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
Vvi16g734 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g735 . . Bda05g00085 . Bpe03g00144 . Bma10g01237 Bma14g02052 Cmo16g00115 Cmo18g01289 . . . . Sed07g1007 . Cpe14g00092 Bhi01g01269 Tan01g0216 Cmetu09g1022 . Hepe07g0136 Mch10g1473 . . . . . . . . . . . . Lsi05g01207 . . . Blo07g00395 Blo09g00074 . . . . . . . . . Cma16g00107 Cma18g01262 Car16g00096 Car18g01171 Cpe09g00075 . Bhi12g00810 . . . . . Lcy10g0884 Cla05g00901 Cam05g0985 Cec05g0991 Cco05g0989 Clacu05g0973 Cmu05g0930 Cre05g1015 . Csa03g01736 Chy06g00967 .
Vvi16g736 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g737 . . . . . . . . . . . Cma15g01082 . . . . . . . . . . . . Cla01g00098 Cam01g0100 Cec01g0101 Cco01g0102 Clacu01g0098 Cmu01g0100 Cre09g2407 . . . . . Csa05g00115 . . Blo07g00394 Blo09g00073 . . . . . . . . Cmo15g01142 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g738 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g739 . . . . Bpe03g00145 . Bma10g01238 Bma14g02051 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo09g00072 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g740 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo09g00071 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g741 . . . Bda07g01895 Bpe03g00147 . . . . . . . . Car15g00995 . . . . . . . . . . . . . . . . . . . . . . . Chy09g01381 . . Blo09g00070 . . . . . . . . . . . . . . Cpe13g00267 Bhi12g00020 . . . . . Lcy12g0048 . . . . . . . Lsi09g00087 . . Cme09g01925
Vvi16g742 . . Bda05g00086 . Bpe03g00272 . Bma10g01239 . . Cmo18g01292 . . . . Sed11g1514 . . Bhi01g01267 Tan01g0211 Cmetu11g1479 . Hepe07g0133 . . . . . . . . . Cone1ag1180 Cone5ag0884 . . Lsi05g01205 . . . Blo07g00389 . . . . . . . . . . . Cma18g01263 . Car18g01173 Cpe09g00073 . . . . . . . . Cla05g00903 Cam05g0987 Cec05g0993 Cco05g0991 Clacu05g0975 Cmu05g0932 Cre05g1017 . . . .
Vvi16g743 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 4049552 4051987 - Bda020679.1 Bda05g00085 85
5 4091640 4096192 + Bda020680.1 Bda05g00086 86
7 36346113 36356694 - Bda028868.2 Bda07g01895 1895
1 25828939 25838082 - XM_039022253.1 Bhi01g01267 1267
1 25843484 25846993 - XM_039020031.1 Bhi01g01269 1269
12 431135 435341 + XM_039050747.1 Bhi12g00020 20
12 24403278 24407016 + XM_039019812.1 Bhi12g00810 810
7 6682479 6695886 - BLOR18321 Blo07g00389 389
7 6821864 6826845 + BLOR18326 Blo07g00394 394
7 6862230 6867846 + BLOR18327 Blo07g00395 395
9 1209648 1214628 + BLOR20985 Blo09g00070 70
9 1234594 1240069 + BLOR20986 Blo09g00071 71
9 1303472 1308456 + BLOR20987 Blo09g00072 72
9 1331420 1336079 + BLOR20988 Blo09g00073 73
9 1351318 1361793 + BLOR20989 Blo09g00074 74
10 43937568 43940447 - Bma005323.1 Bma10g01237 1237
10 43945856 43948868 - Bma005324.1 Bma10g01238 1238
10 43954365 43959306 + Bma005325.1 Bma10g01239 1239
14 43862475 43865126 + Bma012860.1 Bma14g02051 2051
14 43872954 43875963 + Bma012861.1 Bma14g02052 2052
3 1941223 1944413 - Bpe025362 Bpe03g00144 144
3 1947882 1950804 - Bpe011988.1 Bpe03g00145 145
3 1967813 1970491 - Bpe011991.1 Bpe03g00147 147
3 3745860 3750443 - Bpe012125.1 Bpe03g00272 272
1 1308123 1311812 + CaPI482276_01g001000.1 Cam01g0100 100
5 8956501 8959676 + CaPI482276_05g009850.1 Cam05g0985 985
5 8969674 8973549 + CaPI482276_05g009870.1 Cam05g0987 987
15 7780382 7784332 + Carg23171-RA Car15g00995 995
16 591438 595150 - Carg15118-RA Car16g00096 96
