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
Vvi16g744 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag1181 Cone5ag0885 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g745 . . . . Bpe03g00148 . . Bma14g02049 Cmo16g00114 . . . . . Sed08g0079 . Cpe14g00091 Bhi01g01266 Tan01g0209 Cmetu10g1511 . Hepe07g0132 Mch10g0135 . . . . . . . . Cone1ag1183 . . . Lsi05g01204 . . . Blo07g00388 . . . . Bpe12g00441 . . . . . Cma16g00106 . . . . . . . . . . . . . . . . . . . . Csa03g01738 Chy06g00969 .
Vvi16g746 . . Bda05g00089 Bda07g01897 Bpe03g00270 . Bma10g01240 . Cmo16g00113 . . . . . . Cpe05g00642 Cpe14g00090 . . . . . . . Cla01g00095 Cam01g0097 Cec01g0097 Cco01g0098 Clacu01g0095 Cmu01g0097 Cre09g2410 . . . Cone15ag0065 Lsi05g01202 Csa05g00110 . . Blo07g00385 . . Bda15g00712 . . . . . . . Cma16g00105 . Car16g00094 . . . . . . . . . . Cla05g00904 Cam05g0988 Cec05g0994 Cco05g0992 Clacu05g0976 Cmu05g0933 Cre05g1018 Lsi09g00083 . . .
Vvi16g747 . . Bda05g00091 . Bpe03g00269 . Bma10g01241 . . . Cma02g01077 . Car02g00820 . . . . . . . . . . . . . . . . . . Cone1ag1186 . . . Lsi05g01201 . Chy09g01385 . Blo07g00382 . . . . . . . . Cmo02g01094 . . . . . . . Bhi12g00788 . . . . . Lcy12g0053 Cla05g00906 Cam05g0991 Cec05g0995 Cco05g0993 Clacu05g0979 Cmu05g0936 Cre05g1019 . Csa03g01739 Chy06g00970 Cme09g01930
Vvi16g748 . Blo15g00177 . . . Bpe07g00927 . . . . Cma02g01078 . Car02g00821 . . Cpe05g00641 . . . . . . . . Cla01g00094 Cam01g0096 Cec01g0096 Cco01g0097 Clacu01g0094 Cmu01g0096 Cre09g2411 . . Cone14ag0061 Cone15ag0064 . Csa05g00109 Chy09g01386 . . . Bda06g00694 . . . . Bma12g01110 . Cmo02g01095 . . . . . . . Bhi12g00787 . . . . . . . . . . . . . Lsi09g00082 . . Cme09g01931
Vvi16g749 . . . Bda07g01898 Bpe03g00149 . . Bma14g02048 Cmo16g00112 Cmo18g01293 . . . . . . Cpe14g00089 . . . . . . . . . . . . . . . . . . Lsi05g01200 . . . . Blo09g00068 . . . . . . . . . Cma16g00104 Cma18g01264 Car16g00093 Car18g01174 Cpe09g00072 . . . . . . . . Cla05g00907 . . . . . . . Csa03g01740 Chy06g00971 .
Vvi16g750 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g751 . . . Bda07g01899 Bpe03g00150 . Bma10g01245 Bma14g02047 Cmo16g00110 Cmo18g01295 . . . . . . . . . . . . . . . . . . . . . Cone1ag1188 Cone5ag0888 . . Lsi05g01199 . . . Blo07g00378 Blo09g00067 . . . . . . . . . Cma16g00103 Cma18g01266 Car16g00092 Car18g01175 Cpe09g00071 . . . . . . . . Cla05g00908 Cam05g0994 Cec05g0997 Cco05g0995 Clacu05g0982 Cmu05g0938 Cre05g1022 . Csa03g01742 Chy06g00972 .
Vvi16g752 . . . Bda07g01900 Bpe03g00151 . Bma10g01246 Bma14g02046 Cmo16g00109 Cmo18g01297 . . . . . . Cpe14g00088 . . . . . . . . . . . . . . . . Cone14ag0060 . Lsi05g01198 . . . . . . . . . . . . . . Cma16g00102 Cma18g01267 . Car18g01176 Cpe09g00070 . . . . . . . . Cla05g00909 Cam05g0995 Cec05g0998 Cco05g0996 Clacu05g0983 Cmu05g0939 Cre05g1023 . Csa03g01743 Chy06g00973 .
