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
Vvi17g716 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone2ag0894 Cone16ag0115 . . . . . . Blo13g00051 . . . . . . Bma08g00172 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g717 . . Bda06g00586 . . . . . . . Cma10g00135 Cma11g00105 Car10g00127 . Sed08g0139 . Cpe04g01547 Bhi02g00424 Tan09g2229 Cmetu02g0557 . Hepe09g0190 . . Cla06g01651 Cam06g1835 Cec06g1886 Cco06g1891 Clacu06g1795 Cmu06g1737 Cre06g2555 . . . . . . . . . Blo15g00275 . . Bpe07g00827 . . . . Cmo10g00141 Cmo11g00107 . . . . . Cpe18g00836 . . . . . . . . . . . . . . Lsi06g01540 Csa01g00164 Chy02g02567 Cme02g01956
Vvi17g718 . . . . . . . . Cmo13g00926 . . . . . . Cpe20g00229 . . . . . . . . . . . . . . . Cone2ag0895 . . . Lsi02g00358 Csa01g00835 Chy12g01283 . . . . . . . . . . . . Cma13g00899 . Car13g00739 . . . Bhi08g01588 . . Lac10g0431 . . . Cla01g01285 Cam01g1443 Cec01g1481 Cco01g1446 Clacu01g1352 Cmu01g1256 Cre01g1280 . . . .
Vvi17g719 . . Bda06g00587 . Bpe12g00587 . . . Cmo13g00925 . Cma10g00133 . Car10g00126 . . Cpe20g00230 . Bhi02g00426 . . . . . . Cla06g01652 Cam06g1836 Cec06g1887 Cco06g1892 Clacu06g1796 Cmu06g1738 Cre06g2556 Cone2ag0896 . . . Lsi02g00359 Csa01g00837 Chy12g01282 Cme12g01707 Blo13g00052 Blo15g00274 . . Bpe07g00828 . . Bma08g00171 Sed08g2494 Cmo10g00140 . Cma13g00898 . Car13g00738 . . Cpe18g00837 Bhi08g01589 Tan05g2027 Cmetu12g1070 Lac10g0432 Hepe07g2240 . . Cla01g01286 Cam01g1442 Cec01g1480 Cco01g1447 Clacu01g1353 Cmu01g1257 Cre01g1279 Lsi06g01542 Csa01g00162 Chy02g02568 Cme02g01957
Vvi17g720 . . . Bda15g00779 . . . . . . . . Car10g00125 . . . . Bhi02g00428 . . . Hepe09g0191 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa01g00161 . .
Vvi17g721 . . . . Bpe12g00588 . . . . . Cma10g00132 . . . . . . Bhi02g00430 . . . . . . Cla06g01653 Cam06g1837 Cec06g1888 Cco06g1893 Clacu06g1797 Cmu06g1739 Cre06g2557 . . Cone13ag0132 . . . . . Blo13g00053 . . . . . . Bma08g00170 . Cmo10g00139 . . . . . . Cpe18g00838 . . . . . . . . . . . . . . Lsi06g01543 . Chy02g02569 Cme02g01958
Vvi17g722 . . . . Bpe12g00589 . . . . . . Cma11g00104 . Car11g00103 Sed12g1882 . Cpe04g01548 Bhi02g00432 Tan09g2233 Cmetu05g1877 . Hepe09g0192 . . Cla06g01654 Cam06g1838 Cec06g1889 Cco06g1894 Clacu06g1798 Cmu06g1740 Cre06g2558 . . Cone13ag0133 . . . . . . . . . . . . . . . Cmo11g00105 . . . . . . . . . . . . . . . . . . . . Lsi06g01544 Csa01g00160 Chy02g02570 Cme02g01959
Vvi17g723 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g724 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g725 . . Bda06g00588 . Bpe12g00591 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00363 Csa01g00840 Chy12g01278 Cme12g01704 Blo13g00054 Blo15g00273 . . Bpe07g00830 . . . . . . . Cma18g00160 . . . . . . . . . . . Cla01g01289 Cam01g1439 Cec01g1477 Cco01g1451 Clacu01g1356 . Cre01g1275 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 8106162 8107978 - Bda023850.1 Bda06g00586 586
