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
Vvi16g784 . . Bda05g00096 . Bpe03g00260 . Bma10g01260 . . Cmo18g01307 . . . . Sed07g2526 . . Bhi01g01417 Tan01g0183 Cmetu10g1018 . Hepe07g0115 Mch10g0118 . . . . . . . . . . Cone14ag0053 . Lsi05g01184 . . Cme06g01045 Blo07g00369 . . . . . . . . . . . Cma18g01276 . Car18g01190 Cpe09g00061 . . . . . . . . Cla05g00923 Cam05g1011 Cec05g1015 Cco05g1011 Clacu05g1000 Cmu05g0953 Cre05g1034 . Csa03g01757 Chy06g00985 .
Vvi16g785 . . . Bda07g01902 Bpe03g00158 . . Bma14g02040 Cmo16g00097 Cmo18g01308 . . . . . . Cpe14g00076 . . . . . . . . . . . . . . . . Cone14ag0052 Cone15ag0058 Lsi05g01183 . . Cme06g01046 . Blo09g00057 . . . . . . . . . Cma16g00092 Cma18g01277 Car16g00082 Car18g01191 Cpe09g00060 . . . . . . . . Cla05g00924 Cam05g1012 Cec05g1016 Cco05g1012 Clacu05g1001 Cmu05g0954 Cre05g1035 . Csa03g01758 Chy06g00986 .
Vvi16g786 . . . Bda07g01903 Bpe03g00159 . . Bma14g02039 . . Cma02g01082 Cma15g01069 Car02g00967 Car15g00989 . Cpe05g00638 . . . . . . . . Cla01g00090 Cam01g0091 Cec01g0091 Cco01g0092 Clacu01g0089 Cmu01g0091 Cre09g2416 . . Cone14ag0051 Cone15ag0056 . Csa05g00102 Chy09g01392 . . Blo09g00056 . . . . . . . Cmo02g01100 Cmo15g01125 . . . . . Cpe13g00276 Bhi12g00775 . . Lac11g0078 Hepe06g0725 . Lcy12g0060 . . . . . . . Lsi09g00077 . . Cme09g01937
Vvi16g787 . . . Bda07g01904 . . . . . . Cma02g01084 Cma15g01067 Car02g00825 Car15g00988 . Cpe05g00637 . . . . . . . . Cla01g00089 Cam01g0090 Cec01g0090 Cco01g0091 Clacu01g0088 Cmu01g0090 Cre09g2417 . . . . . Csa05g00101 . . . Blo09g00055 . . . . . . . . Cmo15g01124 . . . . . Cpe13g00277 Bhi12g00774 . . Lac11g0079 Hepe06g0728 . Lcy12g0061 . . . . . . . Lsi09g00076 . . Cme09g01938
Vvi16g788 . . Bda05g00097 Bda07g01907 Bpe03g00259 . Bma10g01261 Bma14g02038 Cmo16g00096 Cmo18g01309 . . . . Sed07g0975 . . Bhi01g01419 Tan01g0181 Cmetu06g0254 . Hepe07g0113 Mch10g0116 . . . . . . . . Cone1ag1199 Cone5ag0898 . . Lsi05g01182 . . . Blo07g00363 Blo09g00054 . . . . . . . . . . Cma18g01278 Car16g00081 Car18g01192 Cpe09g00059 . . . . . . . . Cla05g00926 Cam05g1013 Cec05g1017 Cco05g1013 Clacu05g1002 Cmu05g0955 Cre05g1036 . Csa03g01759 Chy06g00987 .
Vvi16g789 . . . . . . . . . Cmo18g01310 . . . . . . . Bhi01g01420 . . . . Mch10g0115 . . . . . . . . . Cone5ag0899 . . Lsi05g01181 . . . . . . . . . . . . . . . Cma18g01279 . Car18g01193 . . . . . . . . . Cla05g00927 . . . . . . . . . .
