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
Vvi16g654 . . Bda05g00064 . Bpe03g00291 . Bma10g01219 . . Cmo18g01265 . . . . Sed06g0576 . . Bhi01g01332 Tan01g0264 Cmetu11g0868 . Hepe07g0167 Mch10g0164 . . . . . . . . . . Cone14ag0094 Cone15ag0100 Lsi05g01238 . . Cme06g00987 Blo07g00415 . . . . . . . . . . . Cma18g01242 . Car18g01147 Cpe09g00095 . . . . . . . . Cla05g00870 Cam05g0959 Cec05g0963 Cco05g0963 Clacu05g0945 Cmu05g0902 Cre05g0986 . Csa03g01701 Chy06g00937 .
Vvi16g655 . . . . . . . . Cmo16g00135 . . . . . Sed08g0333 . . Bhi01g01330 Tan01g0263 Cmetu06g0071 . Hepe07g0166 Mch10g0163 . Cla01g00411 Cam01g0429 Cec01g0420 Cco01g0442 Clacu01g0430 Cmu01g0412 Cre09g2100 Cone1ag1153 Cone5ag0862 . . Lsi05g01236 . . Cme06g00988 . Blo09g00106 . . . . . . . . . Cma16g00130 . Car16g00115 . . . . . . . . . . Cla05g00871 Cam05g0960 Cec05g0964 Cco05g0964 Clacu05g0946 Cmu05g0903 Cre05g0987 . Csa03g01702 Chy06g00938 .
Vvi16g656 . Blo15g00164 . . . Bpe07g00941 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda06g00679 Bda15g00733 . Bpe12g00423 Bma08g00337 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g657 . . Bda05g00066 Bda07g01863 Bpe03g00290 . Bma10g01220 Bma14g02087 . . . . . . . . . . . . . . . . . . . . . . . Cone1ag1154 Cone5ag0863 . . . . . . Blo07g00414 Blo09g00108 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g658 . . . . . . . . . . Cma02g01061 . Car02g00804 . . . . . . . . . . . . . . . . . . . Cone5ag0864 Cone14ag0092 Cone15ag0098 . . . . . . . . . Bpe12g00424 . . . Cmo02g01078 . . . . . . . . . . . . . . Cla05g00873 . . . . . . . . . .
Vvi16g659 . . . . . . . . . Cmo18g01267 . . . . Sed13g0120 . . Bhi01g01324 Tan01g0257 Cmetu06g1462 . Hepe07g0162 Mch10g0159 . . . . . . . . . . . . . . . Cme06g00993 . . . . . . . . . . . . Cma18g01244 . Car18g01150 . . . . . . . . . Cla05g00877 Cam05g0965 . Cco05g0969 Clacu05g0953 Cmu05g0909 Cre05g0993 . Csa03g01707 Chy06g00943 .
