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
Vvi16g1024 . . Bda05g00129 . Bpe03g00229 . Bma10g01306 . Cmo16g00043 . . . . . Sed13g0046 . Cpe14g00030 Bhi01g01507 Tan01g0077 Cmetu06g0082 . Hepe07g0048 . . . . . . . . . . . Cone14ag0002 . . . . Cme06g01157 Blo07g00329 . . . . . . . . . . Cma16g00037 . Car16g00037 Car18g01234 Cpe09g00038 . . . . . . . . Cla05g00981 Cam05g1072 Cec05g1079 Cco05g1071 Clacu05g1066 Cmu05g1017 Cre05g1091 . Csa03g01972 Chy06g01185 .
Vvi16g1025 . . . . Bpe03g00230 . . . Cmo16g00045 . . . . . Sed07g0871 . Cpe14g00031 Bhi01g01505 Tan01g0081 Cmetu06g1355 . Hepe07g0050 Mch10g0048 . . . . . . . . Cone1ag0995 Cone5ag0699 . . . . . Cme06g01156 Blo07g00331 . . . . . . . . . . Cma16g00038 Cma18g01323 Car16g00038 Car18g01235 . . . . . . . . . Cla05g00979 Cam05g1071 . . . . Cre05g1090 . Csa03g01974 Chy06g01186 .
Vvi16g1026 . . . . . . . . . . . . . . Sed07g0868 . . Bhi01g01504 Tan01g0082 Cmetu06g0080 . Hepe07g0051 Mch10g0049 . . . . . . . . Cone1ag0994 Cone5ag0698 . . . . . Cme06g01154 . . . . . . . . . . . . . . Car18g01237 . . . . . . . . . Cla05g00978 . Cec05g1077 Cco05g1069 Clacu05g1063 Cmu05g1014 . . Csa03g01975 Chy06g01187 .
Vvi16g1027 . . . . . . . . . . Cma02g01123 . . . . Cpe05g00595 . . . . . . . . Cla01g00037 Cam01g0035 Cec01g0034 Cco01g0036 Clacu01g0038 Cmu01g0035 Cre09g2471 . . Cone14ag0004 . . Csa05g00043 Chy09g01443 . . . Bda06g00789 . . . . . . Cmo02g01152 . . . . . . . Bhi12g00649 . . Lac11g0164 Hepe06g0796 . Lcy12g0140 . . . . . . . Lsi09g00017 . . Cme09g01990
Vvi16g1028 . . . . . . . . . . . . Car02g00932 . . Cpe05g00596 . . . . . . . . . . . . . . . . . . . . Csa05g00045 . . . . . . . . . . . Cmo02g01151 . . . . . . . Bhi12g00647 . . Lac11g0163 . . Lcy12g0139 . . . . . . . . . . Cme09g01989
Vvi16g1029 . Blo15g00085 . . . Bpe07g01018 . . . . Cma02g01122 Cma15g01024 Car02g00931 Car15g00957 . Cpe05g00597 . . . . . . . . Cla01g00038 Cam01g0037 Cec01g0036 Cco01g0038 Clacu01g0039 Cmu01g0037 Cre09g2470 Cone1ag0993 . Cone14ag0005 Cone15ag0008 . Csa05g00046 Chy09g01442 . . . Bda06g00788 . . . . Bma12g01206 . Cmo02g01150 Cmo15g01087 . . . . . Cpe13g00318 Bhi12g00645 . . Lac11g0162 . . Lcy12g0138 . . . . . . . Lsi09g00018 . . Cme09g01988
Vvi16g1030 . . . . Bpe03g00194 . . Bma14g02011 Cmo16g00047 . . . . . Sed13g0050 . Cpe14g00032 Bhi01g01503 Tan01g0083 Cmetu06g0196 . Hepe07g0052 Mch10g0050 . . . . . . . . . Cone5ag0697 . . . . . Cme06g01153 . . . . . . . . . . . . . Car16g00039 Car18g01238 . . . . . . . . . Cla05g00977 Cam05g1070 Cec05g1076 Cco05g1068 Clacu05g1062 Cmu05g1013 Cre05g1089 . Csa03g01976 Chy06g01189 .
