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
Vvi16g1004 . . . Bda07g01945 Bpe03g00200 . . . Cmo16g00039 . . . . . . . Cpe14g00026 Bhi01g01516 Tan01g0067 . . Hepe07g0042 Mch10g0042 . . . . . . . . Cone1ag1002 Cone5ag0710 . . . . . Cme06g01167 . Blo09g00014 . . . . . . . . . Cma16g00033 . Car16g00032 . . . . . . . . . . Cla05g00986 Cam05g1077 Cec05g1085 Cco05g1079 Clacu05g1071 . . . Csa03g01967 . .
Vvi16g1005 . . . . . . . Bma14g02018 . . Cma02g01137 . Car02g00940 Car15g00947 . Cpe05g00587 . . . . . . . . . . . . . . . . Cone5ag0709 . . . Csa05g00033 Chy09g01451 . . . . Bda15g00792 . . Bma08g00395 . . Cmo02g01166 . . . . . . Cpe13g00323 Bhi12g00677 . . . Hepe06g0813 . . . . . . . . . Lsi09g00007 . . Cme09g02000
Vvi16g1006 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00034 Chy09g01450 . . . . . . Bpe12g00342 . . . . Cmo15g01077 . . . . . . Bhi12g00675 . . . Hepe06g0812 . . . . . . . . . . . . Cme09g01999
Vvi16g1007 Blo06g01056 . . . . . . . . . Cma02g01136 Cma15g01013 Car02g00939 . . Cpe05g00588 . . . . . . . . Cla01g00028 Cam01g0027 Cec01g0025 Cco01g0027 Clacu01g0027 Cmu01g0026 Cre09g2480 . . . . . . . . . . . Bda15g00791 . Bpe12g00343 Bma08g00394 . . Cmo02g01164 . . . . . . . Bhi12g00673 . . . Hepe06g0811 . . . . . . . . . Lsi09g00008 . . .
Vvi16g1008 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1009 . . Bda05g00131 Bda07g01944 Bpe03g00228 . Bma10g01308 Bma14g02017 Cmo16g00040 . . Cma15g01014 . Car15g00949 . . Cpe14g00027 Bhi01g01514 . . . Hepe07g0043 Mch10g0043 . Cla01g00029 Cam01g0028 Cec01g0026 Cco01g0028 Clacu01g0028 Cmu01g0027 Cre09g2479 . Cone5ag0708 . . . . . Cme06g01166 Blo07g00326 Blo09g00015 . . . . . . . . Cmo15g01079 Cma16g00034 . Car16g00033 . . Cpe13g00322 Bhi12g00672 . . . . . . Cla05g00985 Cam05g1076 Cec05g1083 Cco05g1076 Clacu05g1070 Cmu05g1021 Cre05g1095 Lsi09g00009 Csa03g01968 Chy06g01178 .
Vvi16g1010 . . . Bda07g01943 Bpe03g00198 . . Bma14g02016 Cmo16g00041 . . . . . . . Cpe14g00028 Bhi01g01513 . . . . . . . . . . . . . Cone1ag1000 . . . . . . Cme06g01165 . Blo09g00016 . . . . . . . . . Cma16g00035 . Car16g00035 . . . . . . . . . . Cla05g00984 Cam05g1075 Cec05g1082 Cco05g1075 Clacu05g1069 Cmu05g1020 Cre05g1094 . Csa03g01969 Chy06g01179 .
Vvi16g1011 Blo06g01057 . . . . . . . . . . Cma15g01016 Car02g00937 Car15g00951 . Cpe05g00589 . . . . . . . . Cla01g00030 Cam01g0029 Cec01g0027 Cco01g0029 Clacu01g0029 Cmu01g0028 Cre09g2478 . . . . . . . . . . . Bda15g00790 . Bpe12g00344 Bma08g00393 . . Cmo02g01162 Cmo15g01080 . . . . . Cpe13g00321 Bhi12g00670 . . . Hepe06g0809 . . . . . . . . . Lsi09g00010 . . .
Vvi16g1012 . Blo15g00080 Bda05g00130 Bda07g01942 Bpe03g00197 Bpe07g01024 Bma10g01307 Bma14g02015 . . Cma02g01133 Cma15g01017 Car02g00936 Car15g00952 . Cpe05g00590 . . . . . . . . Cla01g00031 . Cec01g0028 Cco01g0030 Clacu01g0030 Cmu01g0029 Cre09g2477 Cone1ag0999 Cone5ag0704 . . . . . . Blo07g00327 Blo09g00017 Bda06g00793 Bda15g00789 . Bpe12g00345 Bma08g00392 Bma12g01219 . Cmo02g01161 Cmo15g01081 . . . . . Cpe13g00320 Bhi12g00667 . . . Hepe06g0808 . . . . . . . . . Lsi09g00011 . . .
