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
Vvi19g504 . . . . Bpe09g00179 . . . . . . . . . . . . . . . . . . . Cla10g00511 Cam10g0506 Cec10g0523 Cco10g0510 Clacu10g0527 Cmu10g1353 Cre10g0757 . . . Cone15ag1159 . Csa03g00519 . Cme06g02258 . Blo10g00827 . Bda12g00905 . . . . Sed13g1180 . . Cma04g00947 Cma16g00862 . . . . Bhi11g00628 Tan01g1699 Cmetu06g0121 . . Mch10g1264 . . . . . . . . Lsi05g00604 . Chy06g01811 .
Vvi19g505 . . . . Bpe09g00178 . Bma10g00545 . Cmo16g00900 . . . . . . . . . . . . . . . Cla10g00509 Cam10g0504 Cec10g0521 Cco10g0508 Clacu10g0525 Cmu10g1351 Cre10g0755 . . . . . Csa03g00518 . Cme06g02257 Blo07g00908 Blo10g00828 Bda05g00724 . . Bpe03g00794 . . . . . Cma04g00946 Cma16g00863 . . . . Bhi11g00624 . . . . . . . . . . . . . Lsi05g00603 . Chy06g01812 .
Vvi19g506 . . . . Bpe09g00177 . Bma10g00546 Bma13g01055 . Cmo04g01027 . . . . . . . . . . . . . . Cla10g00508 Cam10g0503 Cec10g0520 Cco10g0507 Clacu10g0523 Cmu10g1349 Cre10g0754 . . Cone14ag1141 . . Csa03g00517 . Cme06g02256 Blo07g00907 Blo10g00829 Bda05g00723 Bda12g00906 . Bpe03g00793 . . . . . . . Car04g00894 . . Cpe01g00867 Bhi11g00622 . . . . Mch10g1268 . . . . . . . . Lsi05g00602 . Chy06g01813 .
Vvi19g507 Blo03g00559 . Bda07g00360 . . . . . . . Cma01g01133 Cma09g00950 . Car09g00863 . Cpe06g00765 Cpe02g00768 . . . . . . . . . . . . . . . . Cone14ag1142 Cone15ag1160 Lsi04g01203 . . . . . . . Bpe11g00547 . . Bma14g00339 . Cmo01g01184 Cmo09g00948 . . . Car16g00544 . . . . . . . . . Cla05g01487 . Cec05g1613 . Clacu05g1583 Cmu05g1486 . . . . .
Vvi19g508 . Blo03g01449 . . . Bpe08g01125 . . . . . Cma09g00951 . Car09g00864 Sed07g2689 Cpe06g00766 . Bhi09g01866 Tan01g4548 Cmetu01g1257 . Hepe01g1279 Mch11g1187 . . . . . . . . . . . . Lsi04g01202 . . . . . . . . . Bma07g01298 . . . Cmo09g00949 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g509 . Blo03g01451 Bda07g00362 Bda09g00401 . Bpe08g01123 Bma10g00547 Bma13g01056 Cmo16g00894 Cmo06g00920 Cma01g01132 Cma09g00953 . Car09g00866 Sed05g0664 Cpe06g00768 Cpe02g00770 Bhi09g01642 Tan01g4552 Cmetu06g1796 . Hepe01g1277 Mch11g1189 . . . . . . . . . . Cone14ag1143 Cone15ag1161 Lsi02g01905 Csa07g01090 . . Blo07g00906 Blo10g00831 . Bda12g00908 Bpe11g00549 . Bma07g01296 Bma14g00337 . Cmo01g01183 Cmo09g00951 . . . Car16g00841 . . . . . . . . . Cla09g01008 Cam09g1065 Cec09g1066 Cco09g1083 . . Cre09g1029 . . . Cme01g01046
Vvi19g510 Blo03g00558 . Bda07g00363 . . . . . . . Cma01g01131 . . Car09g00867 Sed07g2683 Cpe06g00769 Cpe02g00771 Bhi09g01644 Tan01g4553 Cmetu01g1527 . Hepe01g1276 Mch11g1190 . . . . . . . . . . . . Lsi02g01904 Csa07g01091 . . . . . . Bpe11g00550 . . . . Cmo01g01181 Cmo09g00952 . . . Car16g00541 . . . . . . . . . Cla09g01009 Cam09g1067 Cec09g1067 Cco09g1085 . . Cre09g1030 . . . Cme01g01045
Vvi19g511 . . . . Bpe09g00176 . Bma10g00548 . Cmo16g00896 Cmo04g01031 . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1144 Cone15ag1162 . Csa03g00508 . . Blo07g00905 Blo10g00832 Bda05g00722 Bda12g00909 . . . . . . . Cma04g00958 Cma16g00866 Car04g00897 Car16g00843 . Cpe01g00870 . . . . . . . . . . . . . . . . . .
