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
Vvi16g724 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00120 . . . . Bda06g00690 . . . . . . . Cmo15g01146 . . . . . . Bhi12g00031 . . Lac11g0044 . . Lcy12g0041 . . . . . . . Lsi09g00094 . . .
Vvi16g725 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag1173 Cone5ag0880 Cone14ag0073 Cone15ag0076 . . Chy09g01373 . . . . . . . . Bma12g01115 . . . . . . . . . Bhi12g00030 . . Lac11g0045 . . Lcy12g0042 . . . . . . . Lsi09g00093 . . Cme09g01920
Vvi16g726 . . . . . . . . . . . . Car02g00817 . . . . . . . . . . . . . . . . . . . . . . . . Chy09g01374 . . . . . . . . . . . . . . . . . Cpe13g00109 . . . . . . . . . . . . . . Lsi09g00092 . . Cme09g01921
Vvi16g727 Blo06g01135 . . . . . . . Cmo16g00126 Cmo18g01283 . . . . . . Cpe14g00100 Bhi01g01283 . . . . Mch10g0143 . . . . . . . . Cone1ag1174 Cone5ag0881 Cone14ag0072 Cone15ag0075 Lsi05g01214 Csa05g00475 Chy09g01038 Cme06g01017 . . . Bda15g00714 . Bpe12g00439 Bma08g00295 . . . . Cma16g00114 Cma18g01256 Car16g00103 Car18g01166 Cpe09g00079 . Bhi12g00492 . . . . . . Cla05g00892 . . . . . . . Csa03g01727 Chy06g00957 .
Vvi16g728 . Blo15g00174 . . . Bpe07g00931 . . Cmo16g00125 Cmo18g01285 . . . . . . Cpe14g00099 Bhi01g01281 Tan01g0225 . . . . . . . . . . . . . . Cone14ag0071 Cone15ag0073 Lsi05g01213 . . Cme06g01018 . . Bda06g00691 . . . . Bma12g01114 . . . Cma16g00113 Cma18g01258 Car16g00101 Car18g01168 Cpe09g00078 . . . . . . . . Cla05g00894 Cam05g0979 Cec05g0984 Cco05g0982 Clacu05g0966 Cmu05g0924 Cre05g1008 . Csa03g01728 Chy06g00959 .
Vvi16g729 . . Bda05g00082 . Bpe03g00139 . Bma10g01232 . Cmo16g00123 Cmo18g01287 . . . . . . Cpe14g00098 Bhi01g01279 Tan01g5193 . . . . . . . . . . . . . . Cone14ag0069 Cone15ag0072 Lsi05g01212 . . Cme06g01019 . . . . . . . . . . . Cma16g00112 Cma18g01260 Car16g00100 Car18g01169 Cpe09g00077 . . . . . . . . Cla05g00896 Cam05g0980 Cec05g0985 Cco05g0983 Clacu05g0968 Cmu05g0925 Cre05g1009 . Csa03g01730 Chy06g00961 .
Vvi16g730 . . . Bda07g01889 . . . Bma14g02059 Cmo16g00122 . . . . . . . Cpe14g00097 Bhi01g01277 . . . . . . . . . . . . . . . . Cone15ag0071 Lsi05g01211 . . Cme06g01020 . Blo09g00078 . . . . . . . . . Cma16g00111 . Car16g00099 . . . . . . . . . . Cla05g00897 Cam05g0981 Cec05g0986 Cco05g0984 Clacu05g0969 Cmu05g0926 Cre05g1010 . Csa03g01732 Chy06g00963 .
Vvi16g731 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g732 . . . . . . . . Cmo16g00121 . . . . . Sed07g1011 . Cpe14g00096 Bhi01g01274 Tan01g0219 Cmetu06g1581 . Hepe07g0139 Mch10g0139 . . . . . . . . . . . . Lsi05g01210 . . Cme06g01021 . . . . . . . . . . . Cma16g00110 . . . . . . . . . . . . Cla05g00898 Cam05g0982 Cec05g0987 Cco05g0985 Clacu05g0970 Cmu05g0927 Cre05g1011 . Csa03g01733 Chy06g00964 .