Vvi16g1013 . . . Bda07g01940 Bpe03g00195 . . Bma14g02013 Cmo16g00042 . . . . . Sed07g0872 . Cpe14g00029 Bhi01g01510 Tan01g0072 Cmetu06g0962 . Hepe07g0045 Mch10g0045 . . . . . . . . . Cone5ag0703 . . . . . Cme06g01164 . Blo09g00019 . . . . . . . . . Cma16g00036 . Car16g00036 Car18g01230 . . . . . . . . . Cla05g00983 Cam05g1074 Cec05g1081 Cco05g1074 Clacu05g1068 Cmu05g1019 Cre05g1093 . Csa03g01970 Chy06g01181 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 6011416 6013507 - Bda020748.1 Bda05g00130 130
5 6034389 6035198 + Bda020751.1 Bda05g00131 131
6 10998273 11002837 - Bda024116.1 Bda06g00793 793
7 36876618 36877257 - Bda028919.1 Bda07g01940 1940
7 36880142 36883058 - Bda028921.3 Bda07g01942 1942
7 36886499 36890781 + Bda028922.1 Bda07g01943 1943
7 36893264 36894079 + Bda028923.1 Bda07g01944 1944
7 36898657 36901615 + Bda028924.1 Bda07g01945 1945
15 11794083 11797501 - Bda012650.1 Bda15g00789 789
15 11801960 11803499 - Bda012651.1 Bda15g00790 790
15 11804204 11806202 - Bda033320 Bda15g00791 791
15 11808540 11809149 - Bda012652.1 Bda15g00792 792
1 30850302 30854436 - XM_039029555.1 Bhi01g01510 1510
1 30921161 30926298 + XM_039039888.1 Bhi01g01513 1513
1 30926443 30929210 + XM_039039895.1 Bhi01g01514 1514
1 30947248 30952466 + XM_039041716.1 Bhi01g01516 1516
12 19793101 19798522 - XM_039019508.1 Bhi12g00667 667
12 19817520 19820012 - XM_039019622.1 Bhi12g00670 670
12 20013390 20015180 + XM_039050876.1 Bhi12g00672 672
12 20027819 20031028 - XM_039019002.1 Bhi12g00673 673
12 20056701 20058324 - XM_039020349.1 Bhi12g00675 675
12 20056701 20058453 - XM_039020350.1 Bhi12g00677 677
6 33930952 33932919 + BLOR17639 Blo06g01056 1056
6 33941124 33943541 + BLOR17640 Blo06g01057 1057
7 4195737 4198567 - BLOR18258 Blo07g00326 326
7 4246234 4250593 + BLOR18259 Blo07g00327 327
9 141339 147246 - BLOR20929 Blo09g00014 14
9 156727 160924 - BLOR20930 Blo09g00015 15
9 161141 165717 - BLOR20931 Blo09g00016 16
9 174584 177439 + BLOR20932 Blo09g00017 17
9 217142 218375 + BLOR20934 Blo09g00019 19
15 683090 687278 + BLOR06474 Blo15g00080 80
8 9571394 9574825 - Bma027465.1 Bma08g00392 392
8 9578476 9580866 - Bma027466.1 Bma08g00393 393
8 9581775 9583768 - Bma027467.1 Bma08g00394 394
8 9607497 9608109 - Bma027469.1 Bma08g00395 395
10 46463325 46465828 + Bma005416.1 Bma10g01307 1307
10 46481613 46482422 + Bma005418.1 Bma10g01308 1308
12 45091080 45093918 - Bma008581.1 Bma12g01219 1219
14 43523183 43523824 - Bma012822.1 Bma14g02013 2013
14 43527149 43530012 - Bma012824.1 Bma14g02015 2015
14 43532953 43537489 + Bma012825.1 Bma14g02016 2016
14 43539877 43540692 + Bma012826.1 Bma14g02017 2017
14 43545695 43546268 - Bma012827.1 Bma14g02018 2018
3 2325474 2326568 - Bpe012042.1 Bpe03g00195 195
3 2329303 2332203 - Bpe012044.1 Bpe03g00197 197
3 2335292 2339537 + Bpe012045.1 Bpe03g00198 198
3 2350716 2353709 + Bpe012047.1 Bpe03g00200 200
3 3063810 3064382 - Bpe012083.1 Bpe03g00228 228
