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
Vvi16g864 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g865 Blo06g01075 . . . . . . . Cmo16g00075 . . . . . Sed02g0861 . Cpe14g00058 Bhi01g01449 Tan01g0150 Cmetu09g1713 . . Mch10g0089 . . . . . . . . . . . . . . . . . . . Bda15g00774 . Bpe12g00371 . . . . . Cma16g00073 . Car16g00064 . . . . . . . . . . Cla05g00947 Cam05g1037 Cec05g1042 Cco05g1036 Clacu05g1028 Cmu05g0978 Cre05g1057 . Csa03g02195 Chy06g01258 .
Vvi16g866 . . Bda05g00110 . Bpe03g00175 . Bma10g01285 . . Cmo18g01328 . . . . Sed07g0811 . Cpe14g00057 Bhi01g01450 Tan01g0149 Cmetu06g1760 . . Mch10g0088 . . . . . . . . Cone1ag0958 Cone5ag0651 Cone14ag0031 . . . . . Blo07g00350 Blo09g00040 . Bda15g00775 . Bpe12g00372 . . . . . Cma16g00072 Cma18g01299 Car16g00063 Car18g01215 Cpe09g00043 . . . . . . . . . . . . . . . . Csa03g02197 Chy06g01256 .
Vvi16g867 . . Bda05g00111 . Bpe03g00242 . Bma10g01288 . Cmo16g00074 Cmo18g01329 . . . . . . Cpe14g00056 Bhi01g01452 Tan01g0147 . . Hepe07g0088 Mch10g0087 . . . . . . . . . . . . . . . . Blo07g00349 . . . . . . . . . . Cma16g00071 Cma18g01300 Car16g00062 Car18g01216 Cpe09g00042 . . . . . . . . Cla05g00948 Cam05g1039 Cec05g1044 Cco05g1038 Clacu05g1030 Cmu05g0980 Cre05g1059 . Csa03g02198 Chy06g01255 .
Vvi16g868 Blo06g01076 . . . . . . . Cmo16g00073 Cmo18g01330 . . . . Sed07g0818 . Cpe14g00055 Bhi01g01453 Tan01g0146 Cmetu06g0694 . Hepe07g0087 . . . . . . . . . . . Cone14ag0030 Cone15ag0032 . . . . . . . Bda15g00776 . Bpe12g00373 . . . . . Cma16g00070 Cma18g01301 Car16g00061 Car18g01217 Cpe09g00041 . . . . . . . . Cla05g00949 Cam05g1040 Cec05g1045 Cco05g1039 Clacu05g1031 Cmu05g0981 Cre05g1060 . Csa03g02199 Chy06g01254 .
Vvi16g869 . . . . . . . . . . Cma02g01101 Cma15g01040 . . . Cpe05g00615 . . . . . . . . Cla01g00061 Cam01g0060 Cec01g0061 Cco01g0061 Clacu01g0061 Cmu01g0061 Cre09g2447 . . . . . Csa05g00069 Chy09g01421 . . . . . . . . . . Cmo02g01127 Cmo15g01100 . . . . . Cpe13g00305 Bhi12g00613 . . Lac11g0135 Hepe06g0771 . Lcy12g0115 . . . . . . . Lsi09g00040 . . .
