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
Vvi18g100 Blo01g01634 Blo12g00855 . Bda03g00318 Bpe02g00311 Bpe04g00279 Bma04g00286 . . . . Cma09g00057 . . . Cpe06g00025 . . . . . . . . . . . . . . . Cone4ag2017 Cone7ag1933 . . Lsi04g01803 Csa04g02697 . . . . . . . . . . Sed01g2438 . Cmo09g00058 . . . Car09g00049 . . Bhi09g02894 Tan01g5102 Cmetu07g0710 . Hepe01g2337 Mch11g0535 . Cla11g01820 Cam11g1886 Cec11g1911 Cco11g1918 Clacu11g2050 Cmu11g1855 Cre11g2260 . . Chy07g00388 Cme07g00059
Vvi18g101 Blo01g01633 Blo12g00856 . Bda03g00317 Bpe02g00312 Bpe04g00278 Bma04g00285 Bma01g02407 . . Cma01g02010 Cma09g00059 Car01g01580 . . Cpe06g00026 . . . . . . . . . . . . . . . Cone4ag2016 Cone7ag1932 Cone17ag1450 Cone20ag0026 Lsi04g01802 Csa04g02696 . . . . Bda11g00968 . . . . . Sed08g2261 Cmo01g02068 Cmo09g00059 . . . Car09g00050 . Cpe02g00038 Bhi09g02896 Tan01g5100 Cmetu07g0611 . Hepe01g2336 . . Cla11g01819 Cam11g1885 Cec11g1910 Cco11g1917 Clacu11g2049 Cmu11g1854 Cre11g2259 . . Chy07g00387 Cme07g00060
Vvi18g102 . Blo12g00859 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g103 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone20ag0029 . . . . . . Bda08g01169 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g104 . . . . . . . . Cmo05g01003 . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1448 . . . . . . . Bda08g01170 . . . . . . . . . Cma05g00985 Car05g00865 . . . . . . . . . . . . . . . . . Lsi08g00546 . . .
Vvi18g105 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00965 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g106 Blo01g01631 . . Bda03g00315 Bpe02g00313 Bpe04g00277 Bma04g00284 Bma01g02405 Cmo04g02558 . Cma01g02009 Cma09g00061 . . . . . . . . . . . . . . . . . . . Cone4ag2014 Cone7ag1930 . . Lsi04g01800 Csa04g02694 . . . . . . . . . . . . . . . . . . Cpe02g00040 . . . . . . . . . . . . . . . . Chy07g00385 Cme07g00062
Vvi18g107 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car04g02351 . Cpe01g02112 . . . . . . . . . . . . . . . . . . .
Vvi18g108 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g109 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 2714716 2715270 - Bda016275.1 Bda03g00315 315
3 2725511 2726920 + Bda016277.1 Bda03g00317 317
3 2727695 2732339 - Bda016278.3 Bda03g00318 318
8 46723082 46726128 + Bda030114.1 Bda08g01169 1169
8 46726788 46729750 - Bda030115.1 Bda08g01170 1170
11 9419597 9421604 + Bda005727.1 Bda11g00965 965
11 9443956 9445602 + Bda005730.2 Bda11g00968 968
9 76085509 76092332 + XM_039040209.1 Bhi09g02894 2894
9 76092866 76095617 - XM_039040212.1 Bhi09g02896 2896
1 56166834 56168694 - BLOR01631 Blo01g01631 1631
1 56172604 56174282 + BLOR01633 Blo01g01633 1633
1 56174890 56179481 - BLOR01634 Blo01g01634 1634
12 26819523 26824654 + BLOR04874 Blo12g00855 855
12 26825146 26826745 - BLOR04875 Blo12g00856 856
12 26837437 26843603 + BLOR04878 Blo12g00859 859
1 81624185 81625927 - Bma003276.1 Bma01g02405 2405
1 81643545 81645198 + Bma003278.1 Bma01g02407 2407
4 2286686 2288693 - Bma018738.1 Bma04g00284 284
4 2292305 2293959 + Bma018739.1 Bma04g00285 285
4 2294487 2306011 - Bma018740.4 Bma04g00286 286
2 2046511 2055631 + Bpe008153.1 Bpe02g00311 311
2 2050767 2052410 - Bpe025072 Bpe02g00312 312
2 2058876 2060622 + Bpe008154.1 Bpe02g00313 313
4 1785490 1786044 - Bpe014983.1 Bpe04g00277 277
4 1789783 1791372 + Bpe014984.1 Bpe04g00278 278
4 1791905 1796472 - Bpe025596 Bpe04g00279 279
11 31397067 31399791 + CaPI482276_11g018850.1 Cam11g1885 1885
11 31400647 31406535 - CaPI482276_11g018860.1 Cam11g1886 1886
1 13101407 13104467 + Carg21375-RA Car01g01580 1580
4 18912948 18919018 - Carg15785-RA Car04g02351 2351
5 8475857 8481320 + Carg21874-RA Car05g00865 865
9 248228 254389 + Carg08632-RA Car09g00049 49
9 254424 256852 - Carg08633-RA Car09g00050 50