7 15814925 15817860 - Bpe021868.1 Bpe07g01024 1024
12 8512717 8513333 + Bpe024888 Bpe12g00342 342
12 8514057 8516078 + Bpe005598.1 Bpe12g00343 343
12 8516957 8519399 + Bpe005599.1 Bpe12g00344 344
12 8523026 8526428 + Bpe005600.1 Bpe12g00345 345
1 661188 663674 + CaPI482276_01g000270.1 Cam01g0027 27
1 667267 669462 - CaPI482276_01g000280.1 Cam01g0028 28
1 682175 686295 + CaPI482276_01g000290.1 Cam01g0029 29
5 9808225 9811369 - CaPI482276_05g010740.1 Cam05g1074 1074
5 9813633 9818284 + CaPI482276_05g010750.1 Cam05g1075 1075
5 9820023 9820800 + CaPI482276_05g010760.1 Cam05g1076 1076
5 9826349 9831177 + CaPI482276_05g010770.1 Cam05g1077 1077
2 6626209 6630610 - Carg14005-RA Car02g00936 936
2 6638882 6641286 - Carg14004-RA Car02g00937 937
2 6644500 6646953 - Carg14002-RA Car02g00939 939
2 6649255 6650596 - Carg14001-RA Car02g00940 940
15 6756993 6757689 + Carg26771-RA Car15g00947 947
15 6917930 6919231 - Carg26604-RA Car15g00949 949
15 6934791 6936281 + Carg26606-RA Car15g00951 951
15 6943536 6947954 + Carg26607-RA Car15g00952 952
16 257733 261947 - Carg15051-RA Car16g00032 32
16 263121 263914 - Carg15052-RA Car16g00033 33
16 267253 269750 - Carg15054-RA Car16g00035 35
16 269981 271944 + Carg15055-RA Car16g00036 36
18 11825003 11826225 + Carg20340-RA Car18g01230 1230
1 172246 174763 + CcPI632755_01g000270.1 Cco01g0027 27
1 179321 180583 - CcPI632755_01g000280.1 Cco01g0028 28
1 191295 195686 + CcPI632755_01g000290.1 Cco01g0029 29
1 208336 219880 + CcPI632755_01g000300.1 Cco01g0030 30
5 9567307 9570449 - CcPI632755_05g010740.1 Cco05g1074 1074
5 9572700 9577213 + CcPI632755_05g010750.1 Cco05g1075 1075
5 9579135 9579927 + CcPI632755_05g010760.1 Cco05g1076 1076
5 9594764 9597053 + CcPI632755_05g010790.1 Cco05g1079 1079
1 196342 198641 + CePI673135_01g000250.1 Cec01g0025 25
1 211257 212523 - CePI673135_01g000260.1 Cec01g0026 26
1 223053 227200 + CePI673135_01g000270.1 Cec01g0027 27
1 240021 251584 + CePI673135_01g000280.1 Cec01g0028 28
5 9548968 9552110 - CePI673135_05g010810.1 Cec05g1081 1081
5 9554351 9558871 + CePI673135_05g010820.1 Cec05g1082 1082
5 9560793 9561570 + CePI673135_05g010830.1 Cec05g1083 1083
5 9574080 9577150 + CePI673135_05g010850.1 Cec05g1085 1085
6 10463150 10463920 - Chy6G117060.1 Chy06g01178 1178
6 10465951 10476286 - Chy6G117070.1 Chy06g01179 1179
6 10503952 10507013 + Chy6G117090.1 Chy06g01181 1181
9 16026392 16027184 + Chy9G171660.1 Chy09g01450 1450
9 16029122 16029712 + Chy9G171670.1 Chy09g01451 1451
1 265110 267410 + ClG42_01g0002700.10 Clacu01g0027 27
1 271276 273468 - ClG42_01g0002800.10 Clacu01g0028 28
1 286516 290627 + ClG42_01g0002900.10 Clacu01g0029 29
1 303526 308504 + ClG42_01g0003000.10 Clacu01g0030 30
5 9540415 9543555 - ClG42_05g0106800.10 Clacu05g1068 1068
5 9545773 9550219 + ClG42_05g0106900.10 Clacu05g1069 1069
5 9552146 9552923 + ClG42_05g0107000.10 Clacu05g1070 1070
