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
Vvi18g940 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g941 Blo01g01561 . Bda01g00531 . Bpe02g00393 . . Bma01g02319 . . Cma01g01907 . Car01g01489 . . . . . . . . . . . . . . . . . . Cone4ag1910 Cone7ag1824 . . Lsi04g01660 Csa03g04205 Chy04g00513 . . . . . . . . . . Cmo01g01970 . . . . . . Cpe02g00129 . . . . . . . Cla05g01944 Cam05g2087 Cec05g2100 Cco05g2154 Clacu05g2082 Cmu05g1958 Cre05g2077 . . . Cme04g00572
Vvi18g942 . Blo12g00909 Bda01g00530 Bda03g00259 Bpe02g00392 Bpe04g00212 Bma04g00208 Bma01g02320 . . Cma01g01908 . Car01g01490 . . . . . . . . . . . . . . . . . . . . Cone17ag1339 . Lsi04g01664 Csa03g04207 Chy04g00511 . . . . . . . . . . Cmo01g01971 . . . . . . Cpe02g00128 . . . . . . . Cla05g01942 Cam05g2085 Cec05g2098 Cco05g2152 Clacu05g2080 Cmu05g1955 Cre05g2075 . . . Cme04g00566
Vvi18g943 . . . . . . . . . Cmo12g00420 . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1340 Cone20ag0141 . . . . . Blo18g00816 . Bda01g01492 Bpe02g01688 . Bma01g00764 . . . . Cma12g00471 . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g944 . . . . . . . . Cmo05g00250 . . . . . . . . Bhi04g00169 . . . Hepe10g0636 . . . . . . . . . . . Cone17ag1341 Cone20ag0140 . . . . Blo17g00802 . Bda08g01286 . . Bpe05g00089 . Bma05g00118 . . . . Cma05g00242 Car05g00203 . Cpe11g00201 . . . . . . . . . . . . . . . . . Chy03g01459 .
Vvi18g945 . Blo12g00908 . Bda03g00260 . Bpe04g00213 Bma04g00209 . . . . . . Car12g00446 . . Cpe07g00424 . . . . . . . Cla08g01488 Cam08g1978 Cec08g1552 Cco08g1689 Clacu08g1668 . Cre08g1451 . . Cone17ag1342 Cone20ag0139 . . . Cme03g01956 . Blo18g00815 Bda08g01284 Bda01g01493 Bpe02g01689 Bpe05g00090 . Bma05g00120 . . . . . . . . . . . . . . . . . . . . . . . Lsi08g01395 Csa02g02053 . .
Vvi18g946 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g947 Blo01g01562 . Bda01g00529 . Bpe02g00391 Bpe04g00214 . . . . Cma01g01910 Cma09g00158 Car01g01491 . . Cpe06g00113 . . . . . . . . . . . . . . . Cone4ag1911 Cone7ag1825 . . Lsi04g01665 Csa03g04208 Chy04g00510 . . . . . . . . . . Cmo01g01972 Cmo09g00157 . . . Car09g00140 . Cpe02g00127 . . . . . . . Cla05g01941 . . . . . . . . . Cme04g00565
Vvi18g948 Blo01g01563 . Bda01g00528 . Bpe02g00390 . . Bma01g02321 . . Cma01g01911 Cma09g00157 Car01g01492 . Sed05g2314 Cpe06g00112 . Bhi04g00244 Tan02g0788 Cmetu01g0968 . Hepe02g0493 . Lcy13g1988 . . . . . . . Cone4ag1912 . Cone17ag1343 Cone20ag0138 Lsi04g01666 Csa03g04211 Chy04g00508 . Blo17g00801 Blo18g00814 Bda08g01283 Bda01g01494 Bpe02g01690 Bpe05g00091 Bma01g00763 . . Cmo01g01973 Cmo09g00156 . . . Car09g00139 . Cpe02g00126 . . . . . . . Cla05g01939 Cam05g2083 Cec05g2096 Cco05g2147 Clacu05g2079 Cmu05g1953 Cre05g2074 . . . Cme04g00564
Vvi18g949 . . . . . . . . . . Cma01g01912 Cma09g00156 Car01g01493 . . Cpe06g00111 . . . . . . . . . . . . . . . . . Cone17ag1344 . Lsi04g01667 Csa03g04212 Chy04g00507 . Blo17g00799 . . . . . . Bma05g00121 . Cmo01g01974 Cmo09g00155 . . . Car09g00138 . Cpe02g00125 . . . . . . . Cla05g01938 Cam05g2082 Cec05g2095 Cco05g2146 Clacu05g2078 Cmu05g1952 Cre05g2073 . . . Cme04g00563
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 32266888 32267181 - Bda002539.1 Bda01g00528 528