18 11441970 11445103 + Carg22119-RA Car18g01171 1171
18 11448750 11453630 + Carg22121-RA Car18g01173 1173
1 841935 845563 + CcPI632755_01g001020.1 Cco01g0102 102
5 8722565 8725730 + CcPI632755_05g009890.1 Cco05g0989 989
5 8735713 8739720 + CcPI632755_05g009910.1 Cco05g0991 991
1 874606 878279 + CePI673135_01g001010.1 Cec01g0101 101
5 8702550 8705730 + CePI673135_05g009910.1 Cec05g0991 991
5 8715264 8719138 + CePI673135_05g009930.1 Cec05g0993 993
6 7132507 7135376 + Chy6G114950.1 Chy06g00967 967
9 15569776 15571290 - Chy9G170970.1 Chy09g01381 1381
1 918366 922101 + ClG42_01g0009800.10 Clacu01g0098 98
5 8673221 8676359 + ClG42_05g0097300.10 Clacu05g0973 973
5 8685631 8689504 + ClG42_05g0097500.10 Clacu05g0975 975
1 887403 891138 + ClCG01G001000.2 Cla01g00098 98
5 8952989 8956129 + ClCG05G008250.2 Cla05g00901 901
5 8965294 8971805 + ClCG05G008280.1 Cla05g00903 903
15 6885859 6889680 + CmaCh15G010820.1 Cma15g01082 1082
16 477548 485377 - CmaCh16G001070.1 Cma16g00107 107
18 9826835 9833687 + CmaCh18G012620.1 Cma18g01262 1262
18 9833796 9838109 + CmaCh18G012630.1 Cma18g01263 1263
9 23332307 23335776 - MELO3C005831.2.1 Cme09g01925 1925
9 4534153 4537934 + PI0008398.1 Cmetu09g1022 1022
11 7981123 7982448 + PI0028069.1 Cmetu11g1479 1479
15 7974567 7978744 + CmoCh15G011420.1 Cmo15g01142 1142
16 522540 528713 - CmoCh16G001150.1 Cmo16g00115 115
18 12444195 12447530 + CmoCh18G012890.1 Cmo18g01289 1289
18 12451328 12457722 + CmoCh18G012920.1 Cmo18g01292 1292
1 863169 866904 + CmPI595203_01g001000.1 Cmu01g0100 100
5 8519936 8523076 + CmPI595203_05g009300.1 Cmu05g0930 930
5 8532349 8536190 + CmPI595203_05g009320.1 Cmu05g0932 932
1 55805774 55810598 + Conep01aG0122900.1 Cone1ag1180 1180
5 3788311 3794740 + Conep05aG0091000.1 Cone5ag0884 884
9 429059 434241 - Cp4.1LG09g00770.1 Cpe09g00073 73
9 438139 441408 - Cp4.1LG09g00780.1 Cpe09g00075 75
13 2074130 2078394 - Cp4.1LG13g02610.1 Cpe13g00267 267
14 497000 503853 - Cp4.1LG14g06180.1 Cpe14g00092 92
5 9406555 9409721 + CrPI670011_05g010150.1 Cre05g1015 1015
5 9419457 9423344 + CrPI670011_05g010170.1 Cre05g1017 1017
9 43434699 43438348 - CrPI670011_09g024070.1 Cre09g2407 2407
3 13016279 13019993 + CsaV3_3G017360.1 Csa03g01736 1736
5 583100 586669 + CsaV3_5G001150.1 Csa05g00115 115
7 1209044 1212807 - Hsped.07g01330.1 Hepe07g0133 133
7 1233288 1237085 - Hsped.07g01360.1 Hepe07g0136 136
10 27499567 27504695 + Maker00020684 Lcy10g0884 884
12 732181 736392 - Maker00038631 Lcy12g0048 48
5 19897934 19902958 - Lsi05G012050.1 Lsi05g01205 1205
5 19909001 19912634 - Lsi05G012070.1 Lsi05g01207 1207
9 779941 784480 + Lsi09G000870.1 Lsi09g00087 87
10 14666183 14669648 + MC10g1161 Mch10g1473 1473
7 7305188 7308433 - Sed0008349.2 Sed07g1007 1007
11 30791201 30801521 + Sed0015133.1 Sed11g1514 1514
1 1884256 1889022 - Tan0020163.2 Tan01g0211 211
1 1897788 1901247 - Tan0013463.1 Tan01g0216 216
16 17811948 17812491 + Vvi16g734 Vvi16g734 734
16 17812497 17816876 + Vvi16g735 Vvi16g735 735
16 17816894 17817823 - Vvi16g736 Vvi16g736 736
16 17818982 17824636 - Vvi16g737 Vvi16g737 737
16 17824938 17825396 - Vvi16g738 Vvi16g738 738
16 17827579 17830662 - Vvi16g739 Vvi16g739 739
16 17832828 17836814 - Vvi16g740 Vvi16g740 740
16 17836934 17840142 - Vvi16g741 Vvi16g741 741
16 17881723 17898213 + Vvi16g742 Vvi16g742 742
16 17903070 17905473 + Vvi16g743 Vvi16g743 743
       

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