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
Vvi16g1034 . . Bda05g00127 Bda07g01937 Bpe03g00231 . Bma10g01304 Bma14g02010 Cmo16g00050 . . . . . . . Cpe14g00035 Bhi01g01496 Tan01g0088 . . . . . . . . . . . . Cone1ag0989 . Cone14ag0007 . . . . Cme06g01147 Blo07g00332 Blo09g00023 . . . . . . . . . Cma16g00041 . . Car18g01242 . . . . . . . . . . . . . . . . . Csa03g01980 Chy06g01195 .
Vvi16g1035 . Blo15g00086 . . . Bpe07g01017 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0008 Cone15ag0009 . . . . . . Bda06g00786 . . . . Bma12g01205 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1036 Blo06g01059 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag0986 Cone5ag0692 . . . . . . . . . Bda15g00786 . Bpe12g00350 Bma08g00388 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1037 . . . Bda07g01935 Bpe03g00191 . . Bma14g02008 Cmo16g00052 . Cma02g01119 . Car02g00929 . Sed01g3489 Cpe05g00598 Cpe14g00036 Bhi01g01494 Tan01g0090 Cmetu09g1788 . . Mch10g0056 . Cla01g00041 Cam01g0039 Cec01g0038 Cco01g0040 Clacu01g0041 Cmu01g0039 Cre09g2468 Cone1ag0985 Cone5ag0691 Cone14ag0010 Cone15ag0011 . Csa05g00047 Chy09g01440 Cme06g01146 . Blo09g00025 . . . . . . . Cmo02g01149 . Cma16g00043 . Car16g00041 Car18g01244 . . Bhi12g00643 . . Lac11g0159 Hepe06g0793 . Lcy12g0136 Cla05g00973 Cam05g1064 Cec05g1070 Cco05g1063 Clacu05g1057 Cmu05g1008 Cre05g1085 Lsi09g00020 Csa03g01982 Chy06g01197 Cme09g01986
Vvi16g1038 . . . . . . . . Cmo16g00053 . . . . Car15g00958 . . Cpe14g00037 Bhi01g01493 Tan01g0091 . . . Mch10g0576 . . . . . . . . Cone1ag0984 . . . . . . Cme06g01145 . . . . . . . . . . . . . Car16g00042 . . . Bhi12g00642 . . Lac11g0158 Hepe06g0792 . Lcy12g0135 Cla05g00972 Cam05g1063 Cec05g1069 Cco05g1062 Clacu05g1056 Cmu05g1007 Cre05g1084 . . . .
Vvi16g1039 . . . Bda07g01934 Bpe03g00190 . . . . . . . Car02g00928 . Sed01g3490 Cpe05g00599 . Bhi01g01492 Tan01g0092 Cmetu06g0095 Lac11g0158 Hepe07g0059 Mch10g0057 . Cla01g00042 Cam01g0040 Cec01g0039 Cco01g0041 Clacu01g0042 Cmu01g0040 Cre09g2467 . Cone5ag0690 . . . Csa05g00048 Chy09g01439 . . Blo09g00026 . . . . . . . Cmo02g01147 . Cma16g00044 . . . . Cpe13g00317 . . . . . . . . . . . . . . Lsi09g00021 Csa03g01983 Chy06g01198 Cme09g01985
Vvi16g1040 . . . . . . . Bma14g02007 . . . . . . . . . . . . . . . . . . . . . . . Cone1ag0983 . . . . . . . . Blo09g00027 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1041 . Blo15g00087 Bda05g00126 . Bpe03g00232 Bpe07g01014 . . Cmo16g00056 Cmo18g01361 . . . . . . Cpe14g00039 . . . . . . . . . . . . . . . . . . . . . Cme06g01140 Blo07g00335 . Bda06g00784 . . . . Bma12g01203 . . . . . Car16g00044 Car18g01246 . . . . . . . . . Cla05g00969 Cam05g1061 Cec05g1067 Cco05g1060 . Cmu05g1004 . . Csa03g01989 Chy06g01203 .