Vvi19g512 . Blo03g01452 Bda07g00364 . . Bpe08g01122 . . . . . Cma09g00954 . Car09g00868 . . . Bhi09g01646 . . . Hepe01g1274 . . . . . . . . . . . . . . Csa07g01092 . . . . . . . . Bma07g01295 Bma14g00336 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g513 . . . . Bpe09g00175 . Bma10g00549 Bma13g01058 Cmo16g00897 Cmo04g01032 . . . . . . . . . . . . . . Cla10g00502 Cam10g0496 Cec10g0513 Cco10g0499 Clacu10g0517 Cmu10g1343 Cre10g0748 . . . . . . . Cme06g02248 Blo07g00904 Blo10g00833 . Bda12g00910 . Bpe03g00792 . . . . . Cma04g00959 . Car04g00898 . . Cpe01g00871 . . . . . . . . . . . . . . Lsi05g00594 . Chy06g01818 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 55608097 55610331 + Bda021864.1 Bda05g00722 722
5 55614670 55616468 + Bda021865.1 Bda05g00723 723
5 55618922 55620088 + Bda021866.1 Bda05g00724 724
7 4596074 4599922 + Bda025445.1 Bda07g00360 360
7 4616904 4620516 + Bda025447.1 Bda07g00362 362
7 4621128 4623896 - Bda025448.1 Bda07g00363 363
7 4643936 4646551 - Bda025449.1 Bda07g00364 364
9 5034150 5035673 + Bda030981.1 Bda09g00401 401
12 39775816 39780906 + Bda009440.2 Bda12g00905 905
12 39792097 39793955 - Bda009442.2 Bda12g00906 906
12 39798270 39801563 + Bda009444.1 Bda12g00908 908
12 39802908 39805061 - Bda009445.1 Bda12g00909 909
12 39806485 39809564 + Bda009446.2 Bda12g00910 910
9 44212576 44215483 + XM_039041828.1 Bhi09g01642 1642
9 44215628 44219641 - XM_039041831.1 Bhi09g01644 1644
9 44221172 44226425 - XM_039041526.1 Bhi09g01646 1646
9 51474386 51478396 + XM_039040974.1 Bhi09g01866 1866
11 14510216 14514072 + XM_039047733.1 Bhi11g00622 622
11 14600618 14608658 + XM_039049660.1 Bhi11g00624 624
11 14610140 14618342 - XM_039050397.1 Bhi11g00628 628
3 22033884 22051218 + BLOR11739 Blo03g00558 558
3 22161794 22171836 - BLOR11740 Blo03g00559 559
3 41134915 41137198 - BLOR12630 Blo03g01449 1449
3 41144950 41148168 + BLOR12632 Blo03g01451 1451
3 41149327 41153282 - BLOR12633 Blo03g01452 1452
7 27968920 27971764 - BLOR18836 Blo07g00904 904
7 27976899 27979246 + BLOR18837 Blo07g00905 905
7 27979929 27983441 - BLOR18838 Blo07g00906 906
7 27989165 27992314 + BLOR18839 Blo07g00907 907
7 28004682 28006202 + BLOR18840 Blo07g00908 908
10 26106790 26112084 + BLOR02617 Blo10g00827 827
10 26116015 26117130 - BLOR02618 Blo10g00828 828
10 26125003 26126709 - BLOR02619 Blo10g00829 829
10 26131292 26132812 + BLOR02621 Blo10g00831 831
10 26134300 26136857 - BLOR02622 Blo10g00832 832
10 26139726 26143651 + BLOR02623 Blo10g00833 833