Vvi16g660 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g661 Blo06g01117 . Bda05g00072 . Bpe03g00289 . . Bma14g02086 . Cmo18g01268 Cma02g01062 . Car02g00805 . . Cpe05g00657 . Bhi01g01322 . . . . . . Cla01g00283 Cam01g0293 Cec01g0286 Cco01g0299 Clacu01g0292 Cmu01g0278 Cre09g2229 Cone1ag1155 Cone5ag0865 Cone14ag0091 Cone15ag0097 Lsi05g01228 Csa05g00303 Chy09g01204 Cme06g00994 Blo07g00413 Blo09g00109 . . . Bpe12g00425 Bma08g00336 . . Cmo02g01079 . . Cma18g01245 . Car18g01151 Cpe09g00093 . Bhi12g00225 . . Lac11g2116 Hepe06g1565 . Lcy12g1673 Cla05g00878 Cam05g0966 Cec05g0970 Cco05g0970 Clacu05g0954 Cmu05g0910 Cre05g0994 . . Chy06g00944 Cme09g01741
Vvi16g662 Blo06g01119 . . . . . . . . . . . Car02g00806 . . Cpe05g00656 . . . . . . . . . . . . . . . . . Cone14ag0090 Cone15ag0096 . . . . . . . Bda15g00732 . Bpe12g00426 Bma08g00335 . . Cmo02g01080 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g663 Blo06g01120 . . . . . . . . . Cma02g01064 . Car02g00807 . . Cpe05g00655 . . . . . . . . Cla01g00281 Cam01g0291 Cec01g0284 Cco01g0297 Clacu01g0290 Cmu01g0277 Cre09g2230 . . Cone14ag0089 Cone15ag0095 . Csa05g00299 Chy09g01206 . . . . Bda15g00731 . Bpe12g00427 . . . Cmo02g01081 Cmo15g01279 . . . . . Cpe13g00164 Bhi12g00227 . . Lac11g2114 Hepe06g1563 . Lcy12g1671 . . . . . . . . . . Cme09g01743
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 3540818 3544719 + Bda020653.1 Bda05g00064 64
5 3546557 3547696 + Bda020655.1 Bda05g00066 66
5 3680765 3682181 - Bda020661.1 Bda05g00072 72
6 9417061 9418218 + Bda023973.1 Bda06g00679 679
7 36044735 36047734 - Bda028833.1 Bda07g01863 1863
15 10770287 10774787 - Bda012586.2 Bda15g00731 731
15 10781039 10784338 + Bda012587.1 Bda15g00732 732
15 10813574 10814725 - Bda012588.1 Bda15g00733 733
1 26621454 26624295 + XM_039019948.1 Bhi01g01322 1322
1 26625480 26628664 + XM_039019964.1 Bhi01g01324 1324
1 26693363 26712749 + XM_039034195.1 Bhi01g01330 1330
1 26743032 26748446 - XM_039034946.1 Bhi01g01332 1332
12 7277180 7281541 - XM_039020207.1 Bhi12g00225 225
12 7385583 7390973 + XM_039018425.1 Bhi12g00227 227
6 34613697 34615758 - BLOR17700 Blo06g01117 1117
6 34627300 34630764 - BLOR17702 Blo06g01119 1119
6 34642525 34646938 + BLOR17703 Blo06g01120 1120
7 7745344 7746319 + BLOR18345 Blo07g00413 413
7 7749000 7751147 - BLOR18346 Blo07g00414 414
7 7792042 7795984 - BLOR18347 Blo07g00415 415
9 1980361 1994738 - BLOR21021 Blo09g00106 106
9 2075201 2082971 + BLOR21023 Blo09g00108 108
9 2084383 2086368 - BLOR21024 Blo09g00109 109
15 1667827 1668984 + BLOR06558 Blo15g00164 164
8 5843934 5846658 + Bma027376.1 Bma08g00335 335
8 5853905 5934331 + Bma027377.1 Bma08g00336 336
8 6003435 6004586 - Bma027379.1 Bma08g00337 337
10 43095332 43099232 + Bma005290.1 Bma10g01219 1219
10 43101960 43104199 + Bma005291.1 Bma10g01220 1220
14 44254215 44255372 + Bma012898.1 Bma14g02086 2086
