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
Vvi16g984 Blo06g01052 . . . . . . . . . Cma02g01144 Cma15g01004 . Car15g00938 . Cpe05g00581 . . . . . . . . Cla01g00017 . . . . . . Cone14ag0451 Cone15ag0481 . Cone18ag0993 . Csa05g00018 Chy09g01463 . . . . Bda15g00796 . Bpe12g00336 Bma08g00398 . . Cmo02g01175 . . . . . . Cpe13g00332 . . . . . . . . . . . . . . . . . Cme09g02014
Vvi16g985 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g986 . . Bda05g00138 Bda07g01954 . . Bma10g01316 Bma14g02025 Cmo16g00028 Cmo18g01371 . . . . . . . . . . . . . . . . . . . . . Cone1ag1012 Cone5ag0719 . . . . . . . . . . . . . . . . . Cma16g00024 Cma18g01338 Car16g00022 Car18g01252 . . . . . . . . . . . . . . . . . . . .
Vvi16g987 Blo06g01053 . . . . . . . . . . Cma15g01005 . Car15g00939 . . . . . . . . . . Cla01g00019 Cam01g0018 Cec01g0016 Cco01g0020 Clacu01g0019 Cmu01g0018 Cre09g2489 . . . . . Csa05g00021 . . . . . Bda15g00795 . Bpe12g00339 Bma08g00397 . . . Cmo15g01068 . . . . . Cpe13g00331 Bhi12g00686 . . . . . . . . . . . . . . . . Cme09g02012
Vvi16g988 . . . . . . . . Cmo16g00029 Cmo18g01370 Cma02g01143 . . . . . . . . . . . . . . . . . . . . Cone1ag1011 . . . . . . . . . . . . . . . . Cmo02g01174 . Cma16g00025 Cma18g01337 . . . . . . . . . . . . . . . . . . . . . .
Vvi16g989 . . Bda05g00137 . Bpe03g00225 . Bma10g01315 . Cmo16g00030 . Cma02g01142 Cma15g01007 Car02g00946 Car15g00940 . Cpe05g00582 Cpe14g00020 . . . . . . . Cla01g00021 Cam01g0020 Cec01g0018 Cco01g0022 Clacu01g0021 Cmu01g0020 Cre09g2487 Cone1ag1010 Cone5ag0718 . . . Csa05g00023 Chy09g01460 . Blo07g00320 . . . . . . . . Cmo02g01173 Cmo15g01070 Cma16g00026 . Car16g00023 . . Cpe13g00330 Bhi12g00684 . . . Hepe06g0819 . . . . . . . . . Lsi09g00001 . . Cme09g02009
Vvi16g990 . . Bda05g00136 Bda07g01953 . . Bma10g01314 Bma14g02024 Cmo16g00032 Cmo18g01368 Cma02g01140 Cma15g01009 Car02g00945 Car15g00941 . Cpe05g00583 Cpe14g00021 Bhi01g01525 . . . Hepe07g0036 Mch10g0034 . Cla01g00022 Cam01g0021 Cec01g0019 Cco01g0023 Clacu01g0022 Cmu01g0021 Cre09g2486 Cone1ag1009 Cone5ag0717 . . . Csa05g00024 Chy09g01459 Cme06g01172 Blo07g00321 Blo09g00006 . . . . . . . Cmo02g01172 Cmo15g01072 Cma16g00027 Cma18g01336 Car16g00024 Car18g01251 Cpe09g00012 Cpe13g00328 Bhi12g00683 . . . Hepe06g0818 . . Cla05g00990 Cam05g1081 Cec05g1089 Cco05g1083 Clacu05g1075 Cmu05g1025 Cre05g1099 Lsi09g00002 Csa03g01962 Chy06g01174 Cme09g02008
Vvi16g991 . . . Bda07g01952 . . . Bma14g02023 . . Cma02g01139 Cma15g01010 Car02g00943 Car15g00942 . Cpe05g00584 . . . . . . . . Cla01g00023 Cam01g0022 Cec01g0020 Cco01g0024 Clacu01g0023 Cmu01g0022 Cre09g2485 Cone1ag1008 Cone5ag0716 . . . Csa05g00025 Chy09g01458 . . Blo09g00007 . . . . . . . Cmo02g01170 Cmo15g01073 . . . . . Cpe13g00327 Bhi12g00682 . . . Hepe06g0817 . . . . . . . . . Lsi09g00003 . . Cme09g02007