Vvi16g1031 . . . Bda07g01938 Bpe03g00193 . . . Cmo16g00048 . . . . . . . Cpe14g00033 Bhi01g01500 . . . . . . . . . . . . . Cone1ag0991 Cone5ag0696 . . . . . Cme06g01152 . Blo09g00021 . . . . . . . . . Cma16g00040 . . Car18g01239 . . . . . . . . . Cla05g00976 Cam05g1069 Cec05g1075 Cco05g1067 Clacu05g1061 Cmu05g1012 Cre05g1088 . Csa03g01977 Chy06g01190 .
Vvi16g1032 . . . . . . . . . . . . . . Sed05g1782 . . Bhi01g01498 Tan01g0086 Cmetu03g1368 . Hepe07g0054 Mch10g0052 . . . . . . . . . . Cone14ag0006 . . . . Cme06g01149 . . . . . Bpe12g00349 Bma08g00389 . . . . . . . Car18g01240 . . . . . . . . . Cla05g00975 Cam05g1067 Cec05g1073 Cco05g1065 Clacu05g1059 Cmu05g1010 Cre05g1087 . Csa03g01978 Chy06g01193 .
Vvi16g1033 . . . . Bpe03g00192 . . . Cmo16g00049 . . . . . Sed01g3487 . Cpe14g00034 Bhi01g01497 Tan01g0087 Cmetu06g0291 . Hepe07g0055 Mch10g0053 . . . . . . . . Cone1ag0990 Cone5ag0694 . . . . . Cme06g01148 . . Bda06g00787 . . . . . . . . . . Car16g00040 Car18g01241 . . . . . . . . . Cla05g00974 Cam05g1066 Cec05g1072 Cco05g1064 Clacu05g1058 Cmu05g1009 Cre05g1086 . Csa03g01979 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 6002537 6005068 + Bda020747.1 Bda05g00129 129
6 10898012 10898772 + Bda024110.1 Bda06g00787 787
6 10938381 10942389 + Bda024111.1 Bda06g00788 788
6 10948702 10951247 - Bda024112.1 Bda06g00789 789
7 36869637 36871852 + Bda028917.1 Bda07g01938 1938
1 30739162 30740488 + XM_039026997.1 Bhi01g01497 1497
1 30740895 30742548 - XM_039030733.1 Bhi01g01498 1498
1 30804179 30808190 + XM_039039593.1 Bhi01g01500 1500
1 30808395 30810096 - XM_039039636.1 Bhi01g01503 1503
1 30810194 30813357 + XM_039039624.1 Bhi01g01504 1504
1 30824139 30829647 + XM_039035490.1 Bhi01g01505 1505
1 30834957 30838896 + XM_039020977.1 Bhi01g01507 1507
12 19646543 19650893 - XM_039019962.1 Bhi12g00645 645
12 19651856 19655457 - XM_039019701.1 Bhi12g00647 647
12 19657524 19663751 - XM_039020077.1 Bhi12g00649 649
7 4261195 4263827 - BLOR18261 Blo07g00329 329
7 4265892 4269183 + BLOR18263 Blo07g00331 331
9 251786 257103 - BLOR20936 Blo09g00021 21
15 715851 719846 + BLOR06479 Blo15g00085 85
8 9461394 9462087 - Bma027459.1 Bma08g00389 389
10 46439350 46441925 + Bma005415.1 Bma10g01306 1306
12 44980381 44983520 - Bma008564.1 Bma12g01206 1206
14 43514547 43518630 - Bma012820.1 Bma14g02011 2011
3 2311069 2315783 + Bpe012039.3 Bpe03g00192 192
3 2318232 2320438 + Bpe012040.1 Bpe03g00193 193
3 2320818 2321899 - Bpe012041.1 Bpe03g00194 194
3 3079683 3082400 - Bpe012084.1 Bpe03g00229 229
3 3084462 3087678 + Bpe025363 Bpe03g00230 230