Vvi16g790 . . Bda05g00098 Bda07g01908 Bpe03g00160 . Bma10g01265 Bma14g02037 Cmo16g00095 Cmo18g01311 . . . . Sed07g0976 . Cpe14g00075 Bhi01g01421 Tan01g0179 Cmetu06g2016 . Hepe07g0111 Mch10g0114 . . . . . . . . Cone1ag1200 Cone5ag0900 . . Lsi05g01180 . . . Blo07g00360 Blo09g00053 . . . . . . . . . Cma16g00091 Cma18g01280 . Car18g01194 Cpe09g00058 . . . . . . . . Cla05g00928 Cam05g1015 Cec05g1019 Cco05g1015 Clacu05g1004 Cmu05g0957 Cre05g1038 . Csa03g01760 Chy06g00988 .
Vvi16g791 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g792 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g793 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 4929323 4931168 + Bda020701.1 Bda05g00096 96
5 4959642 4960792 + Bda020702.1 Bda05g00097 97
5 4964404 4968463 + Bda020703.1 Bda05g00098 98
7 36425296 36429300 - Bda028876.1 Bda07g01902 1902
7 36432517 36441218 + Bda028877.1 Bda07g01903 1903
7 36452845 36454114 + Bda028878.1 Bda07g01904 1904
7 36509068 36509686 + Bda028881.1 Bda07g01907 1907
7 36512771 36516465 + Bda028882.1 Bda07g01908 1908
1 28896506 28897481 + XM_039025547.1 Bhi01g01417 1417
1 28932438 28934165 + XM_039019035.1 Bhi01g01419 1419
1 28934238 28937364 - XM_039019030.1 Bhi01g01420 1420
1 28967229 28970889 + XM_039040716.1 Bhi01g01421 1421
12 23250334 23252149 - XM_039020142.1 Bhi12g00774 774
12 23270088 23284397 - XM_039018618.1 Bhi12g00775 775
7 5802866 5808740 - BLOR18292 Blo07g00360 360
7 5889780 5897966 - BLOR18295 Blo07g00363 363
7 6015391 6017197 - BLOR18301 Blo07g00369 369
9 876775 880472 - BLOR20968 Blo09g00053 53
9 913780 914397 - BLOR20969 Blo09g00054 54
9 922230 923481 - BLOR20970 Blo09g00055 55
9 947143 952322 - BLOR20971 Blo09g00056 56
9 965908 970459 + BLOR20972 Blo09g00057 57
10 44626176 44628030 + Bma005354.1 Bma10g01260 1260
10 44659966 44661094 + Bma030403 Bma10g01261 1261
10 44943303 44947352 + Bma005362.1 Bma10g01265 1265
14 43737054 43741014 - Bma012845.1 Bma14g02037 2037
14 43749435 43750049 - Bma012847.1 Bma14g02038 2038
14 43772223 43780453 - Bma012848.1 Bma14g02039 2039
14 43804572 43808597 + Bma012850.1 Bma14g02040 2040
3 2035363 2040159 - Bpe012002.1 Bpe03g00158 158
3 2041566 2049885 + Bpe012003.1 Bpe03g00159 159
3 2061002 2064828 + Bpe012005.1 Bpe03g00160 160
3 3530217 3531370 - Bpe012112.1 Bpe03g00259 259
3 3546718 3548569 - Bpe012113.1 Bpe03g00260 260
1 1181597 1183198 - CaPI482276_01g000900.1 Cam01g0090 90
1 1197381 1205511 - CaPI482276_01g000910.1 Cam01g0091 91
5 9126480 9129011 + CaPI482276_05g010110.1 Cam05g1011 1011
5 9130495 9134489 - CaPI482276_05g010120.1 Cam05g1012 1012
5 9144007 9145440 + CaPI482276_05g010130.1 Cam05g1013 1013