Vvi16g753 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag1190 Cone5ag0890 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 4284758 4285105 - Bda020685.1 Bda05g00089 89
5 4341936 4366128 - Bda020687.1 Bda05g00091 91
6 9558028 9558647 - Bda023991.1 Bda06g00694 694
7 36365324 36368256 - Bda028870.1 Bda07g01897 1897
7 36373003 36375854 + Bda028871.1 Bda07g01898 1898
7 36379362 36381249 + Bda028872.1 Bda07g01899 1899
7 36382074 36382944 - Bda028873.1 Bda07g01900 1900
15 10531615 10535208 + Bda012566.1 Bda15g00712 712
1 25824556 25828868 + XM_039022252.1 Bhi01g01266 1266
12 23479998 23484638 + XM_039019270.1 Bhi12g00787 787
12 23485576 23490380 + XM_039050729.1 Bhi12g00788 788
7 6343311 6345239 - BLOR18310 Blo07g00378 378
7 6541790 6545816 + BLOR18314 Blo07g00382 382
7 6645739 6648079 + BLOR18317 Blo07g00385 385
7 6680392 6682005 + BLOR18320 Blo07g00388 388
9 1146355 1148270 - BLOR20982 Blo09g00067 67
9 1156024 1158892 - BLOR20983 Blo09g00068 68
15 1803545 1811725 - BLOR06571 Blo15g00177 177
10 44074547 44078182 - Bma005329.1 Bma10g01240 1240
10 44079873 44083457 - Bma005330.1 Bma10g01241 1241
10 44122728 44124533 + Bma005335.1 Bma10g01245 1245
10 44125293 44125886 - Bma005336.1 Bma10g01246 1246
12 43374169 43374779 + Bma008455.1 Bma12g01110 1110
14 43838928 43839843 + Bma012855.1 Bma14g02046 2046
14 43840641 43842495 - Bma012856.1 Bma14g02047 2047
14 43846303 43848198 - Bma012857.1 Bma14g02048 2048
14 43853406 43856054 + Bma012858.1 Bma14g02049 2049
3 1973917 1976868 - Bpe011992.1 Bpe03g00148 148
3 1981649 1984545 + Bpe011993.1 Bpe03g00149 149
3 1987264 1989119 + Bpe011994.1 Bpe03g00150 150
3 1989940 1990808 - Bpe011995.1 Bpe03g00151 151
3 3705326 3708816 + Bpe012122.1 Bpe03g00269 269
3 3718359 3721364 + Bpe012123.1 Bpe03g00270 270
7 15205248 15205861 + Bpe021768.1 Bpe07g00927 927
12 10168932 10177904 - Bpe005701.1 Bpe12g00441 441
1 1246412 1249108 + CaPI482276_01g000960.1 Cam01g0096 96
1 1250835 1256219 + CaPI482276_01g000970.1 Cam01g0097 97
5 8974244 8977939 - CaPI482276_05g009880.1 Cam05g0988 988
5 8992542 8997545 - CaPI482276_05g009910.1 Cam05g0991 991
5 9018794 9021765 + CaPI482276_05g009940.1 Cam05g0994 994
5 9022416 9023665 - CaPI482276_05g009950.1 Cam05g0995 995
2 5924802 5929915 - Carg08401-RA Car02g00820 820
2 5930995 5934704 - Carg08400-RA Car02g00821 821
16 570474 573846 - Carg15114-RA Car16g00092 92
16 575153 577630 - Carg15115-RA Car16g00093 93
16 579481 582577 + Carg15116-RA Car16g00094 94
18 11456071 11458554 + Carg22122-RA Car18g01174 1174
18 11459841 11463086 + Carg22123-RA Car18g01175 1175
18 11463855 11464508 - Carg22124-RA Car18g01176 1176
1 776828 779470 + CcPI632755_01g000970.1 Cco01g0097 97
1 781288 785958 + CcPI632755_01g000980.1 Cco01g0098 98
5 8740415 8745201 - CcPI632755_05g009920.1 Cco05g0992 992
5 8749052 8753943 - CcPI632755_05g009930.1 Cco05g0993 993
5 8775392 8778351 + CcPI632755_05g009950.1 Cco05g0995 995
5 8779058 8782570 - CcPI632755_05g009960.1 Cco05g0996 996
1 809819 812445 + CePI673135_01g000960.1 Cec01g0096 96