7 15789332 15792594 - Bpe021862.2 Bpe07g01018 1018
12 8548588 8549280 + Bpe005605.1 Bpe12g00349 349
1 746655 752147 + CaPI482276_01g000350.1 Cam01g0035 35
1 758802 763044 + CaPI482276_01g000370.1 Cam01g0037 37
5 9756045 9757103 + CaPI482276_05g010660.1 Cam05g1066 1066
5 9757859 9760068 - CaPI482276_05g010670.1 Cam05g1067 1067
5 9770937 9773356 + CaPI482276_05g010690.1 Cam05g1069 1069
5 9774148 9775557 - CaPI482276_05g010700.1 Cam05g1070 1070
5 9776046 9791500 + CaPI482276_05g010710.1 Cam05g1071 1071
5 9793050 9796970 + CaPI482276_05g010720.1 Cam05g1072 1072
2 6580776 6584866 - Carg14010-RA Car02g00931 931
2 6585862 6590775 - Carg14009-RA Car02g00932 932
15 6985650 6991726 + Carg26612-RA Car15g00957 957
16 273292 276426 - Carg15056-RA Car16g00037 37
16 279095 284228 - Carg15057-RA Car16g00038 38
16 284703 286286 + Carg15058-RA Car16g00039 39
16 286387 294973 - Carg15059-RA Car16g00040 40
18 11831260 11834152 - Carg20336-RA Car18g01234 1234
18 11835057 11840337 - Carg20335-RA Car18g01235 1235
18 11841609 11843784 - Carg20333-RA Car18g01237 1237
18 11843937 11845073 + Carg20332-RA Car18g01238 1238
18 11844879 11847307 - Carg20331-RA Car18g01239 1239
18 11849431 11850426 + Carg20330-RA Car18g01240 1240
18 11850037 11851422 - Carg20329-RA Car18g01241 1241
1 256860 264642 + CcPI632755_01g000360.1 Cco01g0036 36
1 272036 276094 + CcPI632755_01g000380.1 Cco01g0038 38
5 9510353 9515256 + CcPI632755_05g010640.1 Cco05g1064 1064
5 9516016 9518224 - CcPI632755_05g010650.1 Cco05g1065 1065
5 9529086 9531519 + CcPI632755_05g010670.1 Cco05g1067 1067
5 9532308 9533728 - CcPI632755_05g010680.1 Cco05g1068 1068
5 9534227 9536692 + CcPI632755_05g010690.1 Cco05g1069 1069
5 9551103 9554888 + CcPI632755_05g010710.1 Cco05g1071 1071
1 287805 293333 + CePI673135_01g000340.1 Cec01g0034 34
1 299898 303953 + CePI673135_01g000360.1 Cec01g0036 36
5 9496098 9497103 + CePI673135_05g010720.1 Cec05g1072 1072
5 9497868 9500075 - CePI673135_05g010730.1 Cec05g1073 1073
5 9509904 9512342 + CePI673135_05g010750.1 Cec05g1075 1075
5 9513144 9514564 - CePI673135_05g010760.1 Cec05g1076 1076
5 9515058 9517523 + CePI673135_05g010770.1 Cec05g1077 1077
5 9534241 9537804 + CePI673135_05g010790.1 Cec05g1079 1079
6 10603003 10606576 - Chy6G117130.1 Chy06g01185 1185
6 10607972 10616035 - Chy6G117140.1 Chy06g01186 1186
6 10620218 10621994 - Chy6G117150.1 Chy06g01187 1187
6 10627297 10628655 + Chy6G117170.1 Chy06g01189 1189
6 10630405 10633502 - Chy6G117180.1 Chy06g01190 1190
6 10649732 10650509 + Chy6G117210.1 Chy06g01193 1193