Vvi16g733 . . . . . . . . . Cmo18g01288 . . . . Sed07g1008 . Cpe14g00093 Bhi01g01270 Tan01g0217 Cmetu06g1400 . Hepe07g0137 . . . . . . . . . . . . . Lsi05g01208 . . Cme06g01023 . . . . . . . . . . . Cma16g00109 Cma18g01261 Car16g00097 Car18g01170 Cpe09g00076 . . . . . . . . Cla05g00900 Cam05g0984 Cec05g0989 Cco05g0987 Clacu05g0972 Cmu05g0929 Cre05g1014 . Csa03g01735 Chy06g00966 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 3932398 3935293 + Bda020672.1 Bda05g00082 82
6 9530779 9536235 + Bda023987.1 Bda06g00690 690
6 9536753 9538937 - Bda023988.1 Bda06g00691 691
7 36314337 36316695 - Bda028862.1 Bda07g01889 1889
15 10541285 10546247 + Bda012568.1 Bda15g00714 714
1 25880974 25882180 + XM_039036143.1 Bhi01g01270 1270
1 25910182 25913177 + XM_039035807.1 Bhi01g01274 1274
1 25914418 25919276 - XM_039035817.1 Bhi01g01277 1277
1 25939187 25942207 + XM_039039926.1 Bhi01g01279 1279
1 25967394 25970951 + XM_039047308.1 Bhi01g01281 1281
1 26087661 26095463 + XM_039028132.1 Bhi01g01283 1283
12 600352 605918 + XM_039020196.1 Bhi12g00030 30
12 600356 605918 + XM_039020197.1 Bhi12g00031 31
12 15573403 15580360 - XM_039051354.1 Bhi12g00492 492
6 34801017 34806033 - BLOR17718 Blo06g01135 1135
9 1385026 1395541 + BLOR20993 Blo09g00078 78
15 1773882 1779341 - BLOR06568 Blo15g00174 174
8 4102153 4104845 + Bma027317.2 Bma08g00295 295
10 43896921 43899186 + Bma005318.1 Bma10g01232 1232
12 43391664 43393913 + Bma008460.1 Bma12g01114 1114
12 43395479 43402929 - Bma008461.1 Bma12g01115 1115
14 43925355 43927910 + Bma012868.1 Bma14g02059 2059
3 1906385 1909243 + Bpe011983.1 Bpe03g00139 139
7 15221925 15224242 + Bpe021772.1 Bpe07g00931 931
12 10156906 10161898 - Bpe005699.1 Bpe12g00439 439
5 8862304 8864785 - CaPI482276_05g009790.1 Cam05g0979 979
5 8887499 8890312 - CaPI482276_05g009800.1 Cam05g0980 980
5 8905758 8911125 + CaPI482276_05g009810.1 Cam05g0981 981
5 8913280 8915902 - CaPI482276_05g009820.1 Cam05g0982 982
5 8931808 8932668 - CaPI482276_05g009840.1 Cam05g0984 984
2 5908223 5910940 - Carg08404-RA Car02g00817 817
16 597241 598155 + Carg15119-RA Car16g00097 97
16 610502 613164 - Carg15121-RA Car16g00099 99
16 617042 619821 + Carg15122-RA Car16g00100 100
16 624897 627808 + Carg15123-RA Car16g00101 101
16 632279 637986 + Carg15125-RA Car16g00103 103
18 11408514 11414670 - Carg22114-RA Car18g01166 1166
18 11420149 11424129 - Carg22116-RA Car18g01168 1168
18 11432956 11436174 - Carg22117-RA Car18g01169 1169
18 11439067 11439924 - Carg22118-RA Car18g01170 1170
5 8630240 8632717 - CcPI632755_05g009820.1 Cco05g0982 982
5 8654724 8657503 - CcPI632755_05g009830.1 Cco05g0983 983
5 8672830 8678195 + CcPI632755_05g009840.1 Cco05g0984 984
5 8680426 8683047 - CcPI632755_05g009850.1 Cco05g0985 985
5 8701869 8702729 - CcPI632755_05g009870.1 Cco05g0987 987
5 8618555 8621866 - CePI673135_05g009840.1 Cec05g0984 984
5 8642665 8645472 - CePI673135_05g009850.1 Cec05g0985 985
5 8660740 8666073 + CePI673135_05g009860.1 Cec05g0986 986
5 8668274 8670888 - CePI673135_05g009870.1 Cec05g0987 987
5 8686334 8687194 - CePI673135_05g009890.1 Cec05g0989 989
6 7050402 7055710 - Chy6G114850.1 Chy06g00957 957
6 7067529 7068725 - Chy6G114870.1 Chy06g00959 959
6 7089964 7092779 - Chy6G114890.1 Chy06g00961 961