7 48570884 48571653 + Bma026570.1 Bma07g01295 1295
7 48574989 48578070 - Bma026571.2 Bma07g01296 1296
7 48590192 48592988 + Bma026573.1 Bma07g01298 1298
10 6626330 6627498 - Bma004244.2 Bma10g00545 545
10 6629578 6631415 - Bma004245.1 Bma10g00546 546
10 6638556 6643252 + Bma004247.1 Bma10g00547 547
10 6644397 6646606 - Bma004248.1 Bma10g00548 548
10 6659073 6661619 + Bma004249.1 Bma10g00549 549
13 43289930 43291619 - Bma010175.5 Bma13g01055 1055
13 43293777 43297057 + Bma010176.1 Bma13g01056 1056
13 43309543 43312888 + Bma010178.2 Bma13g01058 1058
14 4188521 4190440 + Bma010757.1 Bma14g00336 336
14 4199135 4202564 - Bma010758.1 Bma14g00337 337
14 4220531 4224620 - Bma010760.1 Bma14g00339 339
3 27883815 27886565 - Bpe012704.1 Bpe03g00792 792
3 27896269 27898109 + Bpe012705.1 Bpe03g00793 793
3 27904712 27905875 + Bpe012706.1 Bpe03g00794 794
8 13183576 13184344 + Bpe023248.1 Bpe08g01122 1122
8 13186904 13189577 - Bpe023249.1 Bpe08g01123 1123
8 13194295 13196806 + Bpe023251.1 Bpe08g01125 1125
9 1206001 1209469 - Bpe023846.2 Bpe09g00175 175
9 1210926 1213094 + Bpe023847.1 Bpe09g00176 176
9 1220897 1222790 + Bpe023848.1 Bpe09g00177 177
9 1230112 1231266 + Bpe023849.1 Bpe09g00178 178
9 1235098 1240204 - Bpe023850.1 Bpe09g00179 179
11 4192068 4195943 + Bpe003914.1 Bpe11g00547 547
11 4205122 4208615 + Bpe003916.1 Bpe11g00549 549
11 4209173 4212001 - Bpe003917.1 Bpe11g00550 550
9 11006564 11009066 + CaPI482276_09g010650.1 Cam09g1065 1065
9 11009722 11018605 - CaPI482276_09g010670.1 Cam09g1067 1067
10 7432432 7436589 + CaPI482276_10g004960.1 Cam10g0496 496
10 7497365 7501272 + CaPI482276_10g005030.1 Cam10g0503 503
10 7513665 7515114 + CaPI482276_10g005040.1 Cam10g0504 504
10 7529748 7538587 - CaPI482276_10g005060.1 Cam10g0506 506
4 5128526 5131039 - Carg00069-RA Car04g00894 894
4 5141178 5144023 - Carg00072-RA Car04g00897 897
4 5146694 5150243 + Carg00073-RA Car04g00898 898
9 5277378 5286087 + Carg12817-RA Car09g00863 863
9 5287590 5290963 - Carg12818-RA Car09g00864 864
9 5301316 5303732 + Carg12820-RA Car09g00866 866
9 5303948 5308052 - Carg12821-RA Car09g00867 867
9 5309015 5310795 - Carg12822-RA Car09g00868 868
16 3433298 3438494 + Carg05626-RA Car16g00541 541
16 3446538 3451546 - Carg05629-RA Car16g00544 544
16 6057221 6061587 + Carg27844-RA Car16g00841 841
16 6107240 6108679 - Carg28143-RA Car16g00843 843
9 10335689 10338186 + CcPI632755_09g010830.1 Cco09g1083 1083
9 10338694 10347639 - CcPI632755_09g010850.1 Cco09g1085 1085