9 15972379 15979649 - Chy9G171580.1 Chy09g01442 1442
9 15983620 15992688 - Chy9G171590.1 Chy09g01443 1443
1 356602 361371 + ClG42_01g0003800.10 Clacu01g0038 38
1 365437 372967 + ClG42_01g0003900.10 Clacu01g0039 39
5 9484353 9489195 + ClG42_05g0105800.10 Clacu05g1058 1058
5 9489951 9492173 - ClG42_05g0105900.10 Clacu05g1059 1059
5 9503881 9506291 + ClG42_05g0106100.10 Clacu05g1061 1061
5 9507040 9508461 - ClG42_05g0106200.10 Clacu05g1062 1062
5 9508914 9511428 + ClG42_05g0106300.10 Clacu05g1063 1063
5 9525063 9529196 + ClG42_05g0106600.10 Clacu05g1066 1066
1 286932 293711 + ClCG01G000360.2 Cla01g00037 37
1 295102 306601 + ClCG01G000370.2 Cla01g00038 38
5 9832434 9839270 + ClCG05G008980.2 Cla05g00974 974
5 9839757 9842003 - ClCG05G009000.1 Cla05g00975 975
5 9854265 9858443 + ClCG05G009010.2 Cla05g00976 976
5 9858597 9860373 - ClCG05G009020.1 Cla05g00977 977
5 9860797 9863455 + ClCG05G009030.1 Cla05g00978 978
5 9867049 9872417 + ClCG05G009040.2 Cla05g00979 979
5 9876491 9881341 + ClCG05G009060.1 Cla05g00981 981
2 6657999 6667455 - CmaCh02G011220.1 Cma02g01122 1122
2 6669200 6674365 - CmaCh02G011230.1 Cma02g01123 1123
15 6333216 6358060 + CmaCh15G010240.1 Cma15g01024 1024
16 166272 169389 - CmaCh16G000370.1 Cma16g00037 37
16 169751 176748 - CmaCh16G000380.1 Cma16g00038 38
16 178062 181000 - CmaCh16G000400.1 Cma16g00040 40
18 10125793 10134765 - CmaCh18G013230.1 Cma18g01323 1323
6 8855899 8857030 + MELO3C008501.2.1 Cme06g01148 1148
6 8857091 8858201 - MELO3C008502.2.1 Cme06g01149 1149
6 8882902 8886967 + MELO3C008503.2.1 Cme06g01152 1152
6 8888087 8889956 - MELO3C008504.2.1 Cme06g01153 1153
6 8895403 8897472 + MELO3C019369.2.1 Cme06g01154 1154
6 8905560 8913902 + MELO3C019371.2.1 Cme06g01156 1156
6 8916370 8920711 + MELO3C019373.2.1 Cme06g01157 1157
9 23713042 23717247 - MELO3C005890.2.1 Cme09g01988 1988
9 23722936 23726120 - MELO3C005891.2.1 Cme09g01989 1989
9 23726960 23730975 - MELO3C005892.2.1 Cme09g01990 1990
3 5961346 5962743 - PI0029031.1 Cmetu03g1368 1368
6 8315547 8321240 + PI0009355.2 Cmetu06g0080 80
6 8337651 8341814 + PI0021750.1 Cmetu06g0082 82
6 8001541 8003735 + PI0009517.1 Cmetu06g0196 196
6 8018692 8019946 - PI0006572.1 Cmetu06g0291 291
6 8327867 8332647 + PI0028724.1 Cmetu06g1355 1355
2 6959249 6963089 - CmoCh02G011500.1 Cmo02g01150 1150
2 6964013 6968964 - CmoCh02G011510.1 Cmo02g01151 1151
2 6970960 6976179 - CmoCh02G011520.1 Cmo02g01152 1152
15 7203733 7215027 + CmoCh15G010870.1 Cmo15g01087 1087
16 187305 190450 - CmoCh16G000430.1 Cmo16g00043 43
16 192974 197728 - CmoCh16G000450.1 Cmo16g00045 45
