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
Vvi1g1001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1002 . . . . . . . . . Cmo18g00244 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1003 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1004 . . . Bda11g01164 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone9ag0516 . . . . . . . Bda11g01164 . . . . . Cmo04g02953 . . . . Car15g00221 Cpe13g00994 . . . . . . . . . . . . . . . . . Chy09g00382 .
Vvi1g1005 Blo01g00465 . Bda01g01785 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone9ag0515 . . . . . . . . . Bpe02g01962 Bma01g00137 . . . Cmo15g00882 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1006 . . . . . . . . . Cmo18g01103 . Cma18g01081 . . Sed06g1812 Cpe09g00242 . Bhi07g01439 Tan04g0951 Cmetu04g2545 Lac13g0412 Hepe10g1827 . . Cla05g02372 Cam05g2540 Cec05g2571 Cco05g2609 Clacu05g2538 Cmu05g2397 Cre05g2514 . . . . Lsi04g00334 Csa05g02536 Chy10g01079 Cme10g00332 . . . . . . . . . . . . . . Car15g00220 Cpe13g00995 . . . . . . . . . . . . . . . . . Chy09g00175 .
Vvi1g1007 . Blo16g01073 . Bda11g01163 Bpe13g01362 . . . . Cmo18g01102 . Cma18g01080 . Car18g01002 Sed08g1853 Cpe09g00244 . Bhi07g01438 Tan04g0950 Cmetu03g1218 Lac13g0414 Hepe10g1828 . . Cla05g02371 Cam05g2539 Cec05g2569 Cco05g2608 Clacu05g2536 Cmu05g2395 Cre05g2512 . . . . Lsi04g00332 Csa05g02538 Chy10g01080 . . . . Bda11g01163 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1008 . . . . . Bpe10g00916 . Bma15g00107 . Cmo18g01101 . Cma18g01078 . Car18g01001 . Cpe09g00245 . Bhi07g01436 Tan04g0948 . Lac13g0415 Hepe10g1829 . . Cla05g02368 . . . . . . . . . . Lsi04g00330 Csa05g02539 Chy10g01081 Cme10g00329 Blo06g00943 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01208 . .
Vvi1g1009 . . . . . . . . Cmo04g01064 . . . Car04g00928 . . Cpe09g00246 . Bhi07g01433 . . . . . . . . . . . . . . . . . . . . . . . Bda07g01508 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1010 Blo01g00466 Blo16g01072 Bda01g02113 Bda11g01162 Bpe13g01361 . . . Cmo04g01641 Cmo18g01098 . Cma18g01076 Car04g01621 Car18g00999 . Cpe09g00247 Cpe01g01393 Bhi07g01428 Tan04g0941 . . . . . Cla05g02367 Cam05g2537 Cec05g2567 Cco05g2606 Clacu05g2534 Cmu05g2393 Cre05g2509 . . . Cone9ag0512 Lsi04g00328 Csa05g02541 Chy10g01083 Cme10g00327 . . . Bda11g01162 . Bpe02g02301 Bma01g00138 Bma06g00747 . . Cmo15g00881 . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 54055893 54057914 - Bda032979 Bda01g01785 1785
1 57180782 57182913 + Bda004444.1 Bda01g02113 2113
7 28020272 28021369 - Bda028357.1 Bda07g01508 1508
11 11889411 11893781 + Bda007653.1 Bda11g01162 1162
11 11897568 11901156 - Bda007654.1 Bda11g01163 1163
11 11937713 11946338 - Bda007656.1 Bda11g01164 1164
7 42380488 42384978 + XM_039037168.1 Bhi07g01428 1428
7 42385823 42390387 + XM_039037103.1 Bhi07g01433 1433
7 42388866 42391503 - XM_039037106.1 Bhi07g01436 1436
7 42393080 42398200 - XM_039036461.1 Bhi07g01438 1438
7 42399461 42408451 - XM_039036462.1 Bhi07g01439 1439
