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
Vvi18g180 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1240 Cone8ag1295 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g181 . . . . . . . . Cmo05g00324 . . . . . . . . . . . . . . . . . . . . . . . Cone7ag1908 Cone17ag1424 . . . . . . . Bda08g01191 . . . . . . . . . Cma05g00323 . . . . . . . . . . . Cla11g01561 Cam11g1626 Cec11g1652 Cco11g1651 Clacu11g1782 Cmu11g1598 Cre11g2016 . . . .
Vvi18g182 Blo01g01342 . Bda01g00702 . Bpe02g00603 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1423 . . . . Cme03g01528 . . Bda08g01192 . . Bpe05g00162 . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy03g01036 .
Vvi18g183 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g184 . . . . . . . . . . Cma01g01986 . Car01g01557 . . . . . . . . . . . . . . . . . . . . . . . . Chy04g00399 . . . Bda08g01193 . . . . . . Cmo01g02044 . . . . . . Cpe02g00059 . . . . . . . Cla05g01605 Cam05g1718 Cec05g1719 Cco05g1779 Clacu05g1707 Cmu05g1594 Cre05g1713 . . . .
Vvi18g185 Blo01g01314 Blo12g01115 Bda01g00684 . Bpe02g00621 Bpe04g00015 Bma04g00022 Bma01g02098 . Cmo15g00650 . . . . . . . Bhi04g01843 Tan11g1214 . . . . . Cla08g00646 Cam08g1070 Cec08g0655 Cco08g0766 Clacu08g0775 . Cre08g0583 Cone4ag1441 . Cone17ag0809 Cone20ag0414 . Csa04g01732 . Cme03g00439 . . . . . . . . . . . . . Car04g02322 Car15g00588 Cpe01g02087 Cpe02g00872 . . . . . . . . . . . . . . Lsi08g00505 . Chy03g00557 .
Vvi18g186 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g187 Blo01g01313 . Bda01g00683 . Bpe02g00622 . . Bma01g02097 Cmo04g02523 Cmo15g00651 . . . . Sed01g0943 . . Bhi04g01844 Tan11g1216 Cmetu09g0061 . Hepe02g2741 . Lcy10g1292 Cla08g00644 Cam08g1066 Cec08g0651 Cco08g0762 Clacu08g0772 . Cre08g0580 . . . Cone20ag0416 . . . Cme03g00440 . . . . . . . . . . . . . Car04g02320 Car15g00589 Cpe01g02086 . . . . . . . . . . . . . . . Lsi08g00503 . Chy03g00556 .
Vvi18g188 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g189 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 33986565 33987503 + Bda002719.1 Bda01g00683 683
1 33988040 33997310 - Bda002720.1 Bda01g00684 684
1 34309219 34310421 + Bda002740.1 Bda01g00702 702
8 48014944 48015784 + Bda030143.1 Bda08g01191 1191
8 48017113 48018495 + Bda030144.1 Bda08g01192 1192
8 48038839 48040108 - Bda030145.1 Bda08g01193 1193
4 45440757 45444956 + XM_039030417.1 Bhi04g01843 1843
4 45536726 45539598 - XM_039028307.1 Bhi04g01844 1844
1 50285556 50286750 + BLOR01313 Blo01g01313 1313
1 50287278 50297023 - BLOR01314 Blo01g01314 1314
1 51064764 51065917 + BLOR01342 Blo01g01342 1342
12 28802490 28805746 + BLOR05134 Blo12g01115 1115
1 77026045 77027190 + Bma002919.1 Bma01g02097 2097
1 77027712 77037287 - Bma002920.1 Bma01g02098 2098
4 275443 280004 - Bma018470.1 Bma04g00022 22
2 3923119 3924309 - Bpe008444.1 Bpe02g00603 603
2 4043353 4052428 + Bpe008462.1 Bpe02g00621 621
2 4052963 4053972 - Bpe008463.1 Bpe02g00622 622
4 164936 169228 - Bpe014742.1 Bpe04g00015 15
5 4751974 4755158 - Bpe017550.1 Bpe05g00162 162
5 25667786 25670277 - CaPI482276_05g017180.1 Cam05g1718 1718
8 17036671 17039029 + CaPI482276_08g010660.1 Cam08g1066 1066
8 17054585 17062431 - CaPI482276_08g010700.1 Cam08g1070 1070
11 29009882 29017256 - CaPI482276_11g016260.1 Cam11g1626 1626
1 13001709 13003868 + Carg17212-RA Car01g01557 1557
4 18730587 18733579 + Carg15754-RA Car04g02320 2320
4 18733567 18736994 - Carg15756-RA Car04g02322 2322
15 3249740 3255948 + Carg01567-RA Car15g00588 588
15 3255690 3258833 - Carg01566-RA Car15g00589 589
5 26444826 26447438 - CcPI632755_05g017790.1 Cco05g1779 1779
8 19439198 19441769 + CcPI632755_08g007620.1 Cco08g0762 762