6 7104365 7110322 + Chy6G114910.1 Chy06g00963 963
6 7110897 7113303 - Chy6G114920.1 Chy06g00964 964
6 7120151 7121026 - Chy6G114940.1 Chy06g00966 966
9 12879506 12884277 - Chy9G167540.1 Chy09g01038 1038
9 15537496 15541012 - Chy9G170890.1 Chy09g01373 1373
9 15541917 15546798 - Chy9G170900.1 Chy09g01374 1374
5 8578359 8580834 - ClG42_05g0096600.10 Clacu05g0966 966
5 8606020 8608796 - ClG42_05g0096800.10 Clacu05g0968 968
5 8624122 8629472 + ClG42_05g0096900.10 Clacu05g0969 969
5 8631650 8634271 - ClG42_05g0097000.10 Clacu05g0970 970
5 8650088 8650948 - ClG42_05g0097200.10 Clacu05g0972 972
5 8826684 8835364 - ClCG05G008180.2 Cla05g00892 892
5 8844865 8848661 - ClCG05G008200.1 Cla05g00894 894
5 8874244 8877421 - ClCG05G008220.2 Cla05g00896 896
5 8892652 8898342 + ClCG05G008230.2 Cla05g00897 897
5 8900245 8903186 - ClCG05G008240.2 Cla05g00898 898
5 8918707 8919567 - ClCG05G008247.1 Cla05g00900 900
16 491986 497674 + CmaCh16G001090.1 Cma16g00109 109
16 498968 500826 + CmaCh16G001100.1 Cma16g00110 110
16 500726 503809 - CmaCh16G001110.1 Cma16g00111 111
16 507342 511576 + CmaCh16G001120.1 Cma16g00112 112
16 516680 522766 + CmaCh16G001130.1 Cma16g00113 113
16 522963 528716 + CmaCh16G001140.1 Cma16g00114 114
18 9793275 9800307 - CmaCh18G012560.1 Cma18g01256 1256
18 9805507 9808036 - CmaCh18G012580.1 Cma18g01258 1258
18 9817774 9821036 - CmaCh18G012600.1 Cma18g01260 1260
18 9824177 9825133 - CmaCh18G012610.1 Cma18g01261 1261
6 7319721 7327357 - MELO3C006925.2.1 Cme06g01017 1017
6 7340735 7345010 - MELO3C006926.2.1 Cme06g01018 1018
6 7360764 7364398 - MELO3C006927.2.1 Cme06g01019 1019
6 7379345 7385025 + MELO3C006928.2.1 Cme06g01020 1020
6 7385038 7387481 - MELO3C006929.2.1 Cme06g01021 1021
6 7394483 7395664 - MELO3C006931.2.1 Cme06g01023 1023
9 23301248 23305093 - MELO3C005826.2.1 Cme09g01920 1920
9 23305578 23311057 - MELO3C005827.2.1 Cme09g01921 1921
6 7371267 7372626 - PI0027894.1 Cmetu06g1400 1400
6 7360342 7362983 - PI0023433.1 Cmetu06g1581 1581
15 8002367 8007816 + CmoCh15G011460.1 Cmo15g01146 1146
16 542193 544073 + CmoCh16G001210.1 Cmo16g00121 121
16 544251 547007 - CmoCh16G001220.1 Cmo16g00122 122
16 550650 554013 + CmoCh16G001230.1 Cmo16g00123 123
16 559944 566009 + CmoCh16G001250.1 Cmo16g00125 125
16 566206 572925 + CmoCh16G001260.1 Cmo16g00126 126
18 12410799 12417034 - CmoCh18G012830.1 Cmo18g01283 1283
18 12422782 12424923 - CmoCh18G012850.1 Cmo18g01285 1285
18 12434906 12438173 - CmoCh18G012870.1 Cmo18g01287 1287
18 12441121 12441978 - CmoCh18G012880.1 Cmo18g01288 1288
5 8424998 8427473 - CmPI595203_05g009240.1 Cmu05g0924 924
5 8452667 8455443 - CmPI595203_05g009250.1 Cmu05g0925 925
5 8470820 8476170 + CmPI595203_05g009260.1 Cmu05g0926 926
5 8478349 8480970 - CmPI595203_05g009270.1 Cmu05g0927 927
5 8496765 8497625 - CmPI595203_05g009290.1 Cmu05g0929 929
1 55779073 55782087 + Conep01aG0122200.1 Cone1ag1173 1173
1 55782217 55788035 - Conep01aG0122300.1 Cone1ag1174 1174
5 3771236 3773903 + Conep05aG0090600.1 Cone5ag0880 880
5 3773994 3779834 - Conep05aG0090700.1 Cone5ag0881 881
14 375802 382596 + Conep14aG0007200.1 Cone14ag0069 69
14 386407 388765 + Conep14aG0007400.1 Cone14ag0071 71
14 390001 393651 + Conep14aG0007500.1 Cone14ag0072 72
14 394425 395927 - Conep14aG0007600.1 Cone14ag0073 73