6 8115044 8117872 - Bda023851.1 Bda06g00587 587
6 8121751 8123068 + Bda023852.1 Bda06g00588 588
15 11637413 11642280 + Bda012636.1 Bda15g00779 779
2 7841759 7846571 - XM_039022995.1 Bhi02g00424 424
2 7926285 7943548 - XM_039023987.1 Bhi02g00426 426
2 7992288 7997953 + XM_039022359.1 Bhi02g00428 428
2 7992288 7997953 + XM_039022361.1 Bhi02g00430 430
2 8062058 8065552 + XM_039024758.1 Bhi02g00432 432
8 45579586 45582724 + XM_039037733.1 Bhi08g01588 1588
8 45581984 45585706 - XM_039037734.1 Bhi08g01589 1589
13 753212 754773 - BLOR05332 Blo13g00051 51
13 772326 777609 - BLOR05333 Blo13g00052 52
13 779490 782661 + BLOR05334 Blo13g00053 53
13 819931 820522 + BLOR05335 Blo13g00054 54
15 2941721 2952067 - BLOR06667 Blo15g00273 273
15 2961432 2963813 + BLOR06668 Blo15g00274 274
15 2979844 2982545 + BLOR06669 Blo15g00275 275
8 2120933 2124311 - Bma027171.1 Bma08g00170 170
8 2130172 2133193 + Bma027172.1 Bma08g00171 171
8 2149183 2149683 + Bma027173.1 Bma08g00172 172
7 14522840 14525580 - Bpe026082 Bpe07g00827 827
7 14531443 14533357 - Bpe021672.1 Bpe07g00828 828
7 14537155 14538447 + Bpe021674.1 Bpe07g00830 830
12 11654547 11656860 - Bpe005850.1 Bpe12g00587 587
12 11659486 11662643 + Bpe005851.1 Bpe12g00588 588
12 11666187 11669023 + Bpe005852.1 Bpe12g00589 589
12 11672888 11673761 + Bpe005854.1 Bpe12g00591 591
1 27981034 27982258 - CaPI482276_01g014390.1 Cam01g1439 1439
1 28005187 28008208 + CaPI482276_01g014420.1 Cam01g1442 1442
1 28008360 28011911 - CaPI482276_01g014430.1 Cam01g1443 1443
6 29369044 29376259 - CaPI482276_06g018350.1 Cam06g1835 1835
6 29393797 29400877 - CaPI482276_06g018360.1 Cam06g1836 1836
6 29405063 29410288 + CaPI482276_06g018370.1 Cam06g1837 1837
6 29414919 29418099 + CaPI482276_06g018380.1 Cam06g1838 1838
10 587288 590378 - Carg10357-RA Car10g00125 125
10 594314 596070 + Carg10358-RA Car10g00126 126
10 601967 604725 + Carg10359-RA Car10g00127 127
11 583895 587197 - Carg18139-RA Car11g00103 103
13 8463360 8465255 + Carg07688-RA Car13g00738 738
13 8464684 8468016 - Carg07689-RA Car13g00739 739
1 26216941 26220566 + CcPI632755_01g014460.1 Cco01g1446 1446
1 26220667 26224109 - CcPI632755_01g014470.1 Cco01g1447 1447
1 26259353 26260540 + CcPI632755_01g014510.1 Cco01g1451 1451
6 29090685 29094416 - CcPI632755_06g018910.1 Cco06g1891 1891
6 29111986 29119238 - CcPI632755_06g018920.1 Cco06g1892 1892
6 29123325 29128561 + CcPI632755_06g018930.1 Cco06g1893 1893
6 29133337 29136512 + CcPI632755_06g018940.1 Cco06g1894 1894
1 29451529 29452757 - CePI673135_01g014770.1 Cec01g1477 1477
1 29475502 29478789 + CePI673135_01g014800.1 Cec01g1480 1480
1 29478941 29482606 - CePI673135_01g014810.1 Cec01g1481 1481
6 32150692 32154817 - CePI673135_06g018860.1 Cec06g1886 1886
6 32171560 32178763 - CePI673135_06g018870.1 Cec06g1887 1887
6 32183045 32188257 + CePI673135_06g018880.1 Cec06g1888 1888
6 32192958 32196107 + CePI673135_06g018890.1 Cec06g1889 1889