Vvi16g870 . . . . . . . . . . Cma02g01102 Cma15g01039 . Car15g00969 . Cpe05g00614 . . . . . . . . Cla01g00060 Cam01g0059 Cec01g0060 Cco01g0060 Clacu01g0060 Cmu01g0060 Cre09g2448 . . . . . Csa05g00068 Chy09g01422 . . . . . . . . . . Cmo02g01128 Cmo15g01099 . . . . . Cpe13g00306 Bhi12g00615 . . Lac11g0136 Hepe06g0772 . Lcy12g0116 . . . . . . . Lsi09g00039 . . Cme09g01965
Vvi16g871 Blo06g01077 . . . . . . . . . Cma02g01103 . . . . Cpe05g00613 . . . . . . . . Cla01g00059 . . . . . . . . . . . Csa05g00067 Chy09g01423 . . . . Bda15g00777 . Bpe12g00374 . . . Cmo02g01130 . . . . . . . Bhi12g00617 . . . Hepe06g0775 . Lcy12g0117 . . . . . . . Lsi09g00038 . . Cme09g01966
Vvi16g872 Blo06g01081 Blo15g00092 Bda05g00116 . . . . . . . . . Car02g00918 . . . . . . . . . . . . . . . . . . . . . . . . . Cme06g01078 . . . Bda15g00779 . Bpe12g00381 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g873 . . . Bda07g01926 . . . . . Cmo18g01333 . . . . . . . . . . . . . . . . . . . . . . Cone5ag0671 Cone14ag0026 Cone15ag0028 . . . Cme06g01081 . Blo09g00036 . . . . . . . . . . Cma18g01303 . Car18g01219 Cpe09g00038 . . . . . . . . . . . . . . . . . Chy06g01251 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 5386189 5387709 + Bda020722.1 Bda05g00110 110
5 5481896 5483023 - Bda020724.1 Bda05g00111 111
5 5709074 5712130 + Bda020732.1 Bda05g00116 116
7 36727788 36736767 - Bda028903.2 Bda07g01926 1926
15 11593471 11594829 + Bda012632.1 Bda15g00774 774
15 11598979 11601575 + Bda012633.1 Bda15g00775 775
15 11604146 11621969 + Bda033319 Bda15g00776 776
15 11610833 11612806 - Bda012634.1 Bda15g00777 777
15 11637413 11642280 + Bda012636.1 Bda15g00779 779
1 29613531 29618450 + XM_039049645.1 Bhi01g01449 1449
1 29632140 29634907 + XM_039050115.1 Bhi01g01450 1450
1 29644576 29646538 - XM_039045981.1 Bhi01g01452 1452
1 29672762 29676977 + XM_039047082.1 Bhi01g01453 1453
12 18862515 18864402 - XM_039019810.1 Bhi12g00613 613
12 18902195 18905829 + XM_039018635.1 Bhi12g00615 615
12 18905538 18911418 - XM_039018632.1 Bhi12g00617 617
6 34087331 34091261 + BLOR17658 Blo06g01075 1075
6 34095945 34102905 + BLOR17659 Blo06g01076 1076
6 34108905 34111067 - BLOR17660 Blo06g01077 1077
6 34137623 34141792 + BLOR17664 Blo06g01081 1081
7 5536929 5538726 + BLOR18281 Blo07g00349 349
7 5558353 5560008 - BLOR18282 Blo07g00350 350
9 503286 506905 + BLOR20951 Blo09g00036 36
9 563293 564694 - BLOR20955 Blo09g00040 40
15 775799 780143 - BLOR06486 Blo15g00092 92
10 45456233 45457971 + Bma005387.1 Bma10g01285 1285
10 45702803 45703947 - Bma005393.1 Bma10g01288 1288
3 2188247 2189554 + Bpe012021.1 Bpe03g00175 175
3 3214440 3215611 + Bpe012095.1 Bpe03g00242 242
12 8986953 8990637 + Bpe005627.3 Bpe12g00371 371