5 9151364 9155123 + CaPI482276_05g010150.1 Cam05g1015 1015
2 5964206 5965494 + Carg08396-RA Car02g00825 825
2 6810325 6813129 + Carg13974-RA Car02g00967 967
15 7577166 7578428 - Carg27021-RA Car15g00988 988
15 7585269 7589058 - Carg27022-RA Car15g00989 989
16 510787 513339 - Carg15100-RA Car16g00081 81
16 514685 518880 + Carg15101-RA Car16g00082 82
18 11506780 11509509 + Carg22138-RA Car18g01190 1190
18 11509338 11513068 - Carg22139-RA Car18g01191 1191
18 11514229 11516677 + Carg22140-RA Car18g01192 1192
18 11516910 11519543 - Carg22141-RA Car18g01193 1193
18 11520067 11523115 + Carg22142-RA Car18g01194 1194
1 704282 705843 - CcPI632755_01g000910.1 Cco01g0091 91
1 720840 728798 - CcPI632755_01g000920.1 Cco01g0092 92
5 8890047 8892526 + CcPI632755_05g010110.1 Cco05g1011 1011
5 8894088 8898082 - CcPI632755_05g010120.1 Cco05g1012 1012
5 8899922 8905040 + CcPI632755_05g010130.1 Cco05g1013 1013
5 8911679 8914877 + CcPI632755_05g010150.1 Cco05g1015 1015
1 744261 745794 - CePI673135_01g000900.1 Cec01g0090 90
1 760318 768472 - CePI673135_01g000910.1 Cec01g0091 91
5 8871801 8874333 + CePI673135_05g010150.1 Cec05g1015 1015
5 8875488 8879487 - CePI673135_05g010160.1 Cec05g1016 1016
5 8885002 8886436 + CePI673135_05g010170.1 Cec05g1017 1017
5 8892845 8896955 + CePI673135_05g010190.1 Cec05g1019 1019
6 7293036 7294939 + Chy6G115130.1 Chy06g00985 985
6 7295859 7299541 - Chy6G115140.1 Chy06g00986 986
6 7301994 7303417 + Chy6G115150.1 Chy06g00987 987
6 7305541 7308691 + Chy6G115160.1 Chy06g00988 988
9 15643740 15652957 + Chy9G171080.1 Chy09g01392 1392
1 792167 793757 - ClG42_01g0008800.10 Clacu01g0088 88
1 807919 816049 - ClG42_01g0008900.10 Clacu01g0089 89
5 8842981 8845513 + ClG42_05g0100000.10 Clacu05g1000 1000
5 8847003 8850995 - ClG42_05g0100100.10 Clacu05g1001 1001
5 8860678 8862110 + ClG42_05g0100200.10 Clacu05g1002 1002
5 8867688 8871776 + ClG42_05g0100400.10 Clacu05g1004 1004
1 759937 761527 - ClCG01G000880.1 Cla01g00089 89
1 776495 783817 - ClCG01G000890.2 Cla01g00090 90
5 9135153 9137939 + ClCG05G008480.2 Cla05g00923 923
5 9138928 9144180 - ClCG05G008490.2 Cla05g00924 924
5 9152805 9154578 + ClCG05G008500.1 Cla05g00926 926
5 9154698 9157349 - ClCG05G008505.1 Cla05g00927 927
5 9160627 9164356 + ClCG05G008510.2 Cla05g00928 928
2 6438792 6445158 + CmaCh02G010820.1 Cma02g01082 1082
2 6451561 6452816 + CmaCh02G010840.1 Cma02g01084 1084
15 6759134 6762945 - CmaCh15G010670.1 Cma15g01067 1067
15 6770336 6774455 - CmaCh15G010690.1 Cma15g01069 1069
16 401467 404735 - CmaCh16G000910.1 Cma16g00091 91
16 405179 410197 + CmaCh16G000920.1 Cma16g00092 92