14 44256401 44258401 - Bma030759 Bma14g02087 2087
3 3946608 3947538 + Bpe012141.1 Bpe03g00289 289
3 3950605 3952823 - Bpe012142.1 Bpe03g00290 290
3 3954760 3958674 - Bpe012143.2 Bpe03g00291 291
7 15282151 15283311 - Bpe021783.1 Bpe07g00941 941
12 9828790 9829941 + Bpe005680.1 Bpe12g00423 423
12 9839981 9841304 + Bpe005681.1 Bpe12g00424 424
12 9858599 9860442 - Bpe005682.1 Bpe12g00425 425
12 9864485 9867109 - Bpe005683.1 Bpe12g00426 426
12 9871765 9876252 + Bpe005684.1 Bpe12g00427 427
1 3269962 3274750 - CaPI482276_01g002910.1 Cam01g0291 291
1 3303394 3306157 + CaPI482276_01g002930.1 Cam01g0293 293
1 4700757 4710141 + CaPI482276_01g004290.1 Cam01g0429 429
5 8648141 8653382 + CaPI482276_05g009590.1 Cam05g0959 959
5 8653389 8660954 - CaPI482276_05g009600.1 Cam05g0960 960
5 8686839 8690663 - CaPI482276_05g009650.1 Cam05g0965 965
5 8691877 8693991 - CaPI482276_05g009660.1 Cam05g0966 966
2 5858838 5859687 - Carg08417-RA Car02g00804 804
2 5862435 5863701 - Carg08416-RA Car02g00805 805
2 5867166 5869114 - Carg08415-RA Car02g00806 806
2 5870596 5871802 + Carg08414-RA Car02g00807 807
16 688390 701393 + Carg15137-RA Car16g00115 115
18 11339436 11344009 + Carg22095-RA Car18g01147 1147
18 11347240 11347882 - Carg22098-RA Car18g01150 1150
18 11348172 11349154 - Carg22099-RA Car18g01151 1151
1 2898898 2903693 - CcPI632755_01g002970.1 Cco01g0297 297
1 2938907 2941757 + CcPI632755_01g002990.1 Cco01g0299 299
1 4396978 4406368 + CcPI632755_01g004420.1 Cco01g0442 442
5 8413800 8419463 + CcPI632755_05g009630.1 Cco05g0963 963
5 8419826 8427406 - CcPI632755_05g009640.1 Cco05g0964 964
5 8454907 8458668 - CcPI632755_05g009690.1 Cco05g0969 969
5 8459877 8461982 - CcPI632755_05g009700.1 Cco05g0970 970
1 2868941 2873729 - CePI673135_01g002840.1 Cec01g0284 284
1 2905547 2908427 + CePI673135_01g002860.1 Cec01g0286 286
1 4416330 4425631 + CePI673135_01g004200.1 Cec01g0420 420
5 8396282 8401517 + CePI673135_05g009630.1 Cec05g0963 963
5 8401873 8409423 - CePI673135_05g009640.1 Cec05g0964 964
5 8436917 8443940 - CePI673135_05g009700.1 Cec05g0970 970
6 6879997 6884458 + Chy6G114650.1 Chy06g00937 937
6 6884870 6891753 - Chy6G114660.1 Chy06g00938 938
6 6910052 6911898 - Chy6G114710.1 Chy06g00943 943
6 6913030 6914930 - Chy6G114720.1 Chy06g00944 944
9 14186818 14189395 - Chy9G169200.1 Chy09g01204 1204
9 14203475 14208193 + Chy9G169220.1 Chy09g01206 1206
1 2883407 2888195 - ClG42_01g0029000.10 Clacu01g0290 290
1 2919502 2922414 + ClG42_01g0029200.10 Clacu01g0292 292
1 4342032 4351395 + ClG42_01g0043000.10 Clacu01g0430 430
5 8359169 8362985 + ClG42_05g0094500.10 Clacu05g0945 945
5 8363084 8370915 - ClG42_05g0094600.10 Clacu05g0946 946
5 8397488 8401313 - ClG42_05g0095300.10 Clacu05g0953 953
5 8402516 8404618 - ClG42_05g0095400.10 Clacu05g0954 954
1 2955157 2960375 - ClCG01G002910.2 Cla01g00281 281