10 5995677 5999855 + CcPI632755_10g004990.1 Cco10g0499 499
10 6077178 6081089 + CcPI632755_10g005070.1 Cco10g0507 507
10 6093656 6095747 + CcPI632755_10g005080.1 Cco10g0508 508
10 6109470 6118271 - CcPI632755_10g005100.1 Cco10g0510 510
5 25045948 25051220 + CePI673135_05g016130.1 Cec05g1613 1613
9 10365877 10368372 + CePI673135_09g010660.1 Cec09g1066 1066
9 10368414 10377703 - CePI673135_09g010670.1 Cec09g1067 1067
10 6192428 6196617 + CePI673135_10g005130.1 Cec10g0513 513
10 6266428 6270222 + CePI673135_10g005200.1 Cec10g0520 520
10 6282510 6283961 + CePI673135_10g005210.1 Cec10g0521 521
10 6298562 6307423 - CePI673135_10g005230.1 Cec10g0523 523
6 21778666 21785688 + Chy6G123390.1 Chy06g01811 1811
6 21787206 21788663 - Chy6G123400.1 Chy06g01812 1812
6 21800351 21834300 - Chy6G123410.1 Chy06g01813 1813
6 21872908 21876803 - Chy6G123460.1 Chy06g01818 1818
5 22525136 22530390 + ClG42_05g0158300.10 Clacu05g1583 1583
10 6266804 6270954 + ClG42_10g0051700.10 Clacu10g0517 517
10 6334654 6338704 + ClG42_10g0052300.10 Clacu10g0523 523
10 6351099 6352548 + ClG42_10g0052500.10 Clacu10g0525 525
10 6367148 6375944 - ClG42_10g0052700.10 Clacu10g0527 527
5 23738030 23743442 + ClCG05G014290.2 Cla05g01487 1487
9 10596549 10599046 + ClCG09G010790.2 Cla09g01008 1008
9 10599380 10609248 - ClCG09G010800.2 Cla09g01009 1009
10 6666675 6671533 + ClCG10G005370.1 Cla10g00502 502
10 6736124 6740034 + ClCG10G005430.1 Cla10g00508 508
10 6745232 6754263 + ClCG10G005440.1 Cla10g00509 509
10 6768802 6777987 - ClCG10G005460.2 Cla10g00511 511
1 8282139 8286583 + CmaCh01G011310.1 Cma01g01131 1131
1 8286365 8288903 - CmaCh01G011320.1 Cma01g01132 1132
1 8301299 8306825 - CmaCh01G011330.1 Cma01g01133 1133
4 4857238 4861383 + CmaCh04G009460.1 Cma04g00946 946
4 4861507 4869551 - CmaCh04G009470.1 Cma04g00947 947
4 4914594 4918334 - CmaCh04G009580.1 Cma04g00958 958
4 4922250 4931175 + CmaCh04G009590.1 Cma04g00959 959
9 4772295 4779686 + CmaCh09G009500.1 Cma09g00950 950
9 4779555 4783788 - CmaCh09G009510.1 Cma09g00951 951
9 4792700 4795110 + CmaCh09G009530.1 Cma09g00953 953
9 4795337 4801100 - CmaCh09G009540.1 Cma09g00954 954
16 5120756 5129805 + CmaCh16G008620.1 Cma16g00862 862
16 5130249 5138432 - CmaCh16G008630.1 Cma16g00863 863
16 5212617 5214360 - CmaCh16G008660.1 Cma16g00866 866
1 12893404 12900484 + MELO3C013167.2.1 Cme01g01045 1045
1 12898884 12901727 - MELO3C013168.2.1 Cme01g01046 1046
6 29467259 29471926 + MELO3C025374.2.1 Cme06g02248 2248
6 29567255 29571254 + MELO3C025383.2.1 Cme06g02256 2256