Vvi16g992 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g993 . . Bda05g00135 Bda07g01951 Bpe03g00226 . Bma10g01313 Bma14g02022 Cmo16g00033 Cmo18g01365 . . . . . . Cpe14g00022 Bhi01g01522 Tan01g0058 . . . . . . . . . . . . Cone1ag1007 Cone5ag0715 . . . . . Cme06g01171 Blo07g00323 Blo09g00008 . . . . . . . . . Cma16g00028 Cma18g01334 Car16g00025 Car18g01250 Cpe09g00013 . . . . . . . . Cla05g00989 Cam05g1080 Cec05g1088 Cco05g1082 Clacu05g1074 Cmu05g1024 Cre05g1098 . Csa03g01963 Chy06g01175 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 6172913 6175435 + Bda020760.1 Bda05g00135 135
5 6182113 6185725 - Bda020761.2 Bda05g00136 136
5 6187334 6188846 - Bda020762.1 Bda05g00137 137
5 6189449 6190444 - Bda020763.1 Bda05g00138 138
7 36934946 36937500 + Bda028931.2 Bda07g01951 1951
7 36938338 36939366 + Bda033999 Bda07g01952 1952
7 36939837 36943506 - Bda028932.3 Bda07g01953 1953
7 36946040 36946800 - Bda028933.1 Bda07g01954 1954
15 11839104 11839811 - Bda012655.1 Bda15g00795 795
15 11843971 11844336 + Bda012656.1 Bda15g00796 796
1 31025714 31030237 + XM_039046248.1 Bhi01g01522 1522
1 31030944 31035321 - XM_039040435.1 Bhi01g01525 1525
12 20168531 20170953 + XM_039019722.1 Bhi12g00682 682
12 20171561 20178350 - XM_039019718.1 Bhi12g00683 683
12 20180176 20183354 - XM_039019720.1 Bhi12g00684 684
12 20206825 20209303 + XM_039050536.1 Bhi12g00686 686
6 33900776 33901156 - BLOR17635 Blo06g01052 1052
6 33902534 33910938 + BLOR17636 Blo06g01053 1053
7 4067219 4068816 + BLOR18252 Blo07g00320 320
7 4070385 4073830 + BLOR18253 Blo07g00321 321
7 4121846 4122561 - BLOR18255 Blo07g00323 323
9 57015 60587 + BLOR20921 Blo09g00006 6
9 61155 62997 - BLOR20922 Blo09g00007 7
9 63263 65806 - BLOR20923 Blo09g00008 8
8 9704825 9707099 - Bma027472.1 Bma08g00397 397
8 9726294 9726653 + Bma027473.1 Bma08g00398 398
10 46629216 46631723 + Bma005427.1 Bma10g01313 1313
10 46716520 46719182 - Bma005428.1 Bma10g01314 1314
10 46751192 46752773 - Bma005429.1 Bma10g01315 1315
10 46784129 46784892 - Bma005430.1 Bma10g01316 1316
14 43579588 43582147 + Bma012830.1 Bma14g02022 2022
14 43583012 43584031 + Bma012831.1 Bma14g02023 2023
14 43584537 43588217 - Bma012832.1 Bma14g02024 2024
14 43590656 43591414 - Bma012833.1 Bma14g02025 2025
3 3012606 3014120 + Bpe012080.1 Bpe03g00225 225
3 3020352 3022867 - Bpe012081.3 Bpe03g00226 226
12 8259875 8260237 + Bpe005592.1 Bpe12g00336 336
12 8459335 8461661 + Bpe005596.1 Bpe12g00339 339
1 614255 616237 - CaPI482276_01g000180.1 Cam01g0018 18
1 620222 625554 + CaPI482276_01g000200.1 Cam01g0020 20
1 625661 630358 + CaPI482276_01g000210.1 Cam01g0021 21
1 631760 633343 - CaPI482276_01g000220.1 Cam01g0022 22
5 9851329 9855429 + CaPI482276_05g010800.1 Cam05g1080 1080
5 9856670 9861050 - CaPI482276_05g010810.1 Cam05g1081 1081