Vvi16g1042 . . . . . . Bma10g01303 . . Cmo18g01359 . . . . . . . Bhi01g01488 Tan01g0095 . . . . . . . . . . . . . . Cone14ag0011 . . . . . . . . . . . . . . . . Cma16g00047 . . Car18g01245 . . . . . . . . . . . . . . . . . . . .
Vvi16g1043 . . Bda05g00124 Bda07g01932 Bpe03g00234 . Bma10g01300 Bma14g02006 Cmo16g00057 . . . . . Sed07g0855 . Cpe14g00041 Bhi01g01484 Tan01g0105 Cmetu06g2482 . Hepe07g0065 Mch10g0063 . . . . . . . . . . . . . . . Cme06g01138 Blo07g00337 Blo09g00028 . . . . . . . . . Cma16g00049 . Car16g00046 . . . . . . . . . . Cla05g00967 Cam05g1059 Cec05g1065 Cco05g1058 Clacu05g1052 Cmu05g1002 Cre05g1079 . Csa03g01993 Chy06g01207 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 5968149 5969627 - Bda033624 Bda05g00124 124
5 5975431 5977111 - Bda033625 Bda05g00126 126
5 5994442 5996734 + Bda020745.1 Bda05g00127 127
6 10882064 10886471 - Bda024107.2 Bda06g00784 784
6 10894906 10897536 - Bda024109.2 Bda06g00786 786
7 36827367 36828632 - Bda033998 Bda07g01932 1932
7 36839999 36843741 - Bda028913.1 Bda07g01934 1934
7 36845393 36847212 + Bda028914.1 Bda07g01935 1935
7 36862594 36867389 + Bda028916.1 Bda07g01937 1937
15 11757338 11760284 + Bda012647.1 Bda15g00786 786
1 30555477 30560180 - XM_039025352.1 Bhi01g01484 1484
1 30664510 30671248 - XM_039036405.1 Bhi01g01488 1488
1 30711839 30716017 - XM_039022499.1 Bhi01g01492 1492
1 30711839 30715769 - XM_039022492.1 Bhi01g01493 1493
1 30726673 30730509 + XM_039049332.1 Bhi01g01494 1494
1 30733733 30738676 + XM_039026983.1 Bhi01g01496 1496
12 19565426 19570139 - XM_039019972.1 Bhi12g00642 642
12 19629107 19631363 + XM_039019485.1 Bhi12g00643 643
6 33962532 33973444 - BLOR17642 Blo06g01059 1059
7 4269720 4272300 - BLOR18264 Blo07g00332 332
7 4307006 4308422 + BLOR18267 Blo07g00335 335
7 4344747 4346052 + BLOR18269 Blo07g00337 337
9 261916 262581 - BLOR20938 Blo09g00023 23
9 290840 297984 - BLOR20940 Blo09g00025 25
9 302734 304979 + BLOR20941 Blo09g00026 26
9 306465 317868 + BLOR20942 Blo09g00027 27
9 349943 351361 + BLOR20943 Blo09g00028 28
15 722424 725243 + BLOR06480 Blo15g00086 86
15 726299 731523 - BLOR06481 Blo15g00087 87
8 9456111 9460979 + Bma031442 Bma08g00388 388
10 46414577 46415800 - Bma005410.1 Bma10g01300 1300
10 46423448 46428107 - Bma030404 Bma10g01303 1303
10 46431373 46433691 + Bma005413.2 Bma10g01304 1304
12 44963733 44968159 - Bma008561.1 Bma12g01203 1203
12 44973810 44976472 - Bma008563.1 Bma12g01205 1205
14 43477382 43478669 - Bma012815.1 Bma14g02006 2006
14 43483168 43491268 - Bma012816.2 Bma14g02007 2007
14 43499126 43500059 + Bma012817.1 Bma14g02008 2008
14 43504867 43507341 + Bma012819.2 Bma14g02010 2010
3 2299448 2301785 - Bpe012037.1 Bpe03g00190 190