1 814321 819107 + CePI673135_01g000970.1 Cec01g0097 97
5 8719832 8724455 - CePI673135_05g009940.1 Cec05g0994 994
5 8728346 8733214 - CePI673135_05g009950.1 Cec05g0995 995
5 8754266 8757206 + CePI673135_05g009970.1 Cec05g0997 997
5 8757866 8759115 - CePI673135_05g009980.1 Cec05g0998 998
6 7142144 7146456 - Chy6G114970.1 Chy06g00969 969
6 7151846 7161887 - Chy6G114980.1 Chy06g00970 970
6 7168049 7170532 + Chy6G114990.1 Chy06g00971 971
6 7175672 7178534 + Chy6G115000.1 Chy06g00972 972
6 7179765 7180415 - Chy6G115010.1 Chy06g00973 973
9 15610739 15615476 - Chy9G171010.1 Chy09g01385 1385
9 15616213 15618463 - Chy9G171020.1 Chy09g01386 1386
1 856899 859561 + ClG42_01g0009400.10 Clacu01g0094 94
1 861414 866126 + ClG42_01g0009500.10 Clacu01g0095 95
5 8690199 8693834 - ClG42_05g0097600.10 Clacu05g0976 976
5 8708366 8713367 - ClG42_05g0097900.10 Clacu05g0979 979
5 8734584 8737568 + ClG42_05g0098200.10 Clacu05g0982 982
5 8738222 8739167 - ClG42_05g0098300.10 Clacu05g0983 983
1 823790 828260 + ClCG01G000950.2 Cla01g00094 94
1 829731 835212 + ClCG01G000960.1 Cla01g00095 95
5 8969950 8987831 - ClCG05G008290.1 Cla05g00904 904
5 8991109 8996469 - ClCG05G008310.1 Cla05g00906 906
5 9007152 9009710 + ClCG05G008320.2 Cla05g00907 907
5 9019568 9024919 + ClCG05G008330.2 Cla05g00908 908
5 9025209 9028822 - ClCG05G008340.2 Cla05g00909 909
2 6412194 6418318 - CmaCh02G010770.1 Cma02g01077 1077
2 6419498 6424079 - CmaCh02G010780.1 Cma02g01078 1078
16 459191 459844 + CmaCh16G001020.1 Cma16g00102 102
16 460296 464249 - CmaCh16G001030.1 Cma16g00103 103
16 465761 468238 - CmaCh16G001040.1 Cma16g00104 104
16 469649 472966 + CmaCh16G001050.1 Cma16g00105 105
16 474290 478896 + CmaCh16G001060.1 Cma16g00106 106
18 9840380 9842863 + CmaCh18G012640.1 Cma18g01264 1264
18 9844818 9847832 + CmaCh18G012660.1 Cma18g01266 1266
18 9848459 9852872 - CmaCh18G012670.1 Cma18g01267 1267
9 23367757 23373422 - MELO3C005835.2.1 Cme09g01930 1930
9 23373853 23374799 - MELO3C005837.2.1 Cme09g01931 1931
10 16788677 16793173 - PI0024845.1 Cmetu10g1511 1511
2 6636961 6643856 - CmoCh02G010940.1 Cmo02g01094 1094
2 6644520 6648071 - CmoCh02G010950.1 Cmo02g01095 1095
16 502570 503838 + CmoCh16G001090.1 Cmo16g00109 109
16 503907 507505 - CmoCh16G001100.1 Cmo16g00110 110
16 509021 511355 - CmoCh16G001120.1 Cmo16g00112 112
16 513050 516310 + CmoCh16G001130.1 Cmo16g00113 113
16 517584 522003 + CmoCh16G001140.1 Cmo16g00114 114
18 12459276 12461759 + CmoCh18G012930.1 Cmo18g01293 1293
18 12464538 12467451 + CmoCh18G012950.1 Cmo18g01295 1295
18 12468202 12469194 - CmoCh18G012970.1 Cmo18g01297 1297
1 801366 804019 + CmPI595203_01g000960.1 Cmu01g0096 96
1 805872 811141 + CmPI595203_01g000970.1 Cmu01g0097 97
5 8536885 8540516 - CmPI595203_05g009330.1 Cmu05g0933 933
5 8555026 8560027 - CmPI595203_05g009360.1 Cmu05g0936 936
5 8581193 8584165 + CmPI595203_05g009380.1 Cmu05g0938 938
5 8584817 8588328 - CmPI595203_05g009390.1 Cmu05g0939 939
1 55812186 55818015 + Conep01aG0123000.1 Cone1ag1181 1181