8 19456410 19464320 - CcPI632755_08g007660.1 Cco08g0766 766
11 29376152 29386366 - CcPI632755_11g016510.1 Cco11g1651 1651
5 28724398 28726874 - CePI673135_05g017190.1 Cec05g1719 1719
8 18266524 18268929 + CePI673135_08g006510.1 Cec08g0651 651
8 18283238 18291108 - CePI673135_08g006550.1 Cec08g0655 655
11 30832818 30840521 - CePI673135_11g016520.1 Cec11g1652 1652
3 7930417 7932291 + Chy3G055360.1 Chy03g00556 556
3 7946180 7953461 - Chy3G055370.1 Chy03g00557 557
3 13880093 13881350 + Chy3G060160.1 Chy03g01036 1036
4 3533198 3535934 - Chy4G071170.1 Chy04g00399 399
5 25869105 25871600 - ClG42_05g0170700.10 Clacu05g1707 1707
8 17755685 17758039 + ClG42_08g0077200.10 Clacu08g0772 772
8 17774810 17782673 - ClG42_08g0077500.10 Clacu08g0775 775
11 29030665 29038076 - ClG42_11g0178200.10 Clacu11g1782 1782
5 27322767 27325390 - ClCG05G015500.1 Cla05g01605 1605
8 18604013 18606708 + ClCG08G006210.1 Cla08g00644 644
8 18628507 18636646 - ClCG08G006240.2 Cla08g00646 646
11 29331612 29335545 - ClCG11G016020.2 Cla11g01561 1561
1 12775567 12777637 + CmaCh01G019860.1 Cma01g01986 1986
5 1398559 1400784 + CmaCh05G003230.1 Cma05g00323 323
3 6142765 6146232 + MELO3C008434.2.1 Cme03g00439 439
3 6148908 6150305 - MELO3C008435.2.1 Cme03g00440 440
3 24448350 24449993 + MELO3C011348.2.1 Cme03g01528 1528
9 2482068 2485087 + PI0018442.1 Cmetu09g0061 61
1 14317207 14319394 + CmoCh01G020440.1 Cmo01g02044 2044
4 18562809 18565800 + CmoCh04G025230.1 Cmo04g02523 2523
5 1440978 1442632 + CmoCh05G003240.1 Cmo05g00324 324
15 3149603 3153742 + CmoCh15G006500.1 Cmo15g00650 650
15 3153493 3156807 - CmoCh15G006510.1 Cmo15g00651 651
5 25588395 25590890 - CmPI595203_05g015940.1 Cmu05g1594 1594
11 28284051 28291448 - CmPI595203_11g015980.1 Cmu11g1598 1598
4 11443508 11445968 - Conep04aG0149300.1 Cone4ag1441 1441
7 12234001 12234975 - Conep07aG0196500.1 Cone7ag1908 1908
8 10602721 10606021 - Conep08aG0133300.1 Cone8ag1295 1295
12 9590744 9593938 - Conep12aG0128000.1 Cone12ag1240 1240
17 6396646 6401653 + Conep17aG0082800.1 Cone17ag0809 809
17 9747372 9749374 - Conep17aG0146100.1 Cone17ag1423 1423
17 9750694 9751661 - Conep17aG0146200.1 Cone17ag1424 1424
20 2012290 2017329 + Conep20aG0042800.1 Cone20ag0414 414
20 2021276 2023273 - Conep20aG0043000.1 Cone20ag0416 416
1 17686070 17690323 + Cp4.1LG01g20770.1 Cpe01g02086 2086
1 17686384 17693598 - Cp4.1LG01g20870.1 Cpe01g02087 2087
2 305614 307911 - Cp4.1LG02g08130.1 Cpe02g00059 59
2 5861472 5872071 - Cp4.1LG02g00010.1 Cpe02g00872 872
5 28837171 28839672 - CrPI670011_05g017130.1 Cre05g1713 1713
8 18680399 18682800 + CrPI670011_08g005800.1 Cre08g0580 580
8 18710741 18718650 - CrPI670011_08g005830.1 Cre08g0583 583
11 31933258 31943463 - CrPI670011_11g020160.1 Cre11g2016 2016
4 16812660 16833155 - CsaV3_4G027580.1 Csa04g01732 1732
2 75916013 75921251 + Hsped.02g27410.1 Hepe02g2741 2741
10 35799453 35802873 + Maker00008858 Lcy10g1292 1292
8 12943910 12946193 + Lsi08G005030.1 Lsi08g00503 503
8 12963820 12968069 - Lsi08G005050.1 Lsi08g00505 505
1 6990892 6993790 + Sed0005591.1 Sed01g0943 943
11 10074709 10079263 + Tan0012575.2 Tan11g1214 1214
11 10084924 10087004 - Tan0003189.1 Tan11g1216 1216
18 1772216 1777433 + Vvi18g180 Vvi18g180 180
18 1778794 1780353 + Vvi18g181 Vvi18g181 181
18 1781658 1782994 + Vvi18g182 Vvi18g182 182
18 1783158 1783284 + Vvi18g183 Vvi18g183 183
18 1784959 1786659 - Vvi18g184 Vvi18g184 184
18 1791336 1803062 + Vvi18g185 Vvi18g185 185
18 1806149 1811109 - Vvi18g186 Vvi18g186 186
18 1811108 1814383 - Vvi18g187 Vvi18g187 187
18 1814393 1815552 + Vvi18g188 Vvi18g188 188
18 1818067 1820567 - Vvi18g189 Vvi18g189 189
       

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