16 198005 199781 + CmoCh16G000470.1 Cmo16g00047 47
16 199875 202493 - CmoCh16G000480.1 Cmo16g00048 48
16 204971 206157 - CmoCh16G000490.1 Cmo16g00049 49
1 301459 306228 + CmPI595203_01g000350.1 Cmu01g0035 35
1 313577 317626 + CmPI595203_01g000370.1 Cmu01g0037 37
5 9324362 9329204 + CmPI595203_05g010090.1 Cmu05g1009 1009
5 9331340 9332206 - CmPI595203_05g010100.1 Cmu05g1010 1010
5 9343904 9346325 + CmPI595203_05g010120.1 Cmu05g1012 1012
5 9347074 9348495 - CmPI595203_05g010130.1 Cmu05g1013 1013
5 9348946 9351460 + CmPI595203_05g010140.1 Cmu05g1014 1014
5 9365112 9369245 + CmPI595203_05g010170.1 Cmu05g1017 1017
1 54970390 54971559 + Conep01aG0103500.1 Cone1ag0990 990
1 54976000 54978609 + Conep01aG0103600.1 Cone1ag0991 991
1 54981431 54982050 - Conep01aG0103800.1 Cone1ag0993 993
1 54983211 54985152 - Conep01aG0103900.1 Cone1ag0994 994
1 54985322 54988915 - Conep01aG0104000.1 Cone1ag0995 995
5 2971181 2972622 + Conep05aG0071800.1 Cone5ag0694 694
5 2987940 2990978 + Conep05aG0072000.1 Cone5ag0696 696
5 2991225 2992108 - Conep05aG0072100.1 Cone5ag0697 697
5 2996467 2998342 - Conep05aG0072200.1 Cone5ag0698 698
5 2999079 3001943 - Conep05aG0072300.1 Cone5ag0699 699
14 28189 30890 - Conep14aG0000300.1 Cone14ag0002 2
14 32833 36220 + Conep14aG0000500.1 Cone14ag0004 4
14 45426 48816 + Conep14aG0000600.1 Cone14ag0005 5
14 49551 50490 + Conep14aG0000700.1 Cone14ag0006 6
15 63548 71842 + Conep15aG0000900.1 Cone15ag0008 8
5 3613108 3615899 + Cp4.1LG05g05880.1 Cpe05g00595 595
5 3619731 3622346 + Cp4.1LG05g05820.1 Cpe05g00596 596
5 3623248 3627055 + Cp4.1LG05g05910.1 Cpe05g00597 597
9 231284 235285 + Cp4.1LG09g00340.1 Cpe09g00038 38
13 2748235 2753198 - Cp4.1LG13g03190.1 Cpe13g00318 318
14 165788 168827 - Cp4.1LG14g06750.1 Cpe14g00030 30
14 173557 181198 - Cp4.1LG14g06770.1 Cpe14g00031 31
14 181806 183678 + Cp4.1LG14g06860.1 Cpe14g00032 32
14 181812 186363 - Cp4.1LG14g06740.1 Cpe14g00033 33
14 187416 188665 - Cp4.1LG14g06780.1 Cpe14g00034 34
5 10202151 10207055 + CrPI670011_05g010860.1 Cre05g1086 1086
5 10207638 10209865 - CrPI670011_05g010870.1 Cre05g1087 1087
5 10216733 10221100 + CrPI670011_05g010880.1 Cre05g1088 1088
5 10221887 10223309 - CrPI670011_05g010890.1 Cre05g1089 1089
5 10223755 10239381 + CrPI670011_05g010900.1 Cre05g1090 1090
5 10240663 10244489 + CrPI670011_05g010910.1 Cre05g1091 1091
9 44012214 44016279 - CrPI670011_09g024700.1 Cre09g2470 2470
9 44017576 44028057 - CrPI670011_09g024710.1 Cre09g2471 2471
3 15565173 15570677 - CsaV3_3G019720.1 Csa03g01972 1972
3 15574144 15579898 - CsaV3_3G019740.1 Csa03g01974 1974
