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
Vvi17g806 . . . Bda15g00544 Bpe12g00667 . . . . . . Cma11g00075 Car10g00090 Car11g00067 . . Cpe04g01577 Bhi02g00504 Tan09g2293 . . Hepe09g0228 . . Cla06g01690 . . . . . . Cone2ag0926 Cone16ag0079 . . . . . . Blo13g00141 . . . . . . Bma08g00086 . Cmo10g00105 Cmo11g00076 . . . . . Cpe18g00862 . . . . . . . . . . . . . . Lsi06g01584 Csa01g00119 Chy02g02608 Cme02g02005
Vvi17g807 Blo04g00723 . . . . Bpe13g00253 Bma06g00209 Bma12g01050 Cmo13g00896 Cmo18g00147 Cma10g00101 Cma11g00074 . . . . . Bhi02g00505 . . . . . . Cla06g01691 . . . . . . . . . . Lsi02g00405 Csa01g00878 Chy12g01245 Cme12g01668 . Blo15g00255 Bda11g01664 . . Bpe15g00649 Bma03g00773 . . Cmo10g00104 Cmo11g00075 Cma13g00864 Cma18g00186 Car13g00707 Car18g00178 . . Bhi08g01652 . . . . . . Cla01g01325 . . . . . . Lsi06g01585 Csa01g00118 . Cme02g02006
Vvi17g808 . . . . . . . Bma12g01051 . Cmo18g00148 Cma10g00100 Cma11g00072 Car10g00088 Car11g00064 . . Cpe04g01579 Bhi02g00507 Tan09g2296 . . Hepe09g0230 . . Cla06g01692 Cam06g1880 Cec06g1927 Cco06g1932 Clacu06g1836 Cmu06g1778 Cre06g2593 . . Cone13ag0162 . Lsi02g00406 Csa01g00879 Chy12g01244 Cme12g01667 . Blo15g00254 . . . . . . Sed01g1626 Cmo10g00103 Cmo11g00074 . Cma18g00187 . Car18g00179 Cpe09g01008 Cpe18g00864 Bhi08g01653 Tan05g1977 Cmetu12g1973 Lac10g0487 Hepe07g2202 . . Cla01g01326 Cam01g1402 Cec01g1434 Cco01g1489 Clacu01g1392 Cmu01g1300 Cre01g1240 Lsi06g01586 Csa01g00117 Chy02g02610 Cme02g02007
Vvi17g809 Blo04g00722 . . . . Bpe13g00227 . . Cmo13g00894 Cmo18g00149 . . . . . Cpe20g00261 . . . . . . . . . . . . . . . . . Cone13ag0164 Cone19ag0161 Lsi02g00408 Csa01g00880 Chy12g01243 Cme12g01666 . . . Bda14g00800 . Bpe15g00650 Bma03g00772 . Sed01g1625 . . Cma13g00863 Cma18g00188 Car13g00706 Car18g00180 Cpe09g01007 . Bhi08g01654 Tan05g1976 Cmetu12g0479 Lac10g0488 Hepe07g2201 . . Cla01g01327 Cam01g1401 Cec01g1433 Cco01g1490 Clacu01g1393 . . . . . .
Vvi17g810 . . . . . . . . . . . . . . . . . Bhi02g00508 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo10g00102 . . . . . . . . . . . . . . . . . . . . . Lsi06g01587 Csa01g00116 . .
Vvi17g811 . . . . . . . . . . Cma10g00099 . Car10g00086 . . . . Bhi02g00510 . . . . . . Cla06g01693 Cam06g1881 Cec06g1928 Cco06g1933 Clacu06g1837 Cmu06g1779 Cre06g2594 Cone2ag0927 . . . . . . . . . . . Bpe07g00856 . . . . Cmo10g00101 . . . . . . Cpe18g00865 . . . . . . . . . . . . . . Lsi06g01588 . Chy02g02611 Cme02g02008
Vvi17g812 Blo04g00721 Blo16g00236 . . . . . . . . . . . . . . . Bhi02g00511 . . . Hepe09g0232 . . Cla06g01694 Cam06g1882 Cec06g1929 Cco06g1934 Clacu06g1838 Cmu06g1780 Cre06g2595 . . Cone13ag0165 Cone19ag0162 . . . . . . . Bda14g00799 . Bpe15g00651 Bma03g00771 . . . . . . . . . . . . . . . . . . . . . . . . . Csa01g00113 Chy02g02612 Cme02g02009
Vvi17g813 . . . . . . . . . . Cma10g00097 . Car10g00085 . . . . . . . . . . . . . . . . . . Cone2ag0929 Cone16ag0077 . . . . . . . . . . . . . . . Cmo10g00100 . . . . . . Cpe18g00866 . . . . . . . . . . . . . . . . . .