12 8995190 8996794 + Bpe005628.1 Bpe12g00372 372
12 9001274 9003633 + Bpe024890 Bpe12g00373 373
12 9007880 9010036 - Bpe005629.2 Bpe12g00374 374
12 9134036 9138809 + Bpe005637.1 Bpe12g00381 381
1 936401 940158 - CaPI482276_01g000590.1 Cam01g0059 59
1 945702 948726 + CaPI482276_01g000600.1 Cam01g0060 60
5 9370236 9375423 + CaPI482276_05g010370.1 Cam05g1037 1037
5 9398431 9399834 - CaPI482276_05g010390.1 Cam05g1039 1039
5 9407007 9410270 + CaPI482276_05g010400.1 Cam05g1040 1040
2 6511197 6515070 + Carg14023-RA Car02g00918 918
15 7160650 7163403 - Carg26218-RA Car15g00969 969
16 404051 407577 - Carg15080-RA Car16g00061 61
16 409864 411129 + Carg15081-RA Car16g00062 62
16 411915 413709 - Carg15082-RA Car16g00063 63
16 419705 425465 - Carg15083-RA Car16g00064 64
18 11718364 11719508 + Carg20355-RA Car18g01215 1215
18 11721401 11722660 - Carg20354-RA Car18g01216 1216
18 11723824 11728012 + Carg20353-RA Car18g01217 1217
18 11737181 11740906 - Carg20351-RA Car18g01219 1219
1 452113 455981 - CcPI632755_01g000600.1 Cco01g0060 60
1 464143 464678 + CcPI632755_01g000610.1 Cco01g0061 61
5 9128599 9133790 + CcPI632755_05g010360.1 Cco05g1036 1036
5 9157047 9158419 - CcPI632755_05g010380.1 Cco05g1038 1038
5 9165312 9168587 + CcPI632755_05g010390.1 Cco05g1039 1039
1 479657 483512 - CePI673135_01g000600.1 Cec01g0060 60
1 491788 492321 + CePI673135_01g000610.1 Cec01g0061 61
5 9099471 9105215 + CePI673135_05g010420.1 Cec05g1042 1042
5 9128286 9129665 - CePI673135_05g010440.1 Cec05g1044 1044
5 9136955 9140229 + CePI673135_05g010450.1 Cec05g1045 1045
6 11498707 11503815 + Chy6G117790.1 Chy06g01251 1251
6 11536325 11539603 - Chy6G117820.1 Chy06g01254 1254
6 11545848 11546968 + Chy6G117830.1 Chy06g01255 1255
6 11552370 11554501 - Chy6G117840.1 Chy06g01256 1256
6 11567114 11572181 - Chy6G117860.1 Chy06g01258 1258
9 15823250 15823782 - Chy9G171370.1 Chy09g01421 1421
9 15829902 15832403 + Chy9G171380.1 Chy09g01422 1422
9 15834438 15836570 - Chy9G171390.1 Chy09g01423 1423
1 544801 548626 - ClG42_01g0006000.10 Clacu01g0060 60
1 556643 557178 + ClG42_01g0006100.10 Clacu01g0061 61
5 9089455 9094643 + ClG42_05g0102800.10 Clacu05g1028 1028
5 9123607 9124992 - ClG42_05g0103000.10 Clacu05g1030 1030
5 9132154 9135416 + ClG42_05g0103100.10 Clacu05g1031 1031
1 491441 493642 + ClCG01G000575.1 Cla01g00059 59
1 499567 503597 - ClCG01G000580.2 Cla01g00060 60
1 510885 512502 + ClCG01G000590.2 Cla01g00061 61
5 9412276 9417814 + ClCG05G008710.2 Cla05g00947 947
5 9452389 9453771 - ClCG05G008720.1 Cla05g00948 948
5 9460930 9464434 + ClCG05G008730.1 Cla05g00949 949
2 6544424 6545205 - CmaCh02G011010.1 Cma02g01101 1101
2 6548668 6551294 + CmaCh02G011020.1 Cma02g01102 1102