2 28885919 28888692 - Chy2G048340.1 Chy02g02567 2567
2 28901708 28905741 - Chy2G048350.1 Chy02g02568 2568
2 28909271 28912672 + Chy2G048360.1 Chy02g02569 2569
2 28916466 28919464 + Chy2G048370.1 Chy02g02570 2570
12 17327082 17329332 - Chy12G218780.1 Chy12g01278 1278
12 17343226 17345211 + Chy12G218820.1 Chy12g01282 1282
12 17345232 17347270 - Chy12G218830.1 Chy12g01283 1283
1 24792881 24796495 + ClG42_01g0135200.10 Clacu01g1352 1352
1 24796649 24799753 - ClG42_01g0135300.10 Clacu01g1353 1353
1 24822558 24823783 + ClG42_01g0135600.10 Clacu01g1356 1356
6 28428550 28432271 - ClG42_06g0179500.10 Clacu06g1795 1795
6 28449893 28457123 - ClG42_06g0179600.10 Clacu06g1796 1796
6 28461353 28466800 + ClG42_06g0179700.10 Clacu06g1797 1797
6 28471426 28474598 + ClG42_06g0179800.10 Clacu06g1798 1798
1 26127088 26131664 + ClCG01G013000.1 Cla01g01285 1285
1 26130950 26134166 - ClCG01G013010.1 Cla01g01286 1286
1 26158144 26169334 + ClCG01G013050.1 Cla01g01289 1289
6 30009658 30013018 - ClCG06G016880.1 Cla06g01651 1651
6 30031638 30042180 - ClCG06G016890.2 Cla06g01652 1652
6 30046179 30052129 + ClCG06G016900.2 Cla06g01653 1653
6 30056618 30060111 + ClCG06G016910.1 Cla06g01654 1654
10 600493 604390 - CmaCh10G001320.1 Cma10g00132 132
10 605951 608153 + CmaCh10G001330.1 Cma10g00133 133
10 613343 616102 + CmaCh10G001350.1 Cma10g00135 135
11 552767 555871 - CmaCh11G001040.1 Cma11g00104 104
11 560642 566492 + CmaCh11G001050.1 Cma11g00105 105
13 7223920 7226064 + CmaCh13G008980.1 Cma13g00898 898
13 7224517 7230006 - CmaCh13G008990.1 Cma13g00899 899
18 806181 807357 + CmaCh18G001600.1 Cma18g00160 160
2 25829505 25834114 - MELO3C017104.2.1 Cme02g01956 1956
2 25845568 25849148 - MELO3C017103.2.1 Cme02g01957 1957
2 25852405 25856201 + MELO3C017101.2.1 Cme02g01958 1958
2 25859064 25862430 + MELO3C017100.2.1 Cme02g01959 1959
12 23901102 23902341 - MELO3C002256.2.1 Cme12g01704 1704
12 23916762 23919285 + MELO3C002252.2.1 Cme12g01707 1707
2 24165530 24169230 - PI0016238.1 Cmetu02g0557 557
5 2268849 2272384 - PI0018397.1 Cmetu05g1877 1877
12 2362811 2365607 - PI0028231.1 Cmetu12g1070 1070
10 641446 645307 - CmoCh10G001390.1 Cmo10g00139 139
10 648065 656281 + CmoCh10G001400.1 Cmo10g00140 140
10 656364 659122 + CmoCh10G001410.1 Cmo10g00141 141
11 548605 551653 - CmoCh11G001050.1 Cmo11g00105 105
11 557057 562732 + CmoCh11G001070.1 Cmo11g00107 107
13 8161792 8163681 + CmoCh13G009250.1 Cmo13g00925 925
13 8163379 8166801 - CmoCh13G009260.1 Cmo13g00926 926
1 25134005 25137619 + CmPI595203_01g012560.1 Cmu01g1256 1256
1 25137773 25141028 - CmPI595203_01g012570.1 Cmu01g1257 1257
6 28331807 28335528 - CmPI595203_06g017370.1 Cmu06g1737 1737
6 28353140 28360392 - CmPI595203_06g017380.1 Cmu06g1738 1738
6 28364609 28369777 + CmPI595203_06g017390.1 Cmu06g1739 1739
6 28374396 28377568 + CmPI595203_06g017400.1 Cmu06g1740 1740
2 34799560 34800857 - Conep02aG0192400.1 Cone2ag0894 894
2 34806763 34809143 + Conep02aG0192500.1 Cone2ag0895 895