2 6663140 6665394 + Carg13998-RA Car02g00943 943
2 6666459 6670921 - Carg13996-RA Car02g00945 945
2 6673083 6676050 - Carg13995-RA Car02g00946 946
15 6696450 6698600 - Carg26780-RA Car15g00938 938
15 6700253 6704003 - Carg26779-RA Car15g00939 939
15 6704751 6711955 + Carg26778-RA Car15g00940 940
15 6713355 6718895 + Carg26777-RA Car15g00941 941
15 6720301 6722727 - Carg26776-RA Car15g00942 942
16 227226 229941 + Carg15041-RA Car16g00022 22
16 231953 233604 + Carg15042-RA Car16g00023 23
16 235149 239336 + Carg15043-RA Car16g00024 24
16 241582 244250 - Carg15044-RA Car16g00025 25
18 11884771 11888180 + Carg20320-RA Car18g01250 1250
18 11890309 11896864 - Carg20319-RA Car18g01251 1251
18 11900083 11900902 - Carg20318-RA Car18g01252 1252
1 125562 127530 - CcPI632755_01g000200.1 Cco01g0020 20
1 131617 136930 + CcPI632755_01g000220.1 Cco01g0022 22
1 137037 141808 + CcPI632755_01g000230.1 Cco01g0023 23
1 143104 145076 - CcPI632755_01g000240.1 Cco01g0024 24
5 9612634 9616725 + CcPI632755_05g010820.1 Cco05g1082 1082
5 9618079 9622468 - CcPI632755_05g010830.1 Cco05g1083 1083
1 143827 145785 - CePI673135_01g000160.1 Cec01g0016 16
1 150985 156310 + CePI673135_01g000180.1 Cec01g0018 18
1 156417 161253 + CePI673135_01g000190.1 Cec01g0019 19
1 162483 164457 - CePI673135_01g000200.1 Cec01g0020 20
5 9593578 9597675 + CePI673135_05g010880.1 Cec05g1088 1088
5 9599016 9603387 - CePI673135_05g010890.1 Cec05g1089 1089
6 10423073 10426926 + Chy6G117020.1 Chy06g01174 1174
6 10428465 10431879 - Chy6G117030.1 Chy06g01175 1175
9 16067861 16072290 + Chy9G171740.1 Chy09g01458 1458
9 16078515 16082029 - Chy9G171750.1 Chy09g01459 1459
9 16085542 16088130 - Chy9G171760.1 Chy09g01460 1460
9 16091502 16099670 + Chy9G171790.1 Chy09g01463 1463
1 217932 220349 - ClG42_01g0001900.10 Clacu01g0019 19
1 224309 229647 + ClG42_01g0002100.10 Clacu01g0021 21
1 229754 234444 + ClG42_01g0002200.10 Clacu01g0022 22
1 235846 237784 - ClG42_01g0002300.10 Clacu01g0023 23
5 9585589 9589686 + ClG42_05g0107400.10 Clacu05g1074 1074
5 9590952 9595323 - ClG42_05g0107500.10 Clacu05g1075 1075
1 130052 130423 - ClCG01G000155.1 Cla01g00017 17
1 138286 140447 - ClCG01G000170.1 Cla01g00019 19
1 144544 149882 + ClCG01G000190.2 Cla01g00021 21
1 149529 155623 + ClCG01G000200.1 Cla01g00022 22
1 156146 158349 - ClCG01G000210.1 Cla01g00023 23
5 9941894 9945321 + ClCG05G009150.2 Cla05g00989 989
5 9946572 9951099 - ClCG05G009160.2 Cla05g00990 990
2 6733324 6735930 + CmaCh02G011390.1 Cma02g01139 1139
2 6735836 6741476 - CmaCh02G011400.1 Cma02g01140 1140
2 6743952 6746314 - CmaCh02G011420.1 Cma02g01142 1142
2 6747429 6749205 - CmaCh02G011430.1 Cma02g01143 1143
2 6752352 6752968 + CmaCh02G011440.1 Cma02g01144 1144
15 6068472 6068864 - CmaCh15G010040.1 Cma15g01004 1004
15 6071059 6074725 - CmaCh15G010050.1 Cma15g01005 1005