1 32271517 32274621 + Bda002540.1 Bda01g00529 529
1 32276691 32279093 + Bda002541.1 Bda01g00530 530
1 32280227 32283816 + Bda002542.1 Bda01g00531 531
1 50812678 50814351 + Bda003748.1 Bda01g01492 1492
1 50818163 50825167 + Bda003749.1 Bda01g01493 1493
1 50826229 50826492 + Bda003750.1 Bda01g01494 1494
3 2312733 2315546 - Bda016215.1 Bda03g00259 259
3 2317473 2323441 + Bda016216.3 Bda03g00260 260
8 52102367 52107815 - Bda030302.3 Bda08g01283 1283
8 52130993 52135219 - Bda030304.1 Bda08g01284 1284
8 52317724 52322060 + Bda034048 Bda08g01286 1286
4 4110404 4112616 + XM_039028930.1 Bhi04g00169 169
4 6013876 6015620 + XM_039030373.1 Bhi04g00244 244
1 55375486 55383823 - BLOR01561 Blo01g01561 1561
1 55385654 55391009 - BLOR01562 Blo01g01562 1562
1 55391219 55394320 + BLOR01563 Blo01g01563 1563
12 27261759 27265480 - BLOR04927 Blo12g00908 908
12 27268840 27272786 + BLOR04928 Blo12g00909 909
17 25728200 25731174 - BLOR08345 Blo17g00799 799
17 25764580 25768902 + BLOR08347 Blo17g00801 801
17 25808634 25810183 + BLOR08348 Blo17g00802 802
18 24108441 24108746 - BLOR09302 Blo18g00814 814
18 24127582 24141560 - BLOR09303 Blo18g00815 815
18 24160770 24162121 - BLOR09304 Blo18g00816 816
1 7012514 7012852 - Bma000980.1 Bma01g00763 763
1 7047676 7048317 - Bma000983.1 Bma01g00764 764
1 80708513 80711578 - Bma003181.2 Bma01g02319 2319
1 80712772 80719985 - Bma003182.2 Bma01g02320 2320
1 80725778 80726089 + Bma003183.1 Bma01g02321 2321
4 1810479 1813288 - Bma018657.1 Bma04g00208 208
4 1815085 1819236 + Bma018658.2 Bma04g00209 209
5 3841738 3848396 - Bma020821.1 Bma05g00118 118
5 3867725 3871991 + Bma020824.1 Bma05g00120 120
5 3874790 3880218 + Bma020825.1 Bma05g00121 121
2 2536221 2536514 - Bpe008231.1 Bpe02g00390 390
2 2541530 2544729 + Bpe008232.1 Bpe02g00391 391
2 2546482 2548918 + Bpe008233.1 Bpe02g00392 392
2 2550078 2553668 + Bpe008234.1 Bpe02g00393 393
2 19462156 19463831 + Bpe009522.1 Bpe02g01688 1688
2 19465798 19471379 + Bpe009523.1 Bpe02g01689 1689
2 19472484 19472810 + Bpe009524.1 Bpe02g01690 1690
4 1456776 1459762 - Bpe014930.1 Bpe04g00212 212
4 1462151 1465698 + Bpe025583 Bpe04g00213 213
4 1466208 1469415 - Bpe014931.2 Bpe04g00214 214
5 1528975 1536803 - Bpe017477.2 Bpe05g00089 89
5 1558571 1562809 + Bpe025783 Bpe05g00090 90
5 1577729 1578034 + Bpe017478.1 Bpe05g00091 91
5 29407321 29411546 - CaPI482276_05g020820.1 Cam05g2082 2082
5 29413384 29413647 - CaPI482276_05g020830.1 Cam05g2083 2083
5 29439426 29443727 + CaPI482276_05g020850.1 Cam05g2085 2085
5 29450837 29455281 + CaPI482276_05g020870.1 Cam05g2087 2087
8 25620763 25626856 + CaPI482276_08g019780.1 Cam08g1978 1978
1 12664173 12674749 - Carg17144-RA Car01g01489 1489
1 12672803 12673514 + Carg17145-RA Car01g01490 1490
1 12674852 12681240 - Carg17146-RA Car01g01491 1491
1 12685196 12686083 + Carg17147-RA Car01g01492 1492
1 12688135 12691868 + Carg17148-RA Car01g01493 1493
5 1059328 1061638 + Carg11799-RA Car05g00203 203
9 668055 670729 - Carg08722-RA Car09g00138 138
9 672213 672627 - Carg08723-RA Car09g00139 139
9 677243 680995 + Carg08724-RA Car09g00140 140
12 2817682 2824520 + Carg04054-RA Car12g00446 446