15 395187 396946 - Conep15aG0007300.1 Cone15ag0071 71
15 399747 403377 + Conep15aG0007400.1 Cone15ag0072 72
15 404195 406910 + Conep15aG0007500.1 Cone15ag0073 73
15 412549 417762 + Conep15aG0007700.1 Cone15ag0075 75
15 418365 420150 - Conep15aG0007800.1 Cone15ag0076 76
9 443497 444354 + Cp4.1LG09g00660.1 Cpe09g00076 76
9 447281 450690 + Cp4.1LG09g00650.1 Cpe09g00077 77
9 459801 463425 + Cp4.1LG09g00720.1 Cpe09g00078 78
9 464681 474929 + Cp4.1LG09g00700.1 Cpe09g00079 79
13 787034 789745 - Cp4.1LG13g01190.1 Cpe13g00109 109
14 506256 507116 + Cp4.1LG14g06230.1 Cpe14g00093 93
14 517412 520438 + Cp4.1LG14g06330.1 Cpe14g00096 96
14 517432 522306 - Cp4.1LG14g06150.1 Cpe14g00097 97
14 525885 531598 + Cp4.1LG14g06220.1 Cpe14g00098 98
14 535369 538715 + Cp4.1LG14g06260.1 Cpe14g00099 99
14 541122 549668 + Cp4.1LG14g06270.1 Cpe14g00100 100
5 9313977 9316477 - CrPI670011_05g010080.1 Cre05g1008 1008
5 9339460 9342285 - CrPI670011_05g010090.1 Cre05g1009 1009
5 9358626 9363963 + CrPI670011_05g010100.1 Cre05g1010 1010
5 9366227 9368845 - CrPI670011_05g010110.1 Cre05g1011 1011
5 9385039 9385440 - CrPI670011_05g010140.1 Cre05g1014 1014
3 12943196 12950937 - CsaV3_3G017270.1 Csa03g01727 1727
3 12958675 12960927 - CsaV3_3G017280.1 Csa03g01728 1728
3 12978564 12982069 - CsaV3_3G017300.1 Csa03g01730 1730
3 12991483 12996542 + CsaV3_3G017320.1 Csa03g01732 1732
3 12997072 12999792 - CsaV3_3G017330.1 Csa03g01733 1733
3 13005979 13006854 - CsaV3_3G017350.1 Csa03g01735 1735
5 607480 613022 + CsaV3_5G001200.1 Csa05g00120 120
5 3086912 3094232 + CsaV3_5G004750.1 Csa05g00475 475
7 1245108 1246489 + Hsped.07g01370.1 Hepe07g0137 137
7 1253811 1256441 + Hsped.07g01390.1 Hepe07g0139 139
11 376074 380427 - Lag0030682.1 Lac11g0044 44
11 382622 388367 - Lag0030683.1 Lac11g0045 45
12 662810 663832 - Maker00038776 Lcy12g0041 41
12 666647 676117 - Maker00038535 Lcy12g0042 42
5 19926036 19926914 + Lsi05G012080.1 Lsi05g01208 1208
5 19940193 19942389 + Lsi05G012100.1 Lsi05g01210 1210
5 19943298 19948720 - Lsi05G012110.1 Lsi05g01211 1211
5 19963456 19966627 + Lsi05G012120.1 Lsi05g01212 1212
5 19991345 19995185 + Lsi05G012130.1 Lsi05g01213 1213
5 20005153 20014634 + Lsi05G012140.1 Lsi05g01214 1214
9 816008 825801 + Lsi09G000920.1 Lsi09g00092 92
9 828349 830112 + Lsi09G000930.1 Lsi09g00093 93
9 830137 832249 + Lsi09G000940.1 Lsi09g00094 94
10 819757 822185 + MC10g0119 Mch10g0139 139
10 856718 864586 + MC10g0122 Mch10g0143 143
7 7313091 7314405 + Sed0008964.1 Sed07g1008 1008
7 7335396 7337008 + Sed0018649.1 Sed07g1011 1011
1 1916958 1918573 + Tan0002531.1 Tan01g0217 217
1 1934085 1936435 + Tan0022709.1 Tan01g0219 219
1 1987455 1991757 + Tan0004687.3 Tan01g0225 225
1 116962844 116976231 - Tan0004656.1 Tan01g5193 5193
16 17682373 17688734 + Vvi16g724 Vvi16g724 724
16 17690131 17699354 + Vvi16g725 Vvi16g725 725
16 17700855 17707425 + Vvi16g726 Vvi16g726 726
16 17707491 17719297 - Vvi16g727 Vvi16g727 727
16 17723467 17727425 - Vvi16g728 Vvi16g728 728
16 17730594 17735820 - Vvi16g729 Vvi16g729 729
16 17739768 17746645 + Vvi16g730 Vvi16g730 730
16 17754300 17767006 - Vvi16g731 Vvi16g731 731
16 17775848 17795068 - Vvi16g732 Vvi16g732 732
16 17800177 17808482 - Vvi16g733 Vvi16g733 733
       

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