5 9560776 9565385 + ClG42_05g0107100.10 Clacu05g1071 1071
1 186772 189072 + ClCG01G000265.1 Cla01g00028 28
1 197749 198600 - ClCG01G000270.1 Cla01g00029 29
1 214584 217219 + ClCG01G000280.2 Cla01g00030 30
1 231120 236420 + ClCG01G000290.1 Cla01g00031 31
5 9894509 9897756 - ClCG05G009090.1 Cla05g00983 983
5 9899881 9904428 + ClCG05G009095.1 Cla05g00984 984
5 9900367 9907325 + ClCG05G009100.1 Cla05g00985 985
5 9911735 9925927 + ClCG05G009110.2 Cla05g00986 986
2 6698172 6702975 - CmaCh02G011330.1 Cma02g01133 1133
2 6714176 6718001 - CmaCh02G011360.1 Cma02g01136 1136
2 6719919 6727696 - CmaCh02G011370.1 Cma02g01137 1137
15 6134973 6137173 + CmaCh15G010130.1 Cma15g01013 1013
15 6266996 6269122 - CmaCh15G010140.1 Cma15g01014 1014
15 6281258 6283715 + CmaCh15G010160.1 Cma15g01016 1016
15 6290271 6295866 + CmaCh15G010170.1 Cma15g01017 1017
16 147900 154315 - CmaCh16G000330.1 Cma16g00033 33
16 154362 156500 - CmaCh16G000340.1 Cma16g00034 34
16 158177 162376 - CmaCh16G000350.1 Cma16g00035 35
16 162477 164592 + CmaCh16G000360.1 Cma16g00036 36
6 9051857 9055640 - MELO3C019377.2.1 Cme06g01164 1164
6 9071717 9077324 + MELO3C019378.2.1 Cme06g01165 1165
6 9078957 9080503 + MELO3C019379.2.1 Cme06g01166 1166
6 9085771 9089971 + MELO3C019380.2.1 Cme06g01167 1167
9 23776851 23777925 + MELO3C005899.2.1 Cme09g01999 1999
9 23778866 23780470 + MELO3C005900.2.1 Cme09g02000 2000
6 8350640 8354038 - PI0018755.1 Cmetu06g0962 962
2 7000290 7005160 - CmoCh02G011610.1 Cmo02g01161 1161
2 7014565 7021336 - CmoCh02G011620.1 Cmo02g01162 1162
2 7022923 7026920 - CmoCh02G011640.1 Cmo02g01164 1164
2 7028733 7030321 - CmoCh02G011660.1 Cmo02g01166 1166
15 6998924 7006876 + CmoCh15G010770.1 Cmo15g01077 1077
15 7134402 7135250 - CmoCh15G010790.1 Cmo15g01079 1079
15 7154773 7157090 + CmoCh15G010800.1 Cmo15g01080 1080
15 7163643 7169427 + CmoCh15G010810.1 Cmo15g01081 1081
16 172744 175752 - CmoCh16G000390.1 Cmo16g00039 39
16 176924 177610 - CmoCh16G000400.1 Cmo16g00040 40
16 179157 183577 - CmoCh16G000410.1 Cmo16g00041 41
16 183786 185910 + CmoCh16G000420.1 Cmo16g00042 42
1 210073 212373 + CmPI595203_01g000260.1 Cmu01g0026 26
1 216212 218392 - CmPI595203_01g000270.1 Cmu01g0027 27
1 231424 235535 + CmPI595203_01g000280.1 Cmu01g0028 28
1 248471 253452 + CmPI595203_01g000290.1 Cmu01g0029 29
5 9380484 9383624 - CmPI595203_05g010190.1 Cmu05g1019 1019
5 9385840 9390295 + CmPI595203_05g010200.1 Cmu05g1020 1020
5 9392222 9392999 + CmPI595203_05g010210.1 Cmu05g1021 1021
1 55010010 55014451 - Conep01aG0104500.1 Cone1ag0999 999
1 55019645 55023278 + Conep01aG0104600.1 Cone1ag1000 1000
1 55035113 55038783 + Conep01aG0104800.1 Cone1ag1002 1002
5 3018750 3020189 - Conep05aG0072700.1 Cone5ag0703 703
5 3021125 3025538 - Conep05aG0072800.1 Cone5ag0704 704
5 3040801 3041901 + Conep05aG0073200.1 Cone5ag0708 708
5 3044362 3045180 - Conep05aG0073300.1 Cone5ag0709 709
5 3045608 3049083 + Conep05aG0073400.1 Cone5ag0710 710