15 6079656 6082350 + CmaCh15G010070.1 Cma15g01007 1007
15 6083930 6089719 + CmaCh15G010090.1 Cma15g01009 1009
15 6090522 6093047 - CmaCh15G010100.1 Cma15g01010 1010
16 121192 121617 + CmaCh16G000240.1 Cma16g00024 24
16 122917 124430 - CmaCh16G000250.1 Cma16g00025 25
16 124453 125858 + CmaCh16G000260.1 Cma16g00026 26
16 127988 132313 + CmaCh16G000270.1 Cma16g00027 27
16 134110 136820 - CmaCh16G000280.1 Cma16g00028 28
18 10176428 10179894 + CmaCh18G013340.1 Cma18g01334 1334
18 10182682 10189182 - CmaCh18G013360.1 Cma18g01336 1336
18 10189514 10191372 + CmaCh18G013370.1 Cma18g01337 1337
18 10196929 10197525 - CmaCh18G013380.1 Cma18g01338 1338
6 9116826 9120723 + MELO3C019384.2.1 Cme06g01171 1171
6 9121507 9126291 - MELO3C019385.2.1 Cme06g01172 1172
9 23822042 23824374 + MELO3C005907.2.1 Cme09g02007 2007
9 23824839 23830255 - MELO3C005908.2.1 Cme09g02008 2008
9 23831376 23835308 - MELO3C005909.2.1 Cme09g02009 2009
9 23838556 23841989 + MELO3C005911.2.1 Cme09g02012 2012
9 23847360 23849634 + MELO3C005913.2.1 Cme09g02014 2014
2 7043499 7045407 + CmoCh02G011700.1 Cmo02g01170 1170
2 7046443 7051133 - CmoCh02G011720.1 Cmo02g01172 1172
2 7052839 7056071 - CmoCh02G011730.1 Cmo02g01173 1173
2 7057228 7058998 - CmoCh02G011740.1 Cmo02g01174 1174
2 7062288 7062614 + CmoCh02G011750.1 Cmo02g01175 1175
15 6949560 6953215 - CmoCh15G010680.1 Cmo15g01068 1068
15 6956983 6959571 + CmoCh15G010700.1 Cmo15g01070 1070
15 6961068 6967125 + CmoCh15G010720.1 Cmo15g01072 1072
15 6968038 6970578 - CmoCh15G010730.1 Cmo15g01073 1073
16 137218 139128 + CmoCh16G000280.1 Cmo16g00028 28
16 139251 140789 - CmoCh16G000290.1 Cmo16g00029 29
16 140808 142514 + CmoCh16G000300.1 Cmo16g00030 30
16 149257 153795 + CmoCh16G000320.1 Cmo16g00032 32
16 155618 158339 - CmoCh16G000330.1 Cmo16g00033 33
18 12815949 12820091 + CmoCh18G013650.1 Cmo18g01365 1365
18 12822298 12828334 - CmoCh18G013680.1 Cmo18g01368 1368
18 12828851 12830713 + CmoCh18G013700.1 Cmo18g01370 1370
18 12831625 12832408 - CmoCh18G013710.1 Cmo18g01371 1371
1 162891 165298 - CmPI595203_01g000180.1 Cmu01g0018 18
1 169254 174598 + CmPI595203_01g000200.1 Cmu01g0020 20
1 174705 179395 + CmPI595203_01g000210.1 Cmu01g0021 21
1 180797 182736 - CmPI595203_01g000220.1 Cmu01g0022 22
5 9425707 9429773 + CmPI595203_05g010240.1 Cmu05g1024 1024
5 9431039 9435410 - CmPI595203_05g010250.1 Cmu05g1025 1025
1 55065746 55069154 + Conep01aG0105500.1 Cone1ag1007 1007
1 55070293 55071436 + Conep01aG0105600.1 Cone1ag1008 1008
1 55072215 55076319 - Conep01aG0105700.1 Cone1ag1009 1009
1 55077648 55079641 - Conep01aG0105800.1 Cone1ag1010 1010
1 55079875 55081460 + Conep01aG0105900.1 Cone1ag1011 1011
1 55081851 55082679 - Conep01aG0106000.1 Cone1ag1012 1012
5 3078218 3081659 + Conep05aG0074000.1 Cone5ag0715 715
5 3082824 3084675 + Conep05aG0074100.1 Cone5ag0716 716