6 29574276 29584188 + MELO3C025384.2.1 Cme06g02257 2257
6 29584838 29594761 - MELO3C025386.2.1 Cme06g02258 2258
1 9219814 9223866 - PI0001549.1 Cmetu01g1257 1257
1 10728083 10732088 - PI0028650.1 Cmetu01g1527 1527
6 26150066 26157683 + PI0006465.1 Cmetu06g0121 121
6 26310059 26313512 + PI0014345.1 Cmetu06g1796 1796
1 9611098 9617981 + CmoCh01G011810.1 Cmo01g01181 1181
1 9618144 9620687 - CmoCh01G011830.1 Cmo01g01183 1183
1 9626023 9630560 - CmoCh01G011840.1 Cmo01g01184 1184
4 5141883 5150880 - CmoCh04G010270.1 Cmo04g01027 1027
4 5159300 5163562 - CmoCh04G010310.1 Cmo04g01031 1031
4 5164440 5168006 + CmoCh04G010320.1 Cmo04g01032 1032
6 6618306 6629205 - CmoCh06G009200.1 Cmo06g00920 920
9 4976312 4985160 + CmoCh09G009480.1 Cmo09g00948 948
9 4986200 4990167 - CmoCh09G009490.1 Cmo09g00949 949
9 4999968 5002442 + CmoCh09G009510.1 Cmo09g00951 951
9 5002570 5009449 - CmoCh09G009520.1 Cmo09g00952 952
16 5138988 5143020 + CmoCh16G008940.1 Cmo16g00894 894
16 5204595 5206074 - CmoCh16G008960.1 Cmo16g00896 896
16 5267062 5271580 + CmoCh16G008970.1 Cmo16g00897 897
16 5302709 5304215 + CmoCh16G009000.1 Cmo16g00900 900
5 22249912 22255167 + CmPI595203_05g014860.1 Cmu05g1486 1486
10 6388717 6392866 + CmPI595203_10g013430.1 Cmu10g1343 1343
10 6457437 6460460 + CmPI595203_10g013490.1 Cmu10g1349 1349
10 6472858 6474307 + CmPI595203_10g013510.1 Cmu10g1351 1351
10 6488922 6497718 - CmPI595203_10g013530.1 Cmu10g1353 1353
14 9462555 9464901 - Conep14aG0116500.1 Cone14ag1141 1141
14 9469281 9474460 + Conep14aG0116600.1 Cone14ag1142 1142
14 9476714 9480827 + Conep14aG0116700.1 Cone14ag1143 1143
14 9481143 9483112 - Conep14aG0116800.1 Cone14ag1144 1144
15 9367669 9371258 + Conep15aG0118800.1 Cone15ag1159 1159
15 9398779 9404034 + Conep15aG0118900.1 Cone15ag1160 1160
15 9406158 9410056 + Conep15aG0119000.1 Cone15ag1161 1161
15 9410346 9412786 - Conep15aG0119100.1 Cone15ag1162 1162
1 5112590 5114825 - Cp4.1LG01g08130.1 Cpe01g00867 867
1 5125359 5128667 - Cp4.1LG01g08100.1 Cpe01g00870 870
1 5131024 5134554 + Cp4.1LG01g08030.1 Cpe01g00871 871
2 4899184 4904638 + Cp4.1LG02g01130.1 Cpe02g00768 768
2 4909989 4913964 + Cp4.1LG02g01080.1 Cpe02g00770 770
2 4911062 4917648 - Cp4.1LG02g01030.1 Cpe02g00771 771
6 4827600 4836288 + Cp4.1LG06g08940.1 Cpe06g00765 765
6 4837116 4840884 - Cp4.1LG06g08810.1 Cpe06g00766 766
6 4850389 4854420 + Cp4.1LG06g08920.1 Cpe06g00768 768
6 4851394 4857727 - Cp4.1LG06g08870.1 Cpe06g00769 769
9 10539030 10541526 + CrPI670011_09g010290.1 Cre09g1029 1029