1 2991388 2994618 + ClCG01G002930.2 Cla01g00283 283
1 4509957 4519320 + ClCG01G004190.1 Cla01g00411 411
5 8612484 8617752 + ClCG05G007970.1 Cla05g00870 870
5 8617823 8625431 - ClCG05G007980.2 Cla05g00871 871
5 8639377 8639949 + ClCG05G007987.1 Cla05g00873 873
5 8656727 8660552 - ClCG05G008020.2 Cla05g00877 877
5 8661755 8663855 - ClCG05G008030.2 Cla05g00878 878
2 6337611 6338475 - CmaCh02G010610.1 Cma02g01061 1061
2 6342177 6343504 - CmaCh02G010620.1 Cma02g01062 1062
2 6351079 6357060 + CmaCh02G010640.1 Cma02g01064 1064
16 582197 588990 + CmaCh16G001300.1 Cma16g00130 130
18 9723529 9727689 + CmaCh18G012420.1 Cma18g01242 1242
18 9730202 9731750 - CmaCh18G012440.1 Cma18g01244 1244
18 9731835 9733066 - CmaCh18G012450.1 Cma18g01245 1245
6 7038549 7043163 + MELO3C006899.2.1 Cme06g00987 987
6 7043015 7051085 - MELO3C006901.2.1 Cme06g00988 988
6 7071248 7073694 - MELO3C031642.2.1 Cme06g00993 993
6 7074692 7076924 - MELO3C006904.2.1 Cme06g00994 994
9 21939369 21942505 - MELO3C005653.2.1 Cme09g01741 1741
9 21956332 21961507 + MELO3C005655.2.1 Cme09g01743 1743
6 7078540 7086881 - PI0020160.1 Cmetu06g0071 71
6 7111943 7114259 - PI0007726.1 Cmetu06g1462 1462
11 105655 109704 - PI0021044.1 Cmetu11g0868 868
2 6569191 6570042 - CmoCh02G010780.1 Cmo02g01078 1078
2 6573333 6574634 - CmoCh02G010790.1 Cmo02g01079 1079
2 6577235 6580357 - CmoCh02G010800.1 Cmo02g01080 1080
2 6581899 6587486 + CmoCh02G010810.1 Cmo02g01081 1081
15 8767724 8772403 + CmoCh15G012790.1 Cmo15g01279 1279
16 625008 633574 + CmoCh16G001350.1 Cmo16g00135 135
18 12341896 12346289 + CmoCh18G012650.1 Cmo18g01265 1265
18 12348859 12350277 - CmoCh18G012670.1 Cmo18g01267 1267
18 12350426 12351498 - CmoCh18G012680.1 Cmo18g01268 1268
1 2839466 2844254 - CmPI595203_01g002770.1 Cmu01g0277 277
1 2875567 2878471 + CmPI595203_01g002780.1 Cmu01g0278 278
1 4298608 4307971 + CmPI595203_01g004120.1 Cmu01g0412 412
5 8204990 8209877 + CmPI595203_05g009020.1 Cmu05g0902 902
5 8210235 8217807 - CmPI595203_05g009030.1 Cmu05g0903 903
5 8244349 8248178 - CmPI595203_05g009090.1 Cmu05g0909 909
5 8249379 8251462 - CmPI595203_05g009100.1 Cmu05g0910 910
1 55701682 55706273 - Conep01aG0120200.1 Cone1ag1153 1153
1 55706503 55709079 + Conep01aG0120300.1 Cone1ag1154 1154
1 55710851 55712681 - Conep01aG0120400.1 Cone1ag1155 1155
5 3679562 3683671 - Conep05aG0088800.1 Cone5ag0862 862
5 3683845 3686182 + Conep05aG0088900.1 Cone5ag0863 863
5 3687023 3688103 + Conep05aG0089000.1 Cone5ag0864 864
5 3688430 3689745 - Conep05aG0089100.1 Cone5ag0865 865
14 443642 447343 - Conep14aG0009200.1 Cone14ag0089 89
14 451141 453502 + Conep14aG0009300.1 Cone14ag0090 90
14 453942 456001 + Conep14aG0009400.1 Cone14ag0091 91
14 456764 458280 - Conep14aG0009500.1 Cone14ag0092 92
14 463520 466799 - Conep14aG0009700.1 Cone14ag0094 94
15 481286 484984 - Conep15aG0009700.1 Cone15ag0095 95