3 15582918 15585341 - CsaV3_3G019750.1 Csa03g01975 1975
3 15591214 15593225 + CsaV3_3G019760.1 Csa03g01976 1976
3 15593485 15597743 - CsaV3_3G019770.1 Csa03g01977 1977
3 15608830 15609539 + CsaV3_3G019780.1 Csa03g01978 1978
3 15609564 15611301 - CsaV3_3G019790.1 Csa03g01979 1979
5 198022 203299 + CsaV3_5G000430.1 Csa05g00043 43
5 205265 207157 + CsaV3_5G000450.1 Csa05g00045 45
5 208526 212373 + CsaV3_5G000460.1 Csa05g00046 46
6 54742895 54747988 - Hsped.06g07960.1 Hepe06g0796 796
7 497620 501631 - Hsped.07g00480.1 Hepe07g0048 48
7 505566 511118 - Hsped.07g00500.1 Hepe07g0050 50
7 513146 515579 - Hsped.07g00510.1 Hepe07g0051 51
7 515821 517444 + Hsped.07g00520.1 Hepe07g0052 52
7 526882 528316 + Hsped.07g00540.1 Hepe07g0054 54
7 529218 531262 - Hsped.07g00550.1 Hepe07g0055 55
11 1494819 1498684 - Lag0030800.1 Lac11g0162 162
11 1500984 1504171 - Lag0030801.1 Lac11g0163 163
11 1506319 1509859 - Lag0030802.1 Lac11g0164 164
12 1715823 1721621 - Maker00039049 Lcy12g0138 138
12 1723324 1725771 - Maker00038841 Lcy12g0139 139
12 1728068 1732845 - Maker00038649 Lcy12g0140 140
9 140609 154609 + Lsi09G000170.1 Lsi09g00017 17
9 156771 163734 + Lsi09G000180.1 Lsi09g00018 18
10 262336 274990 - MC10g0043 Mch10g0048 48
10 276300 280021 - MC10g0044 Mch10g0049 49
10 279377 283230 + MC10g0045 Mch10g0050 50
10 288269 289312 + MC10g0047 Mch10g0052 52
10 290099 291069 - MC10g0048 Mch10g0053 53
1 63971315 63973669 - Sed0003282.1 Sed01g3487 3487
5 31450602 31453309 - Sed0013662.1 Sed05g1782 1782
7 6291082 6293776 + Sed0013694.1 Sed07g0868 868
7 6295315 6300631 + Sed0003761.3 Sed07g0871 871
13 297415 302065 - Sed0016509.2 Sed13g0046 46
13 316394 318654 + Sed0012841.1 Sed13g0050 50
1 831839 838557 - Tan0021740.4 Tan01g0077 77
1 847591 852898 - Tan0016985.2 Tan01g0081 81
1 856507 861102 - Tan0006944.1 Tan01g0082 82
1 861247 862831 + Tan0013478.1 Tan01g0083 83
1 957421 959129 + Tan0009373.1 Tan01g0086 86
1 959636 960944 - Tan0007100.1 Tan01g0087 87
16 21771555 21776235 - Vvi16g1024 Vvi16g1024 1024
16 21779446 21784699 + Vvi16g1025 Vvi16g1025 1025
16 21785848 21788949 + Vvi16g1026 Vvi16g1026 1026
16 21791254 21794906 + Vvi16g1027 Vvi16g1027 1027
16 21798662 21804471 + Vvi16g1028 Vvi16g1028 1028
16 21804594 21808723 + Vvi16g1029 Vvi16g1029 1029
16 21810707 21814197 + Vvi16g1030 Vvi16g1030 1030
16 21814435 21817575 - Vvi16g1031 Vvi16g1031 1031
16 21822210 21823097 + Vvi16g1032 Vvi16g1032 1032
16 21823283 21826992 - Vvi16g1033 Vvi16g1033 1033
       

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