmPI595203_06g005160.1 Cmu06g0516 516
6 5742325 5743299 - CmPI595203_06g005170.1 Cmu06g0517 517
4 727473 729307 + Conep04aG0016200.1 Cone4ag0156 156
4 730912 738797 - Conep04aG0016300.1 Cone4ag0157 157
4 739747 748820 - Conep04aG0016400.1 Cone4ag0158 158
7 657388 668937 - Conep07aG0016100.1 Cone7ag0159 159
7 669439 683573 - Conep07aG0016400.1 Cone7ag0162 162
11 271053 276412 - Conep11aG0006300.1 Cone11ag0062 62
14 4461364 4467849 + Conep14aG0079000.1 Cone14ag0773 773
14 4485559 4490101 + Conep14aG0079200.1 Cone14ag0775 775
15 4719949 4726500 + Conep15aG0079400.1 Cone15ag0779 779
15 4727052 4728997 + Conep15aG0079500.1 Cone15ag0780 780
15 4743249 4748068 + Conep15aG0079700.1 Cone15ag0782 782
18 9609821 9611292 + Conep18aG0146400.1 Cone18ag1417 1417
3 11066061 11069386 + Cp4.1LG03g11450.1 Cpe03g01373 1373
3 11067475 11082534 - Cp4.1LG03g11420.1 Cpe03g01374 1374
3 11100001 11104320 + Cp4.1LG03g11290.1 Cpe03g01375 1375
8 1324815 1337416 - Cp4.1LG08g04800.1 Cpe08g00199 199
8 1347667 1352616 + Cp4.1LG08g04850.1 Cpe08g00200 200
12 1765711 1767887 - Cp4.1LG12g02660.1 Cpe12g00265 265
12 1770247 1776732 + Cp4.1LG12g02560.1 Cpe12g00266 266
17 85427 91804 - Cp4.1LG17g00760.1 Cpe17g00011 11
17 94473 101403 + Cp4.1LG17g00810.1 Cpe17g00012 12
17 103500 105054 - Cp4.1LG17g00900.1 Cpe17g00013 13
5 6431263 6435944 - CrPI670011_05g007250.1 Cre05g0725 725
5 6467419 6468513 - CrPI670011_05g007270.1 Cre05g0727 727
5 6475279 6489214 + CrPI670011_05g007290.1 Cre05g0729 729
5 6493800 6494779 - CrPI670011_05g007300.1 Cre05g0730 730
6 6769903 6776678 - CrPI670011_06g012860.1 Cre06g1286 1286
6 6789631 6795488 + CrPI670011_06g012870.1 Cre06g1287 1287
6 6796636 6800646 - CrPI670011_06g012880.1 Cre06g1288 1288
3 10732393 10736764 - CsaV3_3G014330.1 Csa03g01433 1433
3 10748030 10749142 - CsaV3_3G014360.1 Csa03g01436 1436
3 10774432 10788286 + CsaV3_3G014420.1 Csa03g01442 1442
3 10788445 10789888 - CsaV3_3G014430.1 Csa03g01443 1443
3 1383444 1385255 + Hsped.03g01140.1 Hepe03g0114 114
3 1386548 1393567 - Hsped.03g01150.1 Hepe03g0115 115
3 1408371 1416306 + Hsped.03g01160.1 Hepe03g0116 116
5 63995793 63997236 + Hsped.05g14610.1 Hepe05g1461 1461
5 64010189 64016625 - Hsped.05g14630.1 Hepe05g1463 1463
5 64057579 64062082 + Hsped.05g14660.1 Hepe05g1466 1466
12 41020109 41027954 + Lag0016765.1 Lac12g2393 2393
11 38126145 38127171 + Maker00031695 Lcy11g1429 1429
11 38234292 38238334 + Maker00031426 Lcy11g1433 1433
13 1927965 1929782 + Maker00023715 Lcy13g0186 186
13 1942382 1970300 - Maker00023356 Lcy13g0188 188
13 1979721 1987427 + Maker00023361 Lcy13g0190 190
13 1989255 1990406 - Maker00023898 Lcy13g0191 191
5 22999375 23002807 - Lsi05G015210.1 Lsi05g01521 1521
5 23030608 23031705 - Lsi05G015230.1 Lsi05g01523 1523
5 23036862 23056054 + Lsi05G015240.1 Lsi05g01524 1524
5 23056800 23057987 - Lsi05G015250.1 Lsi05g01525 1525
9 22109545 22114197 + Lsi09G014130.1 Lsi09g01413 1413
9 22119925 22127004 - Lsi09G014140.1 Lsi09g01414 1414
9 22155628 22163056 + Lsi09G014150.1 Lsi09g01415 1415
9 22165768 22167579 - Lsi09G014160.1 Lsi09g01416 1416
2 48927413 48929335 + Sed0007304.1 Sed02g1196 1196
2 48973653 48975037 - Sed0003137.1 Sed02g1207 1207
2 48985279 48989849 + Sed0013782.2 Sed02g1209 1209
9 1771000 1779350 - Sed0025025.1 Sed09g0226 226
9 36360231 36372730 + Sed0012078.3 Sed09g1215 1215
6 7154241 7179546 - Tan0012692.1 Tan06g0860 860
6 7227174 7228985 - Tan0001631.1 Tan06g0862 862
6 78980875 78988616 - Tan0008864.2 Tan06g2644 2644
10 8544136 8548661 - Tan0018479.1 Tan10g0977 977
10 8658021 8659759 - Tan0019544.3 Tan10g0983 983
5 3244890 3246711 + Vvi5g329 Vvi5g329 329
5 3254194 3263072 - Vvi5g330 Vvi5g330 330
5 3274388 3274837 - Vvi5g331 Vvi5g331 331
5 3279942 3300085 + Vvi5g332 Vvi5g332 332
5 3301314 3305240 + Vvi5g333 Vvi5g333 333
5 3307668 3310267 + Vvi5g334 Vvi5g334 334
5 3311938 3336770 - Vvi5g335 Vvi5g335 335
5 3339229 3340547 + Vvi5g336 Vvi5g336 336
5 3341974 3348425 - Vvi5g337 Vvi5g337 337
5 3360723 3368187 + Vvi5g338 Vvi5g338 338
       

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