3 2304893 2306734 + Bpe012038.1 Bpe03g00191 191
3 3088151 3090436 - Bpe012085.2 Bpe03g00231 231
3 3103483 3105162 + Bpe025364 Bpe03g00232 232
3 3122914 3124471 + Bpe012088.1 Bpe03g00234 234
7 15768477 15770261 - Bpe021857.2 Bpe07g01014 1014
7 15783875 15786551 - Bpe021861.3 Bpe07g01017 1017
12 8549655 8553982 - Bpe024889 Bpe12g00350 350
1 770328 772131 - CaPI482276_01g000390.1 Cam01g0039 39
1 775560 779699 + CaPI482276_01g000400.1 Cam01g0040 40
5 9672149 9676790 - CaPI482276_05g010590.1 Cam05g1059 1059
5 9702668 9706352 - CaPI482276_05g010610.1 Cam05g1061 1061
5 9724101 9733220 - CaPI482276_05g010630.1 Cam05g1063 1063
5 9742873 9746991 + CaPI482276_05g010640.1 Cam05g1064 1064
2 6567005 6572110 - Carg14013-RA Car02g00928 928
2 6575689 6577605 + Carg14012-RA Car02g00929 929
15 6993595 7002596 + Carg26613-RA Car15g00958 958
16 296993 299416 - Carg15060-RA Car16g00041 41
16 300515 306848 + Carg15061-RA Car16g00042 42
16 313640 316636 + Carg15063-RA Car16g00044 44
16 324250 326407 + Carg15065-RA Car16g00046 46
18 11851844 11854922 - Carg20328-RA Car18g01242 1242
18 11856862 11859268 - Carg20326-RA Car18g01244 1244
18 11859917 11868929 + Carg20325-RA Car18g01245 1245
18 11869814 11875544 + Carg20324-RA Car18g01246 1246
1 283504 285414 - CcPI632755_01g000400.1 Cco01g0040 40
1 289338 293460 + CcPI632755_01g000410.1 Cco01g0041 41
5 9430018 9434217 - CcPI632755_05g010580.1 Cco05g1058 1058
5 9461056 9464744 - CcPI632755_05g010600.1 Cco05g1060 1060
5 9482267 9491375 - CcPI632755_05g010620.1 Cco05g1062 1062
5 9501604 9505152 + CcPI632755_05g010630.1 Cco05g1063 1063
1 311322 313194 - CePI673135_01g000380.1 Cec01g0038 38
1 315958 321203 + CePI673135_01g000390.1 Cec01g0039 39
5 9406483 9411097 - CePI673135_05g010650.1 Cec05g1065 1065
5 9442992 9446633 - CePI673135_05g010670.1 Cec05g1067 1067
5 9464439 9473562 - CePI673135_05g010690.1 Cec05g1069 1069
5 9483585 9487105 + CePI673135_05g010700.1 Cec05g1070 1070
6 10651028 10656048 - Chy6G117230.1 Chy06g01195 1195
6 10661321 10664163 - Chy6G117250.1 Chy06g01197 1197
6 10672114 10675440 + Chy6G117260.1 Chy06g01198 1198
6 10700024 10702570 + Chy6G117310.1 Chy06g01203 1203
6 10738982 10741664 + Chy6G117350.1 Chy06g01207 1207
9 15959023 15963032 - Chy9G171550.1 Chy09g01439 1439
9 15965108 15967010 + Chy9G171560.1 Chy09g01440 1440
1 380136 381940 - ClG42_01g0004100.10 Clacu01g0041 41
1 382062 389504 + ClG42_01g0004200.10 Clacu01g0042 42
5 9404690 9409053 - ClG42_05g0105200.10 Clacu05g1052 1052
5 9461707 9465731 - ClG42_05g0105600.10 Clacu05g1056 1056
5 9475179 9479138 + ClG42_05g0105700.10 Clacu05g1057 1057
1 314069 315873 - ClCG01G000410.1 Cla01g00041 41
1 319013 323892 + ClCG01G000420.1 Cla01g00042 42