5 30358966 30363858 - CcPI632755_05g021460.1 Cco05g2146 2146
5 30364896 30366005 - CcPI632755_05g021470.1 Cco05g2147 2147
5 30398750 30403056 + CcPI632755_05g021520.1 Cco05g2152 2152
5 30410276 30414719 + CcPI632755_05g021540.1 Cco05g2154 2154
8 28306703 28312891 + CcPI632755_08g016890.1 Cco08g1689 1689
5 32741960 32746186 - CePI673135_05g020950.1 Cec05g2095 2095
5 32747173 32748294 - CePI673135_05g020960.1 Cec05g2096 2096
5 32777871 32782163 + CePI673135_05g020980.1 Cec05g2098 2098
5 32789319 32793745 + CePI673135_05g021000.1 Cec05g2100 2100
8 27169596 27175696 + CePI673135_08g015520.1 Cec08g1552 1552
3 17138263 17140748 - Chy3G064390.1 Chy03g01459 1459
4 4942432 4946849 - Chy4G072250.1 Chy04g00507 507
4 4954715 4955204 - Chy4G072260.1 Chy04g00508 508
4 4985680 4989762 + Chy4G072280.1 Chy04g00510 510
4 4991109 4995165 + Chy4G072290.1 Chy04g00511 511
4 5058854 5063201 + Chy4G072310.1 Chy04g00513 513
5 29615803 29620030 - ClG42_05g0207800.10 Clacu05g2078 2078
5 29621897 29622160 - ClG42_05g0207900.10 Clacu05g2079 2079
5 29641462 29652419 + ClG42_05g0208000.10 Clacu05g2080 2080
5 29659633 29664076 + ClG42_05g0208200.10 Clacu05g2082 2082
8 26364075 26370126 + ClG42_08g0166800.10 Clacu08g1668 1668
5 31224445 31228912 - ClCG05G018940.1 Cla05g01938 1938
5 31229761 31233107 - ClCG05G018950.1 Cla05g01939 1939
5 31251297 31256909 + ClCG05G018970.2 Cla05g01941 1941
5 31259265 31264467 + ClCG05G018980.1 Cla05g01942 1942
5 31273527 31278975 + ClCG05G019000.2 Cla05g01944 1944
8 27744523 27750939 + ClCG08G015070.1 Cla08g01488 1488
1 12448647 12453215 - CmaCh01G019070.1 Cma01g01907 1907
1 12453841 12458424 - CmaCh01G019080.1 Cma01g01908 1908
1 12459300 12463731 - CmaCh01G019100.1 Cma01g01910 1910
1 12467511 12468335 + CmaCh01G019110.1 Cma01g01911 1911
1 12470510 12475551 + CmaCh01G019120.1 Cma01g01912 1912
5 1032222 1035355 + CmaCh05G002420.1 Cma05g00242 242
9 668397 672792 - CmaCh09G001560.1 Cma09g00156 156
9 673083 673627 - CmaCh09G001570.1 Cma09g00157 157
9 678076 682413 + CmaCh09G001580.1 Cma09g00158 158
12 2453683 2455669 + CmaCh12G004710.1 Cma12g00471 471
3 27506979 27513713 + MELO3C010944.2.1 Cme03g01956 1956
4 5054133 5058527 - MELO3C003831.2.1 Cme04g00563 563
4 5062698 5062957 - MELO3C027344.2.1 Cme04g00564 564
4 5090590 5095902 + MELO3C003832.2.1 Cme04g00565 565
4 5097311 5103616 + MELO3C003833.2.1 Cme04g00566 566
4 5204455 5209736 + MELO3C003837.2.1 Cme04g00572 572
1 6077488 6079632 - PI0017426.1 Cmetu01g0968 968
1 13971064 13975639 - CmoCh01G019700.1 Cmo01g01970 1970
1 13976223 13980665 - CmoCh01G019710.1 Cmo01g01971 1971
1 13981213 13985756 - CmoCh01G019720.1 Cmo01g01972 1972
1 13990842 13991639 + CmoCh01G019730.1 Cmo01g01973 1973
1 13993753 13997083 + CmoCh01G019740.1 Cmo01g01974 1974
5 1071079 1076563 + CmoCh05G002500.1 Cmo05g00250 250
9 688307 691038 - CmoCh09G001550.1 Cmo09g00155 155
9 692418 693029 - CmoCh09G001560.1 Cmo09g00156 156
9 697755 702794 + CmoCh09G001570.1 Cmo09g00157 157
12 2581528 2583552 + CmoCh12G004200.1 Cmo12g00420 420
5 29342810 29347038 - CmPI595203_05g019520.1 Cmu05g1952 1952
5 29348900 29349163 - CmPI595203_05g019530.1 Cmu05g1953 1953
5 29374662 29379424 + CmPI595203_05g019550.1 Cmu05g1955 1955