2 6552565 6554769 - CmaCh02G011030.1 Cma02g01103 1103
15 6506504 6508929 - CmaCh15G010390.1 Cma15g01039 1039
15 6512349 6512936 + CmaCh15G010400.1 Cma15g01040 1040
16 297779 301654 - CmaCh16G000700.1 Cma16g00070 70
16 303081 304939 + CmaCh16G000710.1 Cma16g00071 71
16 305173 307123 - CmaCh16G000720.1 Cma16g00072 72
16 312869 319929 - CmaCh16G000730.1 Cma16g00073 73
18 10009273 10010998 + CmaCh18G012990.1 Cma18g01299 1299
18 10012040 10013307 - CmaCh18G013000.1 Cma18g01300 1300
18 10014605 10018641 + CmaCh18G013010.1 Cma18g01301 1301
18 10027315 10031046 - CmaCh18G013030.1 Cma18g01303 1303
6 7991880 7996547 - MELO3C006981.2.1 Cme06g01078 1078
6 8009167 8015141 + MELO3C006983.2.1 Cme06g01081 1081
9 23572699 23574844 + MELO3C005869.2.1 Cme09g01965 1965
9 23576833 23578965 - MELO3C005870.2.1 Cme09g01966 1966
6 7877184 7881886 + PI0010377.2 Cmetu06g0694 694
6 7859886 7862109 + PI0010009.1 Cmetu06g1760 1760
9 19171927 19178099 + PI0029118.1 Cmetu09g1713 1713
2 6840178 6840854 - CmoCh02G011270.1 Cmo02g01127 1127
2 6844497 6846439 + CmoCh02G011280.1 Cmo02g01128 1128
2 6851453 6853657 - CmoCh02G011300.1 Cmo02g01130 1130
15 7363143 7366192 - CmoCh15G010990.1 Cmo15g01099 1099
15 7381554 7382314 + CmoCh15G011000.1 Cmo15g01100 1100
16 334958 338806 - CmoCh16G000730.1 Cmo16g00073 73
16 340544 341833 + CmoCh16G000740.1 Cmo16g00074 74
16 350683 357329 - CmoCh16G000750.1 Cmo16g00075 75
18 12635767 12637378 + CmoCh18G013280.1 Cmo18g01328 1328
18 12638900 12640156 - CmoCh18G013290.1 Cmo18g01329 1329
18 12641956 12645142 + CmoCh18G013300.1 Cmo18g01330 1330
18 12654519 12658457 - CmoCh18G013330.1 Cmo18g01333 1333
1 489658 493475 - CmPI595203_01g000600.1 Cmu01g0060 60
1 501459 501994 + CmPI595203_01g000610.1 Cmu01g0061 61
5 8934743 8939983 + CmPI595203_05g009780.1 Cmu05g0978 978
5 8969063 8970445 - CmPI595203_05g009800.1 Cmu05g0980 980
5 8977593 8980855 + CmPI595203_05g009810.1 Cmu05g0981 981
1 54816641 54817880 + Conep01aG0100300.1 Cone1ag0958 958
5 2784451 2785744 - Conep05aG0067300.1 Cone5ag0651 651
5 2870663 2873827 - Conep05aG0069500.1 Cone5ag0671 671
14 216001 218032 + Conep14aG0002700.1 Cone14ag0026 26
14 231793 237941 - Conep14aG0003100.1 Cone14ag0030 30
14 240995 242561 - Conep14aG0003200.1 Cone14ag0031 31
15 207232 209395 + Conep15aG0002900.1 Cone15ag0028 28
15 223284 230003 - Conep15aG0003300.1 Cone15ag0032 32
5 3736727 3741765 + Cp4.1LG05g06130.1 Cpe05g00613 613
5 3740951 3742585 - Cp4.1LG05g06230.1 Cpe05g00614 614
5 3746398 3747936 + Cp4.1LG05g06140.1 Cpe05g00615 615
9 231284 235285 + Cp4.1LG09g00340.1 Cpe09g00038 38
9 244032 248126 - Cp4.1LG09g00430.1 Cpe09g00041 41
9 249286 250559 + Cp4.1LG09g00350.1 Cpe09g00042 42