1 55819389 55821218 - Conep01aG0123200.1 Cone1ag1183 1183
1 55832357 55834623 - Conep01aG0123500.1 Cone1ag1186 1186
1 55839072 55842175 + Conep01aG0123700.1 Cone1ag1188 1188
1 55850022 55855238 - Conep01aG0123900.1 Cone1ag1190 1190
5 3796193 3802128 + Conep05aG0091100.1 Cone5ag0885 885
5 3818726 3821749 + Conep05aG0091400.1 Cone5ag0888 888
5 3826495 3830277 - Conep05aG0091600.1 Cone5ag0890 890
14 342519 344393 + Conep14aG0006200.1 Cone14ag0060 60
14 344776 346497 + Conep14aG0006300.1 Cone14ag0061 61
15 364466 368241 + Conep15aG0006600.1 Cone15ag0064 64
15 368596 370528 + Conep15aG0006700.1 Cone15ag0065 65
5 3923460 3928515 + Cp4.1LG05g06510.1 Cpe05g00641 641
5 3928817 3935135 + Cp4.1LG05g06500.1 Cpe05g00642 642
9 415691 419084 + Cp4.1LG09g00690.1 Cpe09g00070 70
9 419239 422630 - Cp4.1LG09g00810.1 Cpe09g00071 71
9 423972 426864 - Cp4.1LG09g00800.1 Cpe09g00072 72
14 475737 476710 + Cp4.1LG14g06310.1 Cpe14g00088 88
14 483688 486437 - Cp4.1LG14g06190.1 Cpe14g00089 89
14 488341 491676 + Cp4.1LG14g06250.1 Cpe14g00090 90
14 493359 497162 + Cp4.1LG14g06280.1 Cpe14g00091 91
5 9423969 9428313 - CrPI670011_05g010180.1 Cre05g1018 1018
5 9432035 9437046 - CrPI670011_05g010190.1 Cre05g1019 1019
5 9462397 9465366 + CrPI670011_05g010220.1 Cre05g1022 1022
5 9466025 9469558 - CrPI670011_05g010230.1 Cre05g1023 1023
9 43499981 43504708 - CrPI670011_09g024100.1 Cre09g2410 2410
9 43506601 43509209 - CrPI670011_09g024110.1 Cre09g2411 2411
3 13026297 13030904 - CsaV3_3G017380.1 Csa03g01738 1738
3 13034177 13039707 - CsaV3_3G017390.1 Csa03g01739 1739
3 13045860 13049345 + CsaV3_3G017400.1 Csa03g01740 1740
3 13051849 13054695 + CsaV3_3G017420.1 Csa03g01742 1742
3 13055267 13058331 - CsaV3_3G017430.1 Csa03g01743 1743
5 543032 544883 + CsaV3_5G001090.1 Csa05g00109 109
5 545580 550233 + CsaV3_5G001100.1 Csa05g00110 110
7 1204432 1208465 + Hsped.07g01320.1 Hepe07g0132 132
12 800583 807925 - Maker00038459 Lcy12g0053 53
5 19845238 19850106 + Lsi05G011980.1 Lsi05g01198 1198
5 19848832 19852715 - Lsi05G011990.1 Lsi05g01199 1199
5 19858103 19860676 - Lsi05G012000.1 Lsi05g01200 1200
5 19874470 19880749 + Lsi05G012010.1 Lsi05g01201 1201
5 19885077 19889767 + Lsi05G012020.1 Lsi05g01202 1202
5 19893304 19897499 + Lsi05G012040.1 Lsi05g01204 1204
9 702995 703834 + Lsi09G000820.1 Lsi09g00082 82
9 704561 710150 + Lsi09G000830.1 Lsi09g00083 83
10 794703 800574 + MC10g0116 Mch10g0135 135
8 426249 429569 - Sed0027604.1 Sed08g0079 79
1 1879561 1884208 + Tan0006858.3 Tan01g0209 209
16 17905498 17910247 + Vvi16g744 Vvi16g744 744
16 17911250 17919834 - Vvi16g745 Vvi16g745 745
16 17920089 17930273 - Vvi16g746 Vvi16g746 746
16 17930994 17936399 - Vvi16g747 Vvi16g747 747
16 17937131 17940515 - Vvi16g748 Vvi16g748 748
16 17944976 17949854 + Vvi16g749 Vvi16g749 749
16 17958290 17958581 - Vvi16g750 Vvi16g750 750
16 17979667 17985100 + Vvi16g751 Vvi16g751 751
16 17986029 17989757 - Vvi16g752 Vvi16g752 752
16 17990805 18010705 - Vvi16g753 Vvi16g753 753
       

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