5 29386639 29391082 + CmPI595203_05g019580.1 Cmu05g1958 1958
4 13579295 13582199 - Conep04aG0197200.1 Cone4ag1910 1910
4 13583060 13586347 - Conep04aG0197300.1 Cone4ag1911 1911
4 13590212 13590914 + Conep04aG0197400.1 Cone4ag1912 1912
7 11888272 11891941 - Conep07aG0187900.1 Cone7ag1824 1824
7 11892211 11896515 - Conep07aG0188000.1 Cone7ag1825 1825
17 9401028 9405374 - Conep17aG0137200.1 Cone17ag1339 1339
17 9406812 9408700 + Conep17aG0137300.1 Cone17ag1340 1340
17 9409256 9411196 - Conep17aG0137400.1 Cone17ag1341 1341
17 9414274 9418005 + Conep17aG0137500.1 Cone17ag1342 1342
17 9421300 9421569 + Conep17aG0137600.1 Cone17ag1343 1343
17 9423162 9426115 + Conep17aG0137700.1 Cone17ag1344 1344
20 624593 624922 - Conep20aG0014600.1 Cone20ag0138 138
20 626607 631137 - Conep20aG0014700.1 Cone20ag0139 139
20 632840 634430 + Conep20aG0014800.1 Cone20ag0140 140
20 634987 637055 - Conep20aG0014900.1 Cone20ag0141 141
2 616368 621091 - Cp4.1LG02g07480.1 Cpe02g00125 125
2 623182 624172 - Cp4.1LG02g07430.1 Cpe02g00126 126
2 628788 632653 + Cp4.1LG02g07630.1 Cpe02g00127 127
2 633236 637697 + Cp4.1LG02g07650.1 Cpe02g00128 128
2 638098 642784 + Cp4.1LG02g07620.1 Cpe02g00129 129
6 545594 549893 - Cp4.1LG06g01140.1 Cpe06g00111 111
6 550395 550658 - Cp4.1LG06g01170.1 Cpe06g00112 112
6 554903 559531 + Cp4.1LG06g01050.1 Cpe06g00113 113
7 2726593 2733494 + Cp4.1LG07g04130.1 Cpe07g00424 424
11 1088907 1094309 + Cp4.1LG11g02020.1 Cpe11g00201 201
5 32654637 32658872 - CrPI670011_05g020730.1 Cre05g2073 2073
5 32660775 32661038 - CrPI670011_05g020740.1 Cre05g2074 2074
5 32680713 32691615 + CrPI670011_05g020750.1 Cre05g2075 2075
5 32698748 32703195 + CrPI670011_05g020770.1 Cre05g2077 2077
8 27431990 27438232 + CrPI670011_08g014510.1 Cre08g1451 1451
2 18841866 18848329 - CsaV3_2G028720.1 Csa02g02053 2053
3 36868813 36874405 - CsaV3_3G045110.1 Csa03g04205 4205
3 36879382 36883004 - CsaV3_3G045130.1 Csa03g04207 4207
3 36884395 36888476 - CsaV3_3G045140.1 Csa03g04208 4208
3 36908217 36909530 + CsaV3_3G045170.1 Csa03g04211 4211
3 36915581 36921216 + CsaV3_3G045180.1 Csa03g04212 4212
2 4917605 4918084 + Hsped.02g04930.1 Hepe02g0493 493
10 7991361 7997468 - Hsped.10g06360.1 Hepe10g0636 636
13 38883049 38885671 + Maker00033710 Lcy13g1988 1988
4 24056103 24061318 - Lsi04G016600.1 Lsi04g01660 1660
4 24066683 24071892 - Lsi04G016640.1 Lsi04g01664 1664
4 24073582 24079123 - Lsi04G016650.1 Lsi04g01665 1665
4 24095584 24100837 + Lsi04G016660.1 Lsi04g01666 1666
4 24101393 24105796 + Lsi04G016670.1 Lsi04g01667 1667
8 22225637 22232187 + Lsi08G013950.1 Lsi08g01395 1395
5 35616637 35633428 + Sed0022574.1 Sed05g2314 2314
2 7744565 7746255 + Tan0016071.1 Tan02g0788 788
18 10663449 10663542 + Vvi18g940 Vvi18g940 940
18 10663602 10668547 - Vvi18g941 Vvi18g941 941
18 10669999 10675930 - Vvi18g942 Vvi18g942 942
18 10677980 10681418 + Vvi18g943 Vvi18g943 943
18 10682032 10684613 - Vvi18g944 Vvi18g944 944
18 10686780 10698400 + Vvi18g945 Vvi18g945 945
18 10698777 10701640 + Vvi18g946 Vvi18g946 946
18 10701652 10708870 - Vvi18g947 Vvi18g947 947
18 10722457 10723347 + Vvi18g948 Vvi18g948 948
18 10724332 10746287 + Vvi18g949 Vvi18g949 949
       

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