15 487348 489192 + Conep15aG0009800.1 Cone15ag0096 96
15 490685 492341 + Conep15aG0009900.1 Cone15ag0097 97
15 493039 494468 - Conep15aG0010000.1 Cone15ag0098 98
15 499539 502827 - Conep15aG0010200.1 Cone15ag0100 100
5 3988577 3994349 - Cp4.1LG05g06560.1 Cpe05g00655 655
5 3995270 3998167 + Cp4.1LG05g06420.1 Cpe05g00656 656
5 4001147 4002479 + Cp4.1LG05g06440.1 Cpe05g00657 657
9 534309 536989 + Cp4.1LG09g00880.1 Cpe09g00093 93
9 539630 545296 - Cp4.1LG09g00980.1 Cpe09g00095 95
13 1233807 1241400 - Cp4.1LG13g01670.1 Cpe13g00164 164
5 9087777 9093496 + CrPI670011_05g009860.1 Cre05g0986 986
5 9093503 9101190 - CrPI670011_05g009870.1 Cre05g0987 987
5 9127089 9130953 - CrPI670011_05g009930.1 Cre05g0993 993
5 9132154 9134239 - CrPI670011_05g009940.1 Cre05g0994 994
9 40000337 40009593 - CrPI670011_09g021000.1 Cre09g2100 2100
9 41436735 41439599 - CrPI670011_09g022290.1 Cre09g2229 2229
9 41469270 41474078 + CrPI670011_09g022300.1 Cre09g2230 2230
3 12773431 12779616 + CsaV3_3G017010.1 Csa03g01701 1701
3 12778406 12785484 - CsaV3_3G017020.1 Csa03g01702 1702
3 12803288 12805319 - CsaV3_3G017070.1 Csa03g01707 1707
5 1888919 1896154 - CsaV3_5G002990.1 Csa05g00299 299
5 1907702 1910983 + CsaV3_5G003030.1 Csa05g00303 303
6 66354005 66359058 - Hsped.06g15630.1 Hepe06g1563 1563
6 66389266 66392501 + Hsped.06g15650.1 Hepe06g1565 1565
7 1472451 1474664 + Hsped.07g01620.1 Hepe07g0162 162
7 1493411 1500809 + Hsped.07g01660.1 Hepe07g0166 166
7 1500896 1504728 - Hsped.07g01670.1 Hepe07g0167 167
11 37107356 37112127 - Lag0032752.1 Lac11g2114 2114
11 37155802 37156576 + Lag0032754.1 Lac11g2116 2116
12 37143132 37148517 - Maker00029213 Lcy12g1671 1671
12 37195172 37196121 + Maker00029250 Lcy12g1673 1673
5 20162204 20166765 + Lsi05G012280.1 Lsi05g01228 1228
5 20213692 20222260 + Lsi05G012360.1 Lsi05g01236 1236
5 20223460 20225994 - Lsi05G012380.1 Lsi05g01238 1238
10 969107 970865 + MC10g0133 Mch10g0159 159
10 982798 989569 + MC10g0136 Mch10g0163 163
10 989034 992331 - MC10g_new0028 Mch10g0164 164
6 5034508 5048399 + Sed0016811.1 Sed06g0576 576
8 2017495 2027751 + Sed0003655.1 Sed08g0333 333
13 797955 801026 - Sed0012701.1 Sed13g0120 120
1 2199664 2201722 + Tan0013459.1 Tan01g0257 257
1 2231710 2239384 + Tan0001948.2 Tan01g0263 263
1 2239410 2243539 - Tan0010646.1 Tan01g0264 264
16 16810874 16818602 + Vvi16g654 Vvi16g654 654
16 16825487 16834648 - Vvi16g655 Vvi16g655 655
16 16867340 16874670 + Vvi16g656 Vvi16g656 656
16 16882272 16895215 + Vvi16g657 Vvi16g657 657
16 16907192 16908873 + Vvi16g658 Vvi16g658 658
16 16909805 16910663 - Vvi16g659 Vvi16g659 659
16 16918858 16920865 + Vvi16g660 Vvi16g660 660
16 16921283 16925918 - Vvi16g661 Vvi16g661 661
16 16936319 16939272 - Vvi16g662 Vvi16g662 662
16 16945005 16949623 + Vvi16g663 Vvi16g663 663
       

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