11 31863051 31865769 + CcPI632755_11g019170.1 Cco11g1917 1917
11 31866628 31872630 - CcPI632755_11g019180.1 Cco11g1918 1918
11 33316856 33319143 + CePI673135_11g019100.1 Cec11g1910 1910
11 33320377 33326258 - CePI673135_11g019110.1 Cec11g1911 1911
7 3083401 3085498 - Chy7G132150.1 Chy07g00385 385
7 3090437 3092271 + Chy7G132170.1 Chy07g00387 387
7 3093446 3099138 - Chy7G132180.1 Chy07g00388 388
11 31436278 31439004 + ClG42_11g0204900.10 Clacu11g2049 2049
11 31439849 31445708 - ClG42_11g0205000.10 Clacu11g2050 2050
11 31843990 31846789 + ClCG11G018690.2 Cla11g01819 1819
11 31847561 31853607 - ClCG11G018700.2 Cla11g01820 1820
1 12869153 12874682 - CmaCh01G020090.1 Cma01g02009 2009
1 12875109 12877672 + CmaCh01G020100.1 Cma01g02010 2010
5 7913362 7918771 + CmaCh05G009850.1 Cma05g00985 985
9 256517 261561 + CmaCh09G000570.1 Cma09g00057 57
9 262668 264809 - CmaCh09G000590.1 Cma09g00059 59
9 266302 276647 + CmaCh09G000610.1 Cma09g00061 61
7 380747 387057 + MELO3C017021.2.1 Cme07g00059 59
7 387498 389904 - MELO3C017020.2.1 Cme07g00060 60
7 398488 400616 + MELO3C017018.2.1 Cme07g00062 62
7 24398306 24400604 + PI0025859.1 Cmetu07g0611 611
7 24400965 24407901 - PI0014021.1 Cmetu07g0710 710
1 14420602 14423961 + CmoCh01G020680.1 Cmo01g02068 2068
4 18750637 18754714 + CmoCh04G025580.1 Cmo04g02558 2558
5 8067574 8072471 + CmoCh05G010030.1 Cmo05g01003 1003
9 262394 267408 + CmoCh09G000580.1 Cmo09g00058 58
9 267368 269851 - CmoCh09G000590.1 Cmo09g00059 59
11 30685940 30688664 + CmPI595203_11g018540.1 Cmu11g1854 1854
11 30689509 30695371 - CmPI595203_11g018550.1 Cmu11g1855 1855
4 14033877 14036069 - Conep04aG0207900.1 Cone4ag2014 2014
4 14038828 14040527 + Conep04aG0208100.1 Cone4ag2016 2016
4 14040790 14043385 - Conep04aG0208200.1 Cone4ag2017 2017
7 12325609 12327818 - Conep07aG0198800.1 Cone7ag1930 1930
7 12330741 12332364 + Conep07aG0199000.1 Cone7ag1932 1932
7 12332451 12338393 - Conep07aG0199100.1 Cone7ag1933 1933
17 9841924 9845094 - Conep17aG0148900.1 Cone17ag1448 1448
17 9848083 9849551 + Conep17aG0149100.1 Cone17ag1450 1450
20 159088 160746 - Conep20aG0002600.1 Cone20ag0026 26
20 168018 171215 - Conep20aG0002900.1 Cone20ag0029 29
1 17875864 17880726 + Cp4.1LG01g21090.1 Cpe01g02112 2112
2 205186 207687 - Cp4.1LG02g08340.1 Cpe02g00038 38
2 212430 213704 + Cp4.1LG02g08460.1 Cpe02g00040 40
6 129128 135853 + Cp4.1LG06g00200.1 Cpe06g00025 25
6 135001 139912 - Cp4.1LG06g00310.1 Cpe06g00026 26
11 34361655 34364374 + CrPI670011_11g022590.1 Cre11g2259 2259
11 34365227 34371214 - CrPI670011_11g022600.1 Cre11g2260 2260
4 26100793 26103303 - CsaV3_4G037200.1 Csa04g02694 2694
4 26107502 26109890 + CsaV3_4G037220.1 Csa04g02696 2696
4 26110424 26117223 - CsaV3_4G037230.1 Csa04g02697 2697
1 87902237 87904519 + Hsped.01g23360.1 Hepe01g2336 2336
1 87904996 87912206 - Hsped.01g23370.1 Hepe01g2337 2337
4 25219360 25225794 - Lsi04G018000.1 Lsi04g01800 1800
4 25232725 25235670 + Lsi04G018020.1 Lsi04g01802 1802
4 25236088 25243045 - Lsi04G018030.1 Lsi04g01803 1803
8 13595065 13596961 - Lsi08G005460.1 Lsi08g00546 546
11 3432881 3436261 - MC11g0436 Mch11g0535 535
1 18174194 18182275 + Sed0015221.1 Sed01g2438 2438
8 36228750 36231175 + Sed0001121.2 Sed08g2261 2261
1 116397473 116399935 + Tan0015626.1 Tan01g5100 5100
1 116400357 116408070 - Tan0022867.2 Tan01g5102 5102
18 937801 944696 + Vvi18g100 Vvi18g100 100
18 945270 948428 - Vvi18g101 Vvi18g101 101
18 949014 961356 - Vvi18g102 Vvi18g102 102
18 961810 966293 + Vvi18g103 Vvi18g103 103
18 978346 983075 - Vvi18g104 Vvi18g104 104
18 987294 992640 - Vvi18g105 Vvi18g105 105
18 993190 996439 - Vvi18g106 Vvi18g106 106
18 1007919 1011012 + Vvi18g107 Vvi18g107 107
18 1039269 1054180 - Vvi18g108 Vvi18g108 108
18 1054581 1057697 - Vvi18g109 Vvi18g109 109
       

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