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
Vvi1g681 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g682 . . . . . Bpe10g00840 . Bma15g00183 . Cmo18g00799 . Cma18g00795 . Car18g00725 Sed06g1642 Cpe09g00507 . Bhi07g01735 Tan04g1243 Cmetu10g1390 Lac13g0196 Hepe10g1636 . . Cla05g02546 Cam05g2736 Cec05g2767 Cco05g2807 Clacu05g2737 Cmu05g2590 Cre05g2704 Cone13ag1046 Cone19ag1035 . . Lsi04g00555 Csa05g02333 Chy10g00901 Cme10g00527 Blo06g00879 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g683 . . . Bda11g01268 Bpe13g01465 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01268 . . . Bma06g00619 . . . . Cma05g00013 . Car05g00012 . . . . . . . . . . . . . . . . . . . .
Vvi1g684 . . . . . . . . . Cmo18g00800 . Cma18g00796 . Car18g00727 Sed06g1641 Cpe09g00506 . Bhi07g01734 Tan04g1242 Cmetu10g1660 Lac13g0197 Hepe10g1637 . . Cla05g02545 Cam05g2735 Cec05g2766 Cco05g2806 Clacu05g2736 Cmu05g2589 Cre05g2703 . . . . Lsi04g00554 Csa05g02334 Chy10g00902 Cme10g00526 Blo06g00878 . Bda07g01607 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g685 Blo01g00394 Blo16g01159 Bda01g02220 Bda11g01267 Bpe13g00497 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0666 . . . . . . . . Bda11g01267 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g686 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma01g00047 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g687 Blo01g00395 . Bda01g02221 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g688 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g689 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g690 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 58039643 58041068 - Bda004560.1 Bda01g02220 2220
1 58042241 58044267 - Bda004561.1 Bda01g02221 2221
7 29756123 29760368 - Bda028475.2 Bda07g01607 1607
11 13312244 13314798 + Bda007785.1 Bda11g01267 1267
11 13317521 13319212 + Bda007786.1 Bda11g01268 1268
7 47832254 47835792 - XM_039037304.1 Bhi07g01734 1734
7 47884833 47888543 - XM_039035567.1 Bhi07g01735 1735
1 4472821 4474274 - BLOR00394 Blo01g00394 394
1 4475468 4477499 - BLOR00395 Blo01g00395 395
6 32063654 32068063 - BLOR17461 Blo06g00878 878
6 32070508 32071749 - BLOR17462 Blo06g00879 879
16 40120854 40127694 + BLOR21946 Blo16g01159 1159
1 525956 527977 - Bma000215.1 Bma01g00047 47
6 32797643 32802661 - Bma031288 Bma06g00619 619
15 1913374 1919148 + Bma013165.1 Bma15g00183 183
10 14369352 14370500 - Bpe003146.1 Bpe10g00840 840
13 12377074 12378716 + Bpe010208.1 Bpe13g00497 497
13 19933275 19936925 + Bpe011130.1 Bpe13g01465 1465
5 34637850 34641530 - CaPI482276_05g027350.1 Cam05g2735 2735
5 34643966 34646803 - CaPI482276_05g027360.1 Cam05g2736 2736
5 55641 60540 + Carg21812-RA Car05g00012 12
18 8414949 8417684 + Carg14473-RA Car18g00725 725
18 8422059 8423269 + Carg14471-RA Car18g00727 727
5 35781025 35784703 - CcPI632755_05g028060.1 Cco05g2806 2806
5 35786254 35789018 - CcPI632755_05g028070.1 Cco05g2807 2807
5 38095088 38098766 - CePI673135_05g027660.1 Cec05g2766 2766
5 38101170 38104069 - CePI673135_05g027670.1 Cec05g2767 2767
10 14724608 14726336 + Chy10G180950.1 Chy10g00901 901
10 14727631 14730721 + Chy10G180960.1 Chy10g00902 902
5 34845853 34849440 - ClG42_05g0273600.10 Clacu05g2736 2736
5 34851820 34854549 - ClG42_05g0273700.10 Clacu05g2737 2737
5 36782336 36785918 - ClCG05G025380.2 Cla05g02545 2545
5 36788280 36791006 - ClCG05G025390.1 Cla05g02546 2546
5 50792 60541 + CmaCh05G000130.1 Cma05g00013 13
18 7006459 7009419 + CmaCh18G007950.1 Cma18g00795 795
18 7010953 7014093 + CmaCh18G007960.1 Cma18g00796 796
10 3382556 3386113 - MELO3C011992.2.1 Cme10g00526 526
10 3387067 3389183 - MELO3C011991.2.1 Cme10g00527 527
10 18621621 18623975 + PI0026616.1 Cmetu10g1390 1390
10 18624925 18628658 + PI0007084.1 Cmetu10g1660 1660
18 9468869 9472138 + CmoCh18G007990.1 Cmo18g00799 799
18 9473278 9477709 + CmoCh18G008000.1 Cmo18g00800 800
5 34583854 34587441 - CmPI595203_05g025890.1 Cmu05g2589 2589
5 34589813 34592549 - CmPI595203_05g025900.1 Cmu05g2590 2590
8 6673268 6677136 + Conep08aG0068900.1 Cone8ag0666 666
13 8626705 8628551 - Conep13aG0107700.1 Cone13ag1046 1046
19 7684179 7686065 - Conep19aG0106700.1 Cone19ag1035 1035
9 3360173 3365063 - Cp4.1LG09g05020.1 Cpe09g00506 506
9 3368001 3371248 - Cp4.1LG09g05290.1 Cpe09g00507 507
5 37945043 37948716 - CrPI670011_05g027030.1 Cre05g2703 2703
5 37951065 37953981 - CrPI670011_05g027040.1 Cre05g2704 2704
5 25717905 25719904 + CsaV3_5G031520.1 Csa05g02333 2333
5 25720349 25724149 + CsaV3_5G031530.1 Csa05g02334 2334
10 53073981 53077945 + Hsped.10g16360.1 Hepe10g1636 1636
10 53083199 53086656 + Hsped.10g16370.1 Hepe10g1637 1637
13 1368633 1371842 + Lag0039992.1 Lac13g0196 196
13 1373579 1378317 + Lag0039993.1 Lac13g0197 197
4 5060153 5063875 - Lsi04G005540.1 Lsi04g00554 554
4 5071861 5076297 - Lsi04G005550.1 Lsi04g00555 555
6 41177166 41182340 - Sed0009202.1 Sed06g1641 1641
6 41184516 41189851 - Sed0024287.1 Sed06g1642 1642
4 11769324 11772866 - Tan0009114.2 Tan04g1242 1242
4 11779834 11783482 - Tan0006498.1 Tan04g1243 1243
1 7813880 7823597 + Vvi1g681 Vvi1g681 681
1 7835561 7837696 + Vvi1g682 Vvi1g682 682
1 7839045 7856993 - Vvi1g683 Vvi1g683 683
1 7860801 7871133 + Vvi1g684 Vvi1g684 684
1 7871320 7875921 - Vvi1g685 Vvi1g685 685
1 7893947 7896384 - Vvi1g686 Vvi1g686 686
1 7904819 7907581 - Vvi1g687 Vvi1g687 687
1 7930543 7932916 - Vvi1g688 Vvi1g688 688
1 7933691 7941206 + Vvi1g689 Vvi1g689 689
1 7941241 7941972 + Vvi1g690 Vvi1g690 690
       

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