Vvi17g814 . . Bda06g00616 Bda15g00542 Bpe12g00669 . . Bma12g01052 . . Cma10g00096 . Car10g00084 . . . . Bhi02g00512 . . . . . . Cla06g01695 . . . . . . . Cone16ag0076 . . . . . . Blo13g00142 Blo15g00253 . . . . . Bma08g00085 . Cmo10g00099 . . . . . . Cpe18g00867 . . . . . . . . . . . . . . Lsi06g01590 . Chy02g02613 Cme02g02010
Vvi17g815 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 8441060 8443045 - Bda023887.1 Bda06g00616 616
11 50769070 50770284 + Bda008557.1 Bda11g01664 1664
14 6159525 6160543 + Bda027568.1 Bda14g00799 799
14 6162016 6162456 + Bda027569.1 Bda14g00800 800
15 8488442 8490412 + Bda012375.1 Bda15g00542 542
15 8497047 8499492 - Bda012377.1 Bda15g00544 544
2 9740456 9743576 - XM_039024256.1 Bhi02g00504 504
2 9761796 9763409 + XM_039023740.1 Bhi02g00505 505
2 9768008 9773621 - XM_039023248.1 Bhi02g00507 507
2 9814548 9819089 - XM_039023213.1 Bhi02g00508 508
2 9815197 9819090 - XM_039023215.1 Bhi02g00510 510
2 9821548 9823514 + XM_039023497.1 Bhi02g00511 511
2 9823746 9826286 - XM_039023496.1 Bhi02g00512 512
8 46660822 46662404 + XM_039039279.1 Bhi08g01652 1652
8 46681991 46685719 - XM_039038392.1 Bhi08g01653 1653
8 46691936 46692635 - XM_039037698.1 Bhi08g01654 1654
4 6645282 6646289 + BLOR13633 Blo04g00721 721
4 6646697 6647137 + BLOR13634 Blo04g00722 722
4 6658686 6659892 - BLOR13635 Blo04g00723 723
13 4441743 4444408 + BLOR05422 Blo13g00141 141
13 4487985 4489961 - BLOR05423 Blo13g00142 142
15 2616308 2618353 + BLOR06647 Blo15g00253 253
15 2638644 2644186 + BLOR06648 Blo15g00254 254
15 2645580 2646750 - BLOR06649 Blo15g00255 255
16 5273322 5281615 + BLOR07484 Blo16g00236 236
3 7053891 7054899 + Bma017073.1 Bma03g00771 771
3 7057314 7057754 + Bma017074.1 Bma03g00772 772
3 7068603 7069817 - Bma017076.2 Bma03g00773 773
6 2500237 2501450 - Bma022823.1 Bma06g00209 209
8 1000536 1002407 + Bma027084.1 Bma08g00085 85
8 1007157 1009573 - Bma027085.1 Bma08g00086 86
12 42589332 42590488 + Bma008398.1 Bma12g01050 1050
12 42592610 42598145 - Bma008399.1 Bma12g01051 1051
12 42625321 42627060 - Bma008401.1 Bma12g01052 1052
7 14710133 14715285 - Bpe021699.1 Bpe07g00856 856
12 12329785 12332213 + Bpe005927.1 Bpe12g00667 667
12 12342232 12343959 - Bpe005929.1 Bpe12g00669 669
13 10286471 10286911 - Bpe006350.1 Bpe13g00227 227
13 10498891 10500095 + Bpe006374.1 Bpe13g00253 253
15 17264500 17265718 + Bpe001582.1 Bpe15g00649 649
15 17270191 17270631 - Bpe001583.1 Bpe15g00650 650
15 17271565 17272534 - Bpe001584.2 Bpe15g00651 651
1 27555573 27555864 + CaPI482276_01g014010.1 Cam01g1401 1401
1 27561095 27563409 + CaPI482276_01g014020.1 Cam01g1402 1402
6 29846090 29852081 - CaPI482276_06g018800.1 Cam06g1880 1880
6 29867140 29871142 - CaPI482276_06g018810.1 Cam06g1881 1881
6 29871359 29874872 + CaPI482276_06g018820.1 Cam06g1882 1882