5 9747619 9752447 - ClCG05G008920.2 Cla05g00967 967
5 9781419 9787581 - ClCG05G008930.2 Cla05g00969 969
5 9811900 9815652 - ClCG05G008960.2 Cla05g00972 972
5 9824932 9829078 + ClCG05G008970.1 Cla05g00973 973
2 6652536 6654273 + CmaCh02G011190.1 Cma02g01119 1119
16 182185 186503 - CmaCh16G000410.1 Cma16g00041 41
16 188489 191232 - CmaCh16G000430.1 Cma16g00043 43
16 192514 196610 + CmaCh16G000440.1 Cma16g00044 44
16 199743 210152 + CmaCh16G000470.1 Cma16g00047 47
16 214851 219028 + CmaCh16G000490.1 Cma16g00049 49
6 8760831 8765690 - MELO3C008492.2.1 Cme06g01138 1138
6 8793153 8796700 - MELO3C008494.2.1 Cme06g01140 1140
6 8833704 8837443 - MELO3C008498.2.1 Cme06g01145 1145
6 8843162 8847215 + MELO3C008499.2.1 Cme06g01146 1146
6 8849536 8854301 + MELO3C008500.2.1 Cme06g01147 1147
9 23699411 23704130 - MELO3C005887.2.1 Cme09g01985 1985
9 23705692 23708462 + MELO3C005888.2.1 Cme09g01986 1986
6 8044194 8048508 + PI0023763.1 Cmetu06g0095 95
6 8104179 8108956 + PI0004232.2 Cmetu06g2482 2482
9 245893 248174 - PI0007618.1 Cmetu09g1788 1788
2 6944672 6950257 - CmoCh02G011470.1 Cmo02g01147 1147
2 6953872 6955895 + CmoCh02G011490.1 Cmo02g01149 1149
16 206203 209306 - CmoCh16G000500.1 Cmo16g00050 50
16 211326 213972 - CmoCh16G000520.1 Cmo16g00052 52
16 215447 218618 + CmoCh16G000530.1 Cmo16g00053 53
16 228802 231889 + CmoCh16G000560.1 Cmo16g00056 56
16 239482 241744 + CmoCh16G000570.1 Cmo16g00057 57
18 12789652 12800100 + CmoCh18G013590.1 Cmo18g01359 1359
18 12800605 12803284 + CmoCh18G013610.1 Cmo18g01361 1361
1 324979 326783 - CmPI595203_01g000390.1 Cmu01g0039 39
1 326905 334337 + CmPI595203_01g000400.1 Cmu01g0040 40
5 9250245 9254608 - CmPI595203_05g010020.1 Cmu05g1002 1002
5 9275390 9279015 - CmPI595203_05g010040.1 Cmu05g1004 1004
5 9301732 9305759 - CmPI595203_05g010070.1 Cmu05g1007 1007
5 9315675 9319160 + CmPI595203_05g010080.1 Cmu05g1008 1008
1 54925645 54931568 - Conep01aG0102800.1 Cone1ag0983 983
1 54931841 54934979 - Conep01aG0102900.1 Cone1ag0984 984
1 54935358 54937484 + Conep01aG0103000.1 Cone1ag0985 985
1 54937975 54943972 + Conep01aG0103100.1 Cone1ag0986 986
1 54967186 54969082 + Conep01aG0103400.1 Cone1ag0989 989
5 2953985 2957098 - Conep05aG0071400.1 Cone5ag0690 690
5 2957586 2959694 + Conep05aG0071500.1 Cone5ag0691 691
5 2959973 2966066 + Conep05aG0071600.1 Cone5ag0692 692
14 52151 55752 - Conep14aG0000800.1 Cone14ag0007 7
14 55968 59111 + Conep14aG0000900.1 Cone14ag0008 8
14 61618 64329 - Conep14aG0001100.1 Cone14ag0010 10
14 85487 89910 + Conep14aG0001200.1 Cone14ag0011 11
15 85260 88347 + Conep15aG0001000.1 Cone15ag0009 9
15 93865 96465 - Conep15aG0001200.1 Cone15ag0011 11
5 3631166 3634794 - Cp4.1LG05g06060.1 Cpe05g00598 598
5 3638213 3643417 + Cp4.1LG05g06000.1 Cpe05g00599 599