9 252234 253663 - Cp4.1LG09g00440.1 Cpe09g00043 43
13 2539988 2541304 - Cp4.1LG13g03040.1 Cpe13g00305 305
13 2561329 2563974 + Cp4.1LG13g03070.1 Cpe13g00306 306
14 306448 310759 - Cp4.1LG14g06570.1 Cpe14g00055 55
14 311927 313222 + Cp4.1LG14g06650.1 Cpe14g00056 56
14 313862 316005 - Cp4.1LG14g06550.1 Cpe14g00057 57
14 321551 327580 - Cp4.1LG14g06540.1 Cpe14g00058 58
5 9816334 9821418 + CrPI670011_05g010570.1 Cre05g1057 1057
5 9842302 9843699 - CrPI670011_05g010590.1 Cre05g1059 1059
5 9850682 9853958 + CrPI670011_05g010600.1 Cre05g1060 1060
9 43820267 43820802 - CrPI670011_09g024470.1 Cre09g2447 2447
9 43831736 43835600 + CrPI670011_09g024480.1 Cre09g2448 2448
3 19055897 19061281 + CsaV3_3G021950.1 Csa03g02195 2195
3 19073471 19076098 + CsaV3_3G021970.1 Csa03g02197 2197
3 19080570 19082350 - CsaV3_3G021980.1 Csa03g02198 2198
3 19086463 19090647 + CsaV3_3G021990.1 Csa03g02199 2199
5 344648 348011 + CsaV3_5G000670.1 Csa05g00067 67
5 348199 351065 - CsaV3_5G000680.1 Csa05g00068 68
5 355126 357556 + CsaV3_5G000690.1 Csa05g00069 69
6 54328575 54329518 - Hsped.06g07710.1 Hepe06g0771 771
6 54337799 54342269 + Hsped.06g07720.1 Hepe06g0772 772
6 54355743 54357944 - Hsped.06g07750.1 Hepe06g0775 775
7 814354 817555 - Hsped.07g00870.1 Hepe07g0087 87
7 821453 825354 + Hsped.07g00880.1 Hepe07g0088 88
11 1235836 1236385 - Lag0030773.1 Lac11g0135 135
11 1247400 1250590 + Lag0030774.1 Lac11g0136 136
12 1462961 1466949 - Maker00038466 Lcy12g0115 115
12 1475095 1478436 + Maker00038890 Lcy12g0116 116
12 1482934 1485135 - Maker00038424 Lcy12g0117 117
9 345868 348069 + Lsi09G000380.1 Lsi09g00038 38
9 350057 353877 - Lsi09G000390.1 Lsi09g00039 39
9 362888 364358 + Lsi09G000400.1 Lsi09g00040 40
10 498149 500305 + MC10g0078 Mch10g0087 87
10 504618 505922 - MC10g0079 Mch10g0088 88
10 514301 519828 - MC10g0080 Mch10g0089 89
2 46175913 46189600 + Sed0025459.2 Sed02g0861 861
7 5986806 5988132 + Sed0020898.1 Sed07g0811 811
7 6022282 6026221 + Sed0009531.4 Sed07g0818 818
1 1350472 1354482 - Tan0016932.2 Tan01g0146 146
1 1369909 1371729 + Tan0022209.1 Tan01g0147 147
1 1380483 1382518 - Tan0017136.1 Tan01g0149 149
1 1393964 1399012 - Tan0003091.1 Tan01g0150 150
16 19455909 19456029 - Vvi16g864 Vvi16g864 864
16 19456030 19462846 + Vvi16g865 Vvi16g865 865
16 19472592 19474275 + Vvi16g866 Vvi16g866 866
16 19477140 19479868 - Vvi16g867 Vvi16g867 867
16 19488835 19492409 + Vvi16g868 Vvi16g868 868
16 19492843 19495932 - Vvi16g869 Vvi16g869 869
16 19512907 19514934 + Vvi16g870 Vvi16g870 870
16 19516021 19518208 - Vvi16g871 Vvi16g871 871
16 19519388 19529594 - Vvi16g872 Vvi16g872 872
16 19543375 19551472 + Vvi16g873 Vvi16g873 873
       

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