10 380276 382246 + Carg10316-RA Car10g00084 84
10 382462 385482 - Carg10317-RA Car10g00085 85
10 387970 393927 + Carg10318-RA Car10g00086 86
10 397853 402451 + Carg10320-RA Car10g00088 88
10 407695 410684 + Carg10322-RA Car10g00090 90
11 355024 359506 + Carg20202-RA Car11g00064 64
11 366512 370146 + Carg20205-RA Car11g00067 67
13 8321565 8322005 + Carg07656-RA Car13g00706 706
13 8326136 8327309 - Carg07657-RA Car13g00707 707
18 986377 987728 + Carg06745-RA Car18g00178 178
18 994559 996574 - Carg06746-RA Car18g00179 179
18 998539 998979 - Carg06747-RA Car18g00180 180
1 26674854 26676692 - CcPI632755_01g014890.1 Cco01g1489 1489
1 26682664 26683104 - CcPI632755_01g014900.1 Cco01g1490 1490
6 29581591 29587517 - CcPI632755_06g019320.1 Cco06g1932 1932
6 29602841 29606841 - CcPI632755_06g019330.1 Cco06g1933 1933
6 29608915 29610528 + CcPI632755_06g019340.1 Cco06g1934 1934
1 28979354 28979645 + CePI673135_01g014330.1 Cec01g1433 1433
1 28985780 28987618 + CePI673135_01g014340.1 Cec01g1434 1434
6 32655565 32661553 - CePI673135_06g019270.1 Cec06g1927 1927
6 32676692 32680687 - CePI673135_06g019280.1 Cec06g1928 1928
6 32682745 32684380 + CePI673135_06g019290.1 Cec06g1929 1929
2 29270383 29272931 - Chy2G048750.1 Chy02g02608 2608
2 29285236 29291231 - Chy2G048770.1 Chy02g02610 2610
2 29301519 29305529 - Chy2G048780.1 Chy02g02611 2611
2 29306563 29308378 + Chy2G048790.1 Chy02g02612 2612
2 29309257 29311227 - Chy2G048800.1 Chy02g02613 2613
12 17078721 17080578 + Chy12G218430.1 Chy12g01243 1243
12 17082362 17084206 + Chy12G218440.1 Chy12g01244 1244
12 17091737 17093076 - Chy12G218450.1 Chy12g01245 1245
1 25249640 25251668 - ClG42_01g0139200.10 Clacu01g1392 1392
1 25257602 25258042 - ClG42_01g0139300.10 Clacu01g1393 1393
6 28896952 28902943 - ClG42_06g0183600.10 Clacu06g1836 1836
6 28918003 28922005 - ClG42_06g0183700.10 Clacu06g1837 1837
6 28922222 28925736 + ClG42_06g0183800.10 Clacu06g1838 1838
1 26611282 26612591 + ClCG01G013430.2 Cla01g01325 1325
1 26629366 26631394 - ClCG01G013440.1 Cla01g01326 1326
1 26636224 26637768 - ClCG01G013450.2 Cla01g01327 1327
6 30490117 30495528 - ClCG06G017290.1 Cla06g01690 1690
6 30510579 30511887 + ClCG06G017300.1 Cla06g01691 1691
6 30522821 30528816 - ClCG06G017310.1 Cla06g01692 1692
6 30544448 30548417 - ClCG06G017320.2 Cla06g01693 1693
6 30548137 30552628 + ClCG06G017330.2 Cla06g01694 1694
6 30553401 30555371 - ClCG06G017340.2 Cla06g01695 1695
10 388019 389992 + CmaCh10G000960.1 Cma10g00096 96
10 390200 393331 - CmaCh10G000970.1 Cma10g00097 97
10 395810 402039 + CmaCh10G000990.1 Cma10g00099 99
10 406293 412264 + CmaCh10G001000.1 Cma10g00100 100
10 413606 415284 - CmaCh10G001010.1 Cma10g00101 101
11 355752 361673 + CmaCh11G000720.1 Cma11g00072 72