13 2736265 2746295 - Cp4.1LG13g03220.1 Cpe13g00317 317
14 188928 192728 - Cp4.1LG14g06760.1 Cpe14g00035 35
14 193668 196278 - Cp4.1LG14g06730.1 Cpe14g00036 36
14 197755 204046 + Cp4.1LG14g06880.1 Cpe14g00037 37
14 210301 216068 + Cp4.1LG14g06800.1 Cpe14g00039 39
14 219332 223096 + Cp4.1LG14g06840.1 Cpe14g00041 41
5 10112883 10117515 - CrPI670011_05g010790.1 Cre05g1079 1079
5 10180570 10183592 - CrPI670011_05g010840.1 Cre05g1084 1084
5 10192797 10196951 + CrPI670011_05g010850.1 Cre05g1085 1085
9 43995084 44002667 - CrPI670011_09g024670.1 Cre09g2467 2467
9 44002806 44004720 + CrPI670011_09g024680.1 Cre09g2468 2468
3 15612223 15615069 - CsaV3_3G019800.1 Csa03g01980 1980
3 15619665 15623621 - CsaV3_3G019820.1 Csa03g01982 1982
3 15629144 15633182 + CsaV3_3G019830.1 Csa03g01983 1983
3 15655856 15659507 + CsaV3_3G019890.1 Csa03g01989 1989
3 15692586 15697399 + CsaV3_3G019930.1 Csa03g01993 1993
5 217410 219727 - CsaV3_5G000470.1 Csa05g00047 47
5 221495 225627 + CsaV3_5G000480.1 Csa05g00048 48
6 54657793 54664982 - Hsped.06g07920.1 Hepe06g0792 792
6 54679659 54684318 + Hsped.06g07930.1 Hepe06g0793 793
7 553201 557269 + Hsped.07g00590.1 Hepe07g0059 59
7 593097 598394 + Hsped.07g00650.1 Hepe07g0065 65
11 1458922 1462278 - Lag0030796.1 Lac11g0158 158
11 1473226 1476152 + Lag0030797.1 Lac11g0159 159
12 1684256 1688319 - Maker00038734 Lcy12g0135 135
12 1698349 1701899 + Maker00038618 Lcy12g0136 136
9 171229 174705 - Lsi09G000200.1 Lsi09g00020 20
9 179635 184713 + Lsi09G000210.1 Lsi09g00021 21
10 297943 300898 - MC10g0051 Mch10g0056 56
10 305244 309161 + MC10g0052 Mch10g0057 57
10 338129 340922 + MC10g0058 Mch10g0063 63
10 3843020 3845490 + MC10g0472 Mch10g0576 576
1 63980014 63985487 - Sed0019654.2 Sed01g3489 3489
1 63997519 64003974 + Sed0011102.1 Sed01g3490 3490
7 6237431 6241848 - Sed0020421.5 Sed07g0855 855
1 962214 966760 - Tan0015162.1 Tan01g0088 88
1 970592 974442 - Tan0020823.1 Tan01g0090 90
1 984729 988337 + Tan0021808.1 Tan01g0091 91
1 984786 988337 + Tan0021808.2 Tan01g0092 92
1 996751 1003482 + Tan0017886.2 Tan01g0095 95
1 1045615 1049744 + Tan0008714.4 Tan01g0105 105
16 21827671 21831491 - Vvi16g1034 Vvi16g1034 1034
16 21836490 21842723 + Vvi16g1035 Vvi16g1035 1035
16 21844740 21851539 - Vvi16g1036 Vvi16g1036 1036
16 21853424 21867415 - Vvi16g1037 Vvi16g1037 1037
16 21873516 21906584 + Vvi16g1038 Vvi16g1038 1038
16 21906819 21912924 + Vvi16g1039 Vvi16g1039 1039
16 21915588 21926695 + Vvi16g1040 Vvi16g1040 1040
16 21934459 21938446 - Vvi16g1041 Vvi16g1041 1041
16 21939675 21947283 - Vvi16g1042 Vvi16g1042 1042
16 21954570 21960272 + Vvi16g1043 Vvi16g1043 1043
       

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