1 5123484 5141891 + BLOR00465 Blo01g00465 465
1 5141924 5144623 - BLOR00466 Blo01g00466 466
6 32661757 32663551 + BLOR17526 Blo06g00943 943
16 39276599 39279494 + BLOR21859 Blo16g01072 1072
16 39280455 39291319 - BLOR21860 Blo16g01073 1073
1 1320533 1325654 + Bma000302.1 Bma01g00137 137
1 1326386 1328504 - Bma000303.1 Bma01g00138 138
6 38766134 38768781 - Bma023736.1 Bma06g00747 747
15 1142140 1143892 - Bma013080.1 Bma15g00107 107
2 21502417 21504440 - Bpe025195 Bpe02g01962 1962
2 23717586 23719702 + Bpe010118.1 Bpe02g02301 2301
10 14791611 14793284 + Bpe003219.3 Bpe10g00916 916
13 18848862 18851208 + Bpe011023.1 Bpe13g01361 1361
13 18852945 18866371 - Bpe011024.1 Bpe13g01362 1362
5 33213339 33216586 + CaPI482276_05g025370.1 Cam05g2537 2537
5 33222124 33230761 - CaPI482276_05g025390.1 Cam05g2539 2539
5 33230893 33240767 - CaPI482276_05g025400.1 Cam05g2540 2540
4 5315731 5320960 + Carg00103-RA Car04g00928 928
4 9365225 9367717 + Carg01779-RA Car04g01621 1621
15 1224321 1234441 - Carg02201-RA Car15g00220 220
15 1235100 1238749 - Carg02202-RA Car15g00221 221
18 10438430 10441744 + Carg21530-RA Car18g00999 999
18 10446262 10448010 - Carg21528-RA Car18g01001 1001
18 10449766 10453664 - Carg21527-RA Car18g01002 1002
5 34317066 34320696 + CcPI632755_05g026060.1 Cco05g2606 2606
5 34325847 34334502 - CcPI632755_05g026080.1 Cco05g2608 2608
5 34334527 34347454 - CcPI632755_05g026090.1 Cco05g2609 2609
5 36652382 36656000 + CePI673135_05g025670.1 Cec05g2567 2567
5 36661156 36669788 - CePI673135_05g025690.1 Cec05g2569 2569
5 36671756 36680190 - CePI673135_05g025710.1 Cec05g2571 2571
9 1484884 1493506 - Chy9G158910.1 Chy09g00175 175
9 3369843 3372512 + Chy9G160980.1 Chy09g00382 382
10 15885617 15893726 + Chy10G182730.1 Chy10g01079 1079
10 15896281 15900752 + Chy10G182740.1 Chy10g01080 1080
10 15902485 15904297 + Chy10G182750.1 Chy10g01081 1081
10 15909181 15911528 - Chy10G182770.1 Chy10g01083 1083
5 33423764 33426971 + ClG42_05g0253400.10 Clacu05g2534 2534
5 33431751 33441108 - ClG42_05g0253600.10 Clacu05g2536 2536
5 33443088 33451131 - ClG42_05g0253800.10 Clacu05g2538 2538
5 35260244 35263692 + ClCG05G023410.1 Cla05g02367 2367
5 35264958 35271180 - ClCG05G023430.2 Cla05g02368 2368
5 35272179 35277782 - ClCG05G023450.1 Cla05g02371 2371
5 35278644 35287741 - ClCG05G023460.1 Cla05g02372 2372
18 8899573 8903891 + CmaCh18G010760.1 Cma18g01076 1076
18 8907647 8909970 - CmaCh18G010780.1 Cma18g01078 1078
18 8910909 8916005 - CmaCh18G010800.1 Cma18g01080 1080
18 8916662 8924858 - CmaCh18G010810.1 Cma18g01081 1081
10 2169290 2172369 + MELO3C012177.2.1 Cme10g00327 327
10 2174915 2178920 - MELO3C012175.2.1 Cme10g00329 329
10 2181330 2189963 - MELO3C012173.2.1 Cme10g00332 332
3 6463697 6478785 + PI0024240.1 Cmetu03g1218 1218
4 16179945 16180638 + PI0020071.1 Cmetu04g2545 2545
4 5332228 5341933 + CmoCh04G010640.1 Cmo04g01064 1064
4 8388080 8390674 + CmoCh04G016410.1 Cmo04g01641 1641
4 20900591 20904874 + CmoCh04G029530.1 Cmo04g02953 2953