11 363238 364766 - CmaCh11G000740.1 Cma11g00074 74
11 365637 369286 + CmaCh11G000750.1 Cma11g00075 75
13 7083862 7084302 + CmaCh13G008630.1 Cma13g00863 863
13 7088748 7090209 - CmaCh13G008640.1 Cma13g00864 864
18 966783 968278 + CmaCh18G001860.1 Cma18g00186 186
18 974862 976934 - CmaCh18G001870.1 Cma18g00187 187
18 977231 979147 - CmaCh18G001880.1 Cma18g00188 188
2 26275912 26279232 - MELO3C026267.2.1 Cme02g02005 2005
2 26287173 26288059 + MELO3C026265.2.1 Cme02g02006 2006
2 26293025 26299361 - MELO3C026264.2.1 Cme02g02007 2007
2 26307652 26312452 - MELO3C026263.2.1 Cme02g02008 2008
2 26313517 26317455 + MELO3C026262.2.1 Cme02g02009 2009
2 26316302 26318389 - MELO3C026261.2.1 Cme02g02010 2010
12 23666257 23667064 + MELO3C002294.2.1 Cme12g01666 1666
12 23669860 23672343 + MELO3C002293.2.1 Cme12g01667 1667
12 23678995 23680642 - MELO3C002292.2.1 Cme12g01668 1668
12 2632377 2633572 - PI0020703.1 Cmetu12g0479 479
12 2625104 2628866 - PI0003182.1 Cmetu12g1973 1973
10 425577 427544 + CmoCh10G000990.1 Cmo10g00099 99
10 426124 431085 - CmoCh10G001000.1 Cmo10g00100 100
10 433222 437579 + CmoCh10G001010.1 Cmo10g00101 101
10 438031 439518 + CmoCh10G001020.1 Cmo10g00102 102
10 444706 450298 + CmoCh10G001030.1 Cmo10g00103 103
10 451776 453729 - CmoCh10G001040.1 Cmo10g00104 104
10 456335 459161 + CmoCh10G001050.1 Cmo10g00105 105
11 344115 349669 + CmoCh11G000740.1 Cmo11g00074 74
11 351186 352716 - CmoCh11G000750.1 Cmo11g00075 75
11 355753 360110 + CmoCh11G000760.1 Cmo11g00076 76
13 8013986 8014426 + CmoCh13G008940.1 Cmo13g00894 894
13 8018346 8019579 - CmoCh13G008960.1 Cmo13g00896 896
18 1039404 1040897 + CmoCh18G001470.1 Cmo18g00147 147
18 1047312 1049327 - CmoCh18G001480.1 Cmo18g00148 148
18 1051138 1051578 - CmoCh18G001490.1 Cmo18g00149 149
1 25588428 25590266 - CmPI595203_01g013000.1 Cmu01g1300 1300
6 28805652 28811417 - CmPI595203_06g017780.1 Cmu06g1778 1778
6 28826444 28830413 - CmPI595203_06g017790.1 Cmu06g1779 1779
6 28830572 28834107 + CmPI595203_06g017800.1 Cmu06g1780 1780
2 35032890 35035875 - Conep02aG0196000.1 Cone2ag0926 926
2 35049284 35050820 - Conep02aG0196100.1 Cone2ag0927 927
2 35055143 35058507 + Conep02aG0196300.1 Cone2ag0929 929
13 1017961 1020336 - Conep13aG0016700.1 Cone13ag0162 162
13 1029151 1030562 - Conep13aG0016900.1 Cone13ag0164 164
13 1030795 1032677 - Conep13aG0017000.1 Cone13ag0165 165
16 376673 379226 + Conep16aG0007700.1 Cone16ag0076 76
16 379740 382887 - Conep16aG0007800.1 Cone16ag0077 77
16 401802 405179 + Conep16aG0008000.1 Cone16ag0079 79
19 928430 929134 - Conep19aG0016700.1 Cone19ag0161 161
19 930016 931813 - Conep19aG0016800.1 Cone19ag0162 162
4 12326760 12333187 - Cp4.1LG04g15830.1 Cpe04g01577 1577
4 12335583 12341661 - Cp4.1LG04g15790.1 Cpe04g01579 1579
9 8908198 8908638 + Cp4.1LG09g09960.1 Cpe09g01007 1007