5 3085052 3089653 - Conep05aG0074200.1 Cone5ag0717 717
5 3091261 3093485 - Conep05aG0074300.1 Cone5ag0718 718
5 3095360 3096674 - Conep05aG0074400.1 Cone5ag0719 719
14 2132839 2133556 + Conep14aG0046200.1 Cone14ag0451 451
15 2284468 2285375 + Conep15aG0049300.1 Cone15ag0481 481
18 7292818 7293162 - Conep18aG0102100.1 Cone18ag0993 993
5 3522182 3524944 - Cp4.1LG05g05810.1 Cpe05g00581 581
5 3530530 3534379 + Cp4.1LG05g05850.1 Cpe05g00582 582
5 3535926 3544216 + Cp4.1LG05g05830.1 Cpe05g00583 583
5 3539455 3544216 - Cp4.1LG05g05960.1 Cpe05g00584 584
9 62742 73006 + Cp4.1LG09g00060.1 Cpe09g00012 12
9 74322 77960 - Cp4.1LG09g00130.1 Cpe09g00013 13
13 2946237 2948618 + Cp4.1LG13g03230.1 Cpe13g00327 327
13 2949661 2955831 - Cp4.1LG13g03350.1 Cpe13g00328 328
13 2961008 2964070 - Cp4.1LG13g03360.1 Cpe13g00330 330
13 2964394 2966884 + Cp4.1LG13g03300.1 Cpe13g00331 331
13 2969818 2970210 + Cp4.1LG13g03320.1 Cpe13g00332 332
14 124308 126411 + Cp4.1LG14g07110.1 Cpe14g00020 20
14 127916 133615 + Cp4.1LG14g07170.1 Cpe14g00021 21
14 133629 137120 - Cp4.1LG14g06950.1 Cpe14g00022 22
5 10299534 10303630 + CrPI670011_05g010980.1 Cre05g1098 1098
5 10304915 10309055 - CrPI670011_05g010990.1 Cre05g1099 1099
9 44142096 44144044 + CrPI670011_09g024850.1 Cre09g2485 2485
9 44145439 44150153 - CrPI670011_09g024860.1 Cre09g2486 2486
9 44150260 44155653 - CrPI670011_09g024870.1 Cre09g2487 2487
9 44159732 44161727 + CrPI670011_09g024890.1 Cre09g2489 2489
3 15507376 15517173 + CsaV3_3G019620.1 Csa03g01962 1962
3 15512531 15517268 - CsaV3_3G019630.1 Csa03g01963 1963
5 94865 96249 - CsaV3_5G000180.1 Csa05g00018 18
5 99876 102581 - CsaV3_5G000210.1 Csa05g00021 21
5 105623 108214 + CsaV3_5G000230.1 Csa05g00023 23
5 110338 115862 + CsaV3_5G000240.1 Csa05g00024 24
5 116589 118084 - CsaV3_5G000250.1 Csa05g00025 25
6 54970997 54973659 + Hsped.06g08170.1 Hepe06g0817 817
6 54973969 54979952 - Hsped.06g08180.1 Hepe06g0818 818
6 54982959 54987196 - Hsped.06g08190.1 Hepe06g0819 819
7 430048 434406 + Hsped.07g00360.1 Hepe07g0036 36
9 12968 20664 + Lsi09G000010.1 Lsi09g00001 1
9 22908 28569 + Lsi09G000020.1 Lsi09g00002 2
9 27466 31313 - Lsi09G000030.1 Lsi09g00003 3
10 193068 198397 + MC10g0030 Mch10g0034 34
1 725063 729713 - Tan0013506.7 Tan01g0058 58
16 21394850 21395632 - Vvi16g984 Vvi16g984 984
16 21420050 21423341 + Vvi16g985 Vvi16g985 985
16 21439500 21441052 + Vvi16g986 Vvi16g986 986
16 21441799 21447160 + Vvi16g987 Vvi16g987 987
16 21447164 21450532 - Vvi16g988 Vvi16g988 988
16 21450858 21454428 + Vvi16g989 Vvi16g989 989
16 21461670 21468729 + Vvi16g990 Vvi16g990 990
16 21470775 21473444 - Vvi16g991 Vvi16g991 991
16 21490737 21492403 + Vvi16g992 Vvi16g992 992
16 21495027 21499010 - Vvi16g993 Vvi16g993 993
       

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