18 9893415 9895786 + CmaCh18G012760.1 Cma18g01276 1276
18 9896245 9900682 - CmaCh18G012770.1 Cma18g01277 1277
18 9901980 9904516 + CmaCh18G012780.1 Cma18g01278 1278
18 9904703 9907336 - CmaCh18G012790.1 Cma18g01279 1279
18 9907780 9911163 + CmaCh18G012800.1 Cma18g01280 1280
6 7595737 7598193 + MELO3C006950.2.1 Cme06g01045 1045
6 7598603 7603505 - MELO3C006951.2.1 Cme06g01046 1046
9 23402573 23407578 + MELO3C005842.2.1 Cme09g01937 1937
9 23415488 23416900 + MELO3C005843.2.1 Cme09g01938 1938
6 7616488 7618369 + PI0026545.1 Cmetu06g0254 254
6 7622177 7626148 + PI0024753.1 Cmetu06g2016 2016
10 15320502 15323007 + PI0024262.1 Cmetu10g1018 1018
2 6665302 6671549 + CmoCh02G011000.1 Cmo02g01100 1100
15 7806671 7807927 - CmoCh15G011240.1 Cmo15g01124 1124
15 7814534 7816772 - CmoCh15G011250.1 Cmo15g01125 1125
16 440921 442560 - CmoCh16G000950.1 Cmo16g00095 95
16 442596 444070 - CmoCh16G000960.1 Cmo16g00096 96
16 444656 449847 + CmoCh16G000970.1 Cmo16g00097 97
18 12512257 12514655 + CmoCh18G013070.1 Cmo18g01307 1307
18 12514598 12519277 - CmoCh18G013080.1 Cmo18g01308 1308
18 12519713 12522157 + CmoCh18G013090.1 Cmo18g01309 1309
18 12522338 12524971 - CmoCh18G013100.1 Cmo18g01310 1310
18 12525429 12528508 + CmoCh18G013110.1 Cmo18g01311 1311
1 736584 738162 - CmPI595203_01g000900.1 Cmu01g0090 90
1 752324 760454 - CmPI595203_01g000910.1 Cmu01g0091 91
5 8688269 8690801 + CmPI595203_05g009530.1 Cmu05g0953 953
5 8692291 8696283 - CmPI595203_05g009540.1 Cmu05g0954 954
5 8705854 8707286 + CmPI595203_05g009550.1 Cmu05g0955 955
5 8712864 8716950 + CmPI595203_05g009570.1 Cmu05g0957 957
1 55881296 55882990 + Conep01aG0124800.1 Cone1ag1199 1199
1 55886175 55895224 + Conep01aG0124900.1 Cone1ag1200 1200
5 3852335 3853915 + Conep05aG0092400.1 Cone5ag0898 898
5 3853950 3856734 - Conep05aG0092500.1 Cone5ag0899 899
5 3859751 3863841 + Conep05aG0092600.1 Cone5ag0900 900
14 315595 318233 - Conep14aG0005300.1 Cone14ag0051 51
14 318404 322345 + Conep14aG0005400.1 Cone14ag0052 52
14 322699 324274 - Conep14aG0005500.1 Cone14ag0053 53
15 339817 342532 - Conep15aG0005800.1 Cone15ag0056 56
15 345245 346446 + Conep15aG0006000.1 Cone15ag0058 58
5 3893194 3894413 - Cp4.1LG05g06330.1 Cpe05g00637 637
5 3900602 3907697 - Cp4.1LG05g06320.1 Cpe05g00638 638
9 352022 355012 - Cp4.1LG09g00620.1 Cpe09g00058 58
9 358473 360891 - Cp4.1LG09g00560.1 Cpe09g00059 59
9 361473 366778 + Cp4.1LG09g00510.1 Cpe09g00060 60
9 365054 368544 - Cp4.1LG09g00580.1 Cpe09g00061 61
13 2194157 2196116 + Cp4.1LG13g02780.1 Cpe13g00276 276
13 2202479 2203743 + Cp4.1LG13g02760.1 Cpe13g00277 277