9 8911146 8913362 + Cp4.1LG09g10050.1 Cpe09g01008 1008
18 7920825 7924030 - Cp4.1LG18g08770.1 Cpe18g00862 862
18 7929019 7934404 - Cp4.1LG18g08730.1 Cpe18g00864 864
18 7938424 7945117 - Cp4.1LG18g08750.1 Cpe18g00865 865
18 7946506 7952467 + Cp4.1LG18g08590.1 Cpe18g00866 866
18 7950210 7952180 - Cp4.1LG18g08720.1 Cpe18g00867 867
20 1472626 1473066 - Cp4.1LG20g02550.1 Cpe20g00261 261
1 25590798 25593965 + CrPI670011_01g012400.1 Cre01g1240 1240
6 33629117 33635111 - CrPI670011_06g025930.1 Cre06g2593 2593
6 33650322 33654294 - CrPI670011_06g025940.1 Cre06g2594 2594
6 33656428 33658079 + CrPI670011_06g025950.1 Cre06g2595 2595
1 640192 645553 - CsaV3_1G001130.1 Csa01g00113 113
1 646275 650322 + CsaV3_1G001160.1 Csa01g00116 116
1 661266 667885 + CsaV3_1G001170.1 Csa01g00117 117
1 670253 672053 - CsaV3_1G001180.1 Csa01g00118 118
1 677610 680881 + CsaV3_1G001190.1 Csa01g00119 119
1 5484067 5485795 + CsaV3_1G008780.1 Csa01g00878 878
1 5490262 5494538 - CsaV3_1G008790.1 Csa01g00879 879
1 5495370 5497696 - CsaV3_1G008800.1 Csa01g00880 880
7 66400516 66401515 + Hsped.07g22010.1 Hepe07g2201 2201
7 66405723 66409622 + Hsped.07g22020.1 Hepe07g2202 2202
9 1964545 1967647 - Hsped.09g02280.1 Hepe09g0228 228
9 1986724 1992187 - Hsped.09g02300.1 Hepe09g0230 230
9 2040158 2041915 - Hsped.09g02320.1 Hepe09g0232 232
10 3754045 3755874 - Lag0024532.1 Lac10g0487 487
10 3759240 3759680 - Lag0024533.1 Lac10g0488 488
2 3417866 3419269 + Lsi02G004050.1 Lsi02g00405 405
2 3429591 3432277 - Lsi02G004060.1 Lsi02g00406 406
2 3435829 3436269 - Lsi02G004080.1 Lsi02g00408 408
6 26245458 26250610 - Lsi06G015840.1 Lsi06g01584 1584
6 26260003 26261515 + Lsi06G015850.1 Lsi06g01585 1585
6 26265780 26272521 - Lsi06G015860.1 Lsi06g01586 1586
6 26286850 26287812 - Lsi06G015870.1 Lsi06g01587 1587
6 26288150 26291485 - Lsi06G015880.1 Lsi06g01588 1588
6 26295136 26297106 - Lsi06G015900.1 Lsi06g01590 1590
1 11802602 11804553 + Sed0010183.1 Sed01g1625 1625
1 11805185 11808616 + Sed0009413.1 Sed01g1626 1626
5 69357467 69358189 + Tan0010913.1 Tan05g1976 1976
5 69362003 69365876 + Tan0019961.1 Tan05g1977 1977
9 72869652 72872823 - Tan0009881.2 Tan09g2293 2293
9 72887852 72894820 - Tan0009971.2 Tan09g2296 2296
17 10614426 10630758 - Vvi17g806 Vvi17g806 806
17 10650117 10651994 + Vvi17g807 Vvi17g807 807
17 10669112 10682432 - Vvi17g808 Vvi17g808 808
17 10706428 10707300 - Vvi17g809 Vvi17g809 809
17 10707718 10708704 - Vvi17g810 Vvi17g810 810
17 10708716 10715399 - Vvi17g811 Vvi17g811 811
17 10736575 10738749 - Vvi17g812 Vvi17g812 812
17 10745401 10748530 + Vvi17g813 Vvi17g813 813
17 10749583 10751781 - Vvi17g814 Vvi17g814 814
17 10759102 10765957 - Vvi17g815 Vvi17g815 815
       

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