2 34809788 34810725 - Conep02aG0192600.1 Cone2ag0896 896
13 761986 764992 + Conep13aG0013700.1 Cone13ag0132 132
13 765770 769967 + Conep13aG0013800.1 Cone13ag0133 133
16 671041 672250 + Conep16aG0011700.1 Cone16ag0115 115
4 12122590 12126661 - Cp4.1LG04g15490.1 Cpe04g01547 1547
4 12131591 12137677 + Cp4.1LG04g15470.1 Cpe04g01548 1548
18 7720004 7727430 - Cp4.1LG18g08450.1 Cpe18g00836 836
18 7732154 7734193 - Cp4.1LG18g08460.1 Cpe18g00837 837
18 7736171 7742588 + Cp4.1LG18g08370.1 Cpe18g00838 838
20 1316247 1320182 + Cp4.1LG20g02260.1 Cpe20g00229 229
20 1318380 1320977 - Cp4.1LG20g02410.1 Cpe20g00230 230
1 26026708 26027953 - CrPI670011_01g012750.1 Cre01g1275 1275
1 26054395 26057695 + CrPI670011_01g012790.1 Cre01g1279 1279
1 26057847 26061545 - CrPI670011_01g012800.1 Cre01g1280 1280
6 33151282 33156350 - CrPI670011_06g025550.1 Cre06g2555 2555
6 33172039 33179186 - CrPI670011_06g025560.1 Cre06g2556 2556
6 33183457 33188695 + CrPI670011_06g025570.1 Cre06g2557 2557
6 33193422 33196608 + CrPI670011_06g025580.1 Cre06g2558 2558
1 1036221 1040968 - CsaV3_1G001600.1 Csa01g00160 160
1 1043898 1047591 - CsaV3_1G001610.1 Csa01g00161 161
1 1051117 1055704 + CsaV3_1G001620.1 Csa01g00162 162
1 1067140 1069916 + CsaV3_1G001640.1 Csa01g00164 164
1 5248390 5251112 + CsaV3_1G008350.1 Csa01g00835 835
1 5250854 5252331 - CsaV3_1G008370.1 Csa01g00837 837
1 5264997 5266701 + CsaV3_1G008400.1 Csa01g00840 840
7 66812405 66814989 + Hsped.07g22400.1 Hepe07g2240 2240
9 1493385 1498938 - Hsped.09g01900.1 Hepe09g0190 190
9 1516181 1521032 + Hsped.09g01910.1 Hepe09g0191 191
9 1523972 1527515 + Hsped.09g01920.1 Hepe09g0192 192
10 3377263 3381913 + Lag0024476.1 Lac10g0431 431
10 3382072 3384014 - Lag0024477.1 Lac10g0432 432
2 3059482 3062575 + Lsi02G003580.1 Lsi02g00358 358
2 3061914 3065916 - Lsi02G003590.1 Lsi02g00359 359
2 3091531 3101671 + Lsi02G003630.1 Lsi02g00363 363
6 25744451 25753323 - Lsi06G015400.1 Lsi06g01540 1540
6 25771974 25779002 - Lsi06G015420.1 Lsi06g01542 1542
6 25786415 25790162 + Lsi06G015430.1 Lsi06g01543 1543
6 25796226 25799926 + Lsi06G015440.1 Lsi06g01544 1544
8 799337 802106 + Sed0025031.1 Sed08g0139 139
8 37777103 37779559 - Sed0002842.1 Sed08g2494 2494
12 30009036 30012851 - Sed0023744.1 Sed12g1882 1882
5 70404494 70406500 + Tan0018574.1 Tan05g2027 2027
9 72247966 72253928 - Tan0021939.2 Tan09g2229 2229
9 72300960 72304519 + Tan0011084.1 Tan09g2233 2233
17 8991056 8992372 - Vvi17g716 Vvi17g716 716
17 8992842 8998935 - Vvi17g717 Vvi17g717 717
17 9003952 9006962 + Vvi17g718 Vvi17g718 718
17 9007208 9010760 - Vvi17g719 Vvi17g719 719
17 9017131 9026798 + Vvi17g720 Vvi17g720 720
17 9032364 9039270 + Vvi17g721 Vvi17g721 721
17 9063731 9068490 + Vvi17g722 Vvi17g722 722
17 9093026 9096725 + Vvi17g723 Vvi17g723 723
17 9097090 9098131 - Vvi17g724 Vvi17g724 724
17 9117590 9119104 + Vvi17g725 Vvi17g725 725
       

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