14 410557 413855 - Cp4.1LG14g06380.1 Cpe14g00075 75
14 414299 419631 + Cp4.1LG14g06470.1 Cpe14g00076 76
5 9572987 9575518 + CrPI670011_05g010340.1 Cre05g1034 1034
5 9577006 9581007 - CrPI670011_05g010350.1 Cre05g1035 1035
5 9582778 9588051 + CrPI670011_05g010360.1 Cre05g1036 1036
5 9594007 9597826 + CrPI670011_05g010380.1 Cre05g1038 1038
9 43556296 43563346 + CrPI670011_09g024160.1 Cre09g2416 2416
9 43577724 43579309 + CrPI670011_09g024170.1 Cre09g2417 2417
3 13162949 13165734 + CsaV3_3G017570.1 Csa03g01757 1757
3 13166059 13171074 - CsaV3_3G017580.1 Csa03g01758 1758
3 13172144 13174222 + CsaV3_3G017590.1 Csa03g01759 1759
3 13175554 13179367 + CsaV3_3G017600.1 Csa03g01760 1760
5 504127 505921 - CsaV3_5G001010.1 Csa05g00101 101
5 514286 519778 - CsaV3_5G001020.1 Csa05g00102 102
6 53224404 53241779 + Hsped.06g07250.1 Hepe06g0725 725
6 53314997 53316292 + Hsped.06g07280.1 Hepe06g0728 728
7 1051760 1055717 - Hsped.07g01110.1 Hepe07g0111 111
7 1060980 1063817 - Hsped.07g01130.1 Hepe07g0113 113
7 1072782 1075880 - Hsped.07g01150.1 Hepe07g0115 115
11 667713 683621 + Lag0030716.1 Lac11g0078 78
11 698579 699818 + Lag0030717.1 Lac11g0079 79
12 887186 898490 + Maker00039064 Lcy12g0060 60
12 922852 924085 + Maker00038445 Lcy12g0061 61
5 19727630 19731261 - Lsi05G011800.1 Lsi05g01180 1180
5 19735520 19738171 + Lsi05G011810.1 Lsi05g01181 1181
5 19738227 19740478 - Lsi05G011820.1 Lsi05g01182 1182
5 19746386 19752098 + Lsi05G011830.1 Lsi05g01183 1183
5 19754060 19757384 - Lsi05G011840.1 Lsi05g01184 1184
9 633526 635293 - Lsi09G000760.1 Lsi09g00076 76
9 649526 656370 - Lsi09G000770.1 Lsi09g00077 77
10 679110 682663 - MC10g0096 Mch10g0114 114
10 684050 686578 + MC10g0097 Mch10g0115 115
10 686776 688434 - MC10g0098 Mch10g0116 116
10 694263 696746 - MC10g0100 Mch10g0118 118
7 7173271 7176115 + Sed0009881.1 Sed07g0975 975
7 7178897 7183317 + Sed0015019.1 Sed07g0976 976
7 40920894 40924942 - Sed0020126.2 Sed07g2526 2526
1 1664654 1668331 - Tan0001222.2 Tan01g0179 179
1 1672604 1674927 - Tan0014127.1 Tan01g0181 181
1 1689715 1692374 - Tan0020759.1 Tan01g0183 183
16 18325241 18328692 + Vvi16g784 Vvi16g784 784
16 18328788 18337702 - Vvi16g785 Vvi16g785 785
16 18338890 18344393 + Vvi16g786 Vvi16g786 786
16 18360078 18360711 + Vvi16g787 Vvi16g787 787
16 18389481 18392891 + Vvi16g788 Vvi16g788 788
16 18393311 18395954 - Vvi16g789 Vvi16g789 789
16 18398944 18408373 + Vvi16g790 Vvi16g790 790
16 18445145 18457691 - Vvi16g791 Vvi16g791 791
16 18461595 18462737 + Vvi16g792 Vvi16g792 792
16 18462908 18465345 - Vvi16g793 Vvi16g793 793
       

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