15 4461494 4465031 + CmoCh15G008810.1 Cmo15g00881 881
15 4464899 4470946 - CmoCh15G008820.1 Cmo15g00882 882
18 1611522 1613282 - CmoCh18G002440.1 Cmo18g00244 244
18 11457766 11459974 + CmoCh18G010980.1 Cmo18g01098 1098
18 11466464 11468185 - CmoCh18G011010.1 Cmo18g01101 1101
18 11469594 11474997 - CmoCh18G011020.1 Cmo18g01102 1102
18 11476070 11484321 - CmoCh18G011030.1 Cmo18g01103 1103
5 33161783 33164990 + CmPI595203_05g023930.1 Cmu05g2393 2393
5 33169770 33179127 - CmPI595203_05g023950.1 Cmu05g2395 2395
5 33181107 33189148 - CmPI595203_05g023970.1 Cmu05g2397 2397
9 2454901 2458986 + Conep09aG0052200.1 Cone9ag0512 512
9 2463417 2468419 - Conep09aG0052500.1 Cone9ag0515 515
9 2468948 2470535 - Conep09aG0052600.1 Cone9ag0516 516
1 8390205 8393337 + Cp4.1LG01g13230.1 Cpe01g01393 1393
9 1398637 1406687 + Cp4.1LG09g02430.1 Cpe09g00242 242
9 1408280 1412181 + Cp4.1LG09g02420.1 Cpe09g00244 244
9 1413633 1415816 + Cp4.1LG09g02410.1 Cpe09g00245 245
9 1415813 1418869 - Cp4.1LG09g02510.1 Cpe09g00246 246
9 1420189 1424545 - Cp4.1LG09g02530.1 Cpe09g00247 247
13 8213304 8217119 + Cp4.1LG13g08110.1 Cpe13g00994 994
13 8217381 8226511 + Cp4.1LG13g08100.1 Cpe13g00995 995
5 36511011 36514257 + CrPI670011_05g025090.1 Cre05g2509 2509
5 36519747 36528374 - CrPI670011_05g025120.1 Cre05g2512 2512
5 36530348 36541172 - CrPI670011_05g025140.1 Cre05g2514 2514
5 12581188 12593170 + CsaV3_5G015320.1 Csa05g01208 1208
5 26823044 26832041 + CsaV3_5G033550.1 Csa05g02536 2536
5 26833398 26838893 + CsaV3_5G033570.1 Csa05g02538 2538
5 26839219 26845224 + CsaV3_5G033580.1 Csa05g02539 2539
5 26846039 26850063 - CsaV3_5G033600.1 Csa05g02541 2541
10 55014870 55024466 + Hsped.10g18270.1 Hepe10g1827 1827
10 55025134 55033109 + Hsped.10g18280.1 Hepe10g1828 1828
10 55037674 55039550 + Hsped.10g18290.1 Hepe10g1829 1829
13 2899866 2907815 + Lag0040208.1 Lac13g0412 412
13 2909812 2914325 + Lag0040210.1 Lac13g0414 414
13 2916206 2917946 + Lag0040211.1 Lac13g0415 415
4 3368247 3372484 + Lsi04G003280.1 Lsi04g00328 328
4 3376561 3379288 - Lsi04G003300.1 Lsi04g00330 330
4 3381127 3385792 - Lsi04G003320.1 Lsi04g00332 332
4 3388300 3397988 - Lsi04G003340.1 Lsi04g00334 334
6 42629978 42640032 + Sed0010723.1 Sed06g1812 1812
8 33172500 33174595 + Sed0009257.1 Sed08g1853 1853
4 8332786 8337450 + Tan0007596.1 Tan04g0941 941
4 8348827 8351976 - Tan0003074.2 Tan04g0948 948
4 8352775 8359209 - Tan0015437.1 Tan04g0950 950
4 8361632 8371306 - Tan0011832.1 Tan04g0951 951
1 15713489 15721119 + Vvi1g1001 Vvi1g1001 1001
1 15722217 15727580 + Vvi1g1002 Vvi1g1002 1002
1 15732426 15732945 - Vvi1g1003 Vvi1g1003 1003
1 15756275 15759027 + Vvi1g1004 Vvi1g1004 1004
1 15794279 15805183 + Vvi1g1005 Vvi1g1005 1005
1 15828941 15858021 + Vvi1g1006 Vvi1g1006 1006
1 15888299 15892532 + Vvi1g1007 Vvi1g1007 1007
1 15895364 15897710 + Vvi1g1008 Vvi1g1008 1008
1 15898500 15900732 - Vvi1g1009 Vvi1g1009 1009
1 15902529 15907102 - Vvi1g1010 Vvi1g1010 1010
       

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