5 3556967 3558607 + Cp4.1LG05g05940.1 Cpe05g00587 587
5 3561055 3564156 + Cp4.1LG05g05840.1 Cpe05g00588 588
5 3564840 3567343 + Cp4.1LG05g05860.1 Cpe05g00589 589
5 3577026 3582022 + Cp4.1LG05g05900.1 Cpe05g00590 590
13 2785369 2791506 - Cp4.1LG13g03210.1 Cpe13g00320 320
13 2798011 2800466 - Cp4.1LG13g03180.1 Cpe13g00321 321
13 2812456 2813716 + Cp4.1LG13g03150.1 Cpe13g00322 322
13 2896540 2900155 - Cp4.1LG13g03270.1 Cpe13g00323 323
14 149609 154210 - Cp4.1LG14g06980.1 Cpe14g00026 26
14 155290 156071 - Cp4.1LG14g06900.1 Cpe14g00027 27
14 158188 161888 - Cp4.1LG14g06890.1 Cpe14g00028 28
14 162127 164170 + Cp4.1LG14g07150.1 Cpe14g00029 29
5 10256000 10259121 - CrPI670011_05g010930.1 Cre05g1093 1093
5 10261302 10265832 + CrPI670011_05g010940.1 Cre05g1094 1094
5 10267756 10268542 + CrPI670011_05g010950.1 Cre05g1095 1095
9 44065964 44077558 - CrPI670011_09g024770.1 Cre09g2477 2477
9 44091057 44095426 - CrPI670011_09g024780.1 Cre09g2478 2478
9 44105917 44107181 + CrPI670011_09g024790.1 Cre09g2479 2479
9 44111963 44114250 - CrPI670011_09g024800.1 Cre09g2480 2480
3 15531249 15540846 - CsaV3_3G019670.1 Csa03g01967 1967
3 15540852 15541631 - CsaV3_3G019680.1 Csa03g01968 1968
3 15543665 15548526 - CsaV3_3G019690.1 Csa03g01969 1969
3 15550898 15554469 + CsaV3_3G019700.1 Csa03g01970 1970
5 157878 158468 - CsaV3_5G000330.1 Csa05g00033 33
5 160273 161075 - CsaV3_5G000340.1 Csa05g00034 34
6 54866251 54871379 - Hsped.06g08080.1 Hepe06g0808 808
6 54888375 54890763 - Hsped.06g08090.1 Hepe06g0809 809
6 54926695 54931164 - Hsped.06g08110.1 Hepe06g0811 811
6 54934410 54935185 - Hsped.06g08120.1 Hepe06g0812 812
6 54938790 54940032 - Hsped.06g08130.1 Hepe06g0813 813
7 467659 472755 - Hsped.07g00420.1 Hepe07g0042 42
7 475965 477777 - Hsped.07g00430.1 Hepe07g0043 43
7 486118 489029 + Hsped.07g00450.1 Hepe07g0045 45
9 53933 54591 + Lsi09G000070.1 Lsi09g00007 7
9 58002 61135 + Lsi09G000080.1 Lsi09g00008 8
9 70140 70994 - Lsi09G000090.1 Lsi09g00009 9
9 80825 83381 + Lsi09G000100.1 Lsi09g00010 10
9 100654 106228 + Lsi09G000110.1 Lsi09g00011 11
10 239174 242783 - MC10g0038 Mch10g0042 42
10 245396 246040 - MC10g0039 Mch10g0043 43
10 253153 255995 + MC10g0041 Mch10g0045 45
7 6305057 6308546 - Sed0026931.1 Sed07g0872 872
1 795680 801415 - Tan0021367.2 Tan01g0067 67
1 819233 822523 + Tan0018954.2 Tan01g0072 72
16 21608208 21615368 - Vvi16g1004 Vvi16g1004 1004
16 21617855 21619627 + Vvi16g1005 Vvi16g1005 1005
16 21621090 21623248 + Vvi16g1006 Vvi16g1006 1006
16 21624564 21629330 + Vvi16g1007 Vvi16g1007 1007
16 21629330 21631151 - Vvi16g1008 Vvi16g1008 1008
16 21635864 21637951 - Vvi16g1009 Vvi16g1009 1009
16 21644191 21676537 - Vvi16g1010 Vvi16g1010 1010
16 21677419 21681935 + Vvi16g1011 Vvi16g1011 1011
16 21690986 21696151 + Vvi16g1012 Vvi16g1012 1012
16 21708614 21712122 + Vvi16g1013 Vvi16g1013 1013
       

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