9 10541568 10550399 - CrPI670011_09g010300.1 Cre09g1030 1030
10 7287539 7292038 + CrPI670011_10g007480.1 Cre10g0748 748
10 7352241 7356135 + CrPI670011_10g007540.1 Cre10g0754 754
10 7368532 7369983 + CrPI670011_10g007550.1 Cre10g0755 755
10 7381582 7390383 - CrPI670011_10g007570.1 Cre10g0757 757
3 4249150 4256495 - CsaV3_3G005080.1 Csa03g00508 508
3 4313319 4317281 + CsaV3_3G005170.1 Csa03g00517 517
3 4320354 4330994 + CsaV3_3G005180.1 Csa03g00518 518
3 4331861 4339499 - CsaV3_3G005190.1 Csa03g00519 519
7 10484949 10489846 + CsaV3_7G021790.1 Csa07g01090 1090
7 10487785 10498710 - CsaV3_7G021800.1 Csa07g01091 1091
7 10505536 10507948 - CsaV3_7G021810.1 Csa07g01092 1092
1 78006162 78008235 + Hsped.01g12740.1 Hepe01g1274 1274
1 78010804 78013762 + Hsped.01g12760.1 Hepe01g1276 1276
1 78014073 78016959 - Hsped.01g12770.1 Hepe01g1277 1277
1 78033296 78038342 + Hsped.01g12790.1 Hepe01g1279 1279
2 24971894 24980899 + Lsi02G019040.1 Lsi02g01904 1904
2 24979602 24983875 - Lsi02G019050.1 Lsi02g01905 1905
4 18476141 18480040 + Lsi04G012020.1 Lsi04g01202 1202
4 18571465 18577644 - Lsi04G012030.1 Lsi04g01203 1203
5 7378496 7381745 + Lsi05G005940.1 Lsi05g00594 594
5 7463114 7465631 + Lsi05G006020.1 Lsi05g00602 602
5 7487985 7495159 + Lsi05G006030.1 Lsi05g00603 603
5 7496434 7505920 - Lsi05G006040.1 Lsi05g00604 604
10 10321243 10333432 + MC10g1043 Mch10g1264 1264
10 10376515 10380294 - MC10g1046 Mch10g1268 1268
11 8335359 8338836 - MC11g0978 Mch11g1187 1187
11 8351141 8355501 + MC11g0980 Mch11g1189 1189
11 8352404 8363007 - MC11g0981 Mch11g1190 1190
5 4924818 4927050 - Sed0003485.1 Sed05g0664 664
7 42217051 42219776 + Sed0027038.2 Sed07g2683 2683
7 42246185 42251059 + Sed0021471.3 Sed07g2689 2689
13 15671723 15682357 - Sed0020363.1 Sed13g1180 1180
1 18076341 18084479 + Tan0004786.1 Tan01g1699 1699
1 111243088 111247062 - Tan0020463.1 Tan01g4548 4548
1 111297955 111300455 + Tan0007346.1 Tan01g4552 4552
1 111301140 111316081 - Tan0005815.1 Tan01g4553 4553
19 6436165 6451656 + Vvi19g504 Vvi19g504 504
19 6453336 6454997 - Vvi19g505 Vvi19g505 505
19 6477610 6482034 - Vvi19g506 Vvi19g506 506
19 6485716 6495683 + Vvi19g507 Vvi19g507 507
19 6497804 6501971 - Vvi19g508 Vvi19g508 508
19 6519949 6524347 + Vvi19g509 Vvi19g509 509
19 6524668 6542013 - Vvi19g510 Vvi19g510 510
19 6547394 6550650 - Vvi19g511 Vvi19g511 511
19 6551524 6553699 - Vvi19g512 Vvi19g512 512
19 6574166 6579250 + Vvi19g513 Vvi19g513 513
       

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