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
Vvi1g1111 . . . . . . . . . . . . . . . . Cpe01g01874 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo04g02260 Cmo15g00906 Cma04g02161 Cma15g00871 Car04g02096 Car15g00818 . . Bhi12g01002 . . . . . . Cla01g00678 Cam01g0710 Cec01g0702 Cco01g0731 Clacu01g0696 Cmu01g0671 Cre09g1834 Lsi09g00735 Csa05g01313 Chy09g00455 Cme09g01261
Vvi1g1112 . . . . . Bpe10g00771 . Bma15g00251 Cmo04g01901 . . . . . Sed04g0545 . Cpe01g01586 Bhi07g01847 Tan04g0120 Cmetu10g0423 . Hepe10g1556 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma04g01801 . Car04g01814 . . . . . . . . . . . . . . . . . . . . .
Vvi1g1113 . Blo16g01181 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0713 . . . . . . . . . . . . Bma06g00586 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1114 . . . . . . . . Cmo04g01902 Cmo18g00713 . Cma18g00726 . Car18g00674 Sed06g1718 Cpe09g00563 Cpe01g01587 Bhi07g01850 Tan04g0116 Cmetu10g1236 Lac13g0100 Hepe10g1555 . . Cla05g02625 Cam05g2815 Cec05g2851 Cco05g2882 Clacu05g2819 Cmu05g2667 Cre05g2783 . . Cone8ag0714 . Lsi04g00640 . . . . Blo11g00999 . . . . . . . . . Cma04g01803 . Car04g01816 . . . . . . . . . . . . . . . . . . . . .
Vvi1g1115 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag1083 Cone19ag1071 . . . . . Cme10g00583 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1116 . . . . . Bpe10g00772 Bma14g01876 . . Cmo18g00712 . Cma18g00725 . Car18g00672 . Cpe09g00564 Cpe01g01588 Bhi07g01852 . . . . . . . . . . . . . . . . . Lsi04g00641 . . Cme10g00618 . . . . . . . . . . . . . Car04g01817 . . . . . . . . . . . . . . . . . . . . .
Vvi1g1117 . . . . . Bpe10g00773 . Bma15g00250 Cmo04g01903 Cmo18g00711 . Cma18g00724 . Car18g00670 . Cpe09g00565 Cpe01g01589 Bhi07g01853 . . . . . . Cla05g02627 . . . . . . . Cone19ag1094 . . Lsi04g00642 . . Cme10g00619 . . . . . . . . . . . Cma04g01805 . Car04g01818 . . . . . . . . . . . . . . . . . . . . .
Vvi1g1118 . . . . . . Bma14g01877 . . . . . . . . . Cpe01g01591 Bhi07g01857 . . . . . . Cla05g02628 Cam05g2819 Cec05g2854 Cco05g2887 Clacu05g2822 Cmu05g2670 Cre05g2787 Cone13ag1107 Cone19ag1095 Cone8ag0715 . Lsi04g00643 . . Cme10g00620 . . . . . . . . . . . Cma04g01807 . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1119 . Blo16g01182 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag1108 Cone19ag1096 Cone8ag0716 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1120 . . . . . . . Bma15g00249 . . . . . . . . . . . . . . . . . . . . . . . Cone13ag1109 Cone19ag1097 . . . . . . . . Bda07g01413 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 16988827 16991124 - Bda026622.1 Bda07g01413 1413
7 50273824 50279440 - XM_039036213.1 Bhi07g01847 1847
7 50355866 50363967 - XM_039036702.1 Bhi07g01850 1850
7 50365743 50367688 - XM_039037297.1 Bhi07g01852 1852
7 50370590 50376020 - XM_039036251.1 Bhi07g01853 1853
7 50494056 50497577 + XM_039037355.1 Bhi07g01857 1857
12 30559107 30563528 + XM_039050684.1 Bhi12g01002 1002
11 25067658 25073523 - BLOR03875 Blo11g00999 999
16 40347598 40353818 - BLOR21968 Blo16g01181 1181
16 40356446 40359618 + BLOR21969 Blo16g01182 1182
6 31295361 31297318 + Bma023512.1 Bma06g00586 586
14 40167770 40178010 - Bma012660.1 Bma14g01876 1876
14 40180133 40181387 + Bma012661.1 Bma14g01877 1877
15 2489923 2491665 + Bma013234.1 Bma15g00249 249
15 2494171 2498912 + Bma013235.1 Bma15g00250 250
15 2506244 2508994 + Bma013236.2 Bma15g00251 251
10 13921919 13924613 - Bpe003076.1 Bpe10g00771 771
10 13925929 13927766 - Bpe003077.1 Bpe10g00772 772
10 13929343 13933989 - Bpe003078.1 Bpe10g00773 773
1 7974085 7977710 + CaPI482276_01g007100.1 Cam01g0710 710
5 35246747 35251222 - CaPI482276_05g028150.1 Cam05g2815 2815
5 35278706 35281955 + CaPI482276_05g028190.1 Cam05g2819 2819
4 10523545 10528321 - Carg14291-RA Car04g01814 1814
4 10530597 10537825 - Carg14289-RA Car04g01816 1816
4 10540014 10542579 - Carg14288-RA Car04g01817 1817
4 10544724 10551251 - Carg14287-RA Car04g01818 1818
4 17103961 17107285 + Carg17703-RA Car04g02096 2096
15 4656766 4660061 - Carg01337-RA Car15g00818 818
18 7911490 7915212 + Carg21253-RA Car18g00670 670
18 7920554 7921703 + Carg21255-RA Car18g00672 672
18 7925238 7932354 + Carg21257-RA Car18g00674 674
1 7769595 7773292 + CcPI632755_01g007310.1 Cco01g0731 731
5 36406836 36411408 - CcPI632755_05g028820.1 Cco05g2882 2882
5 36436894 36438911 + CcPI632755_05g028870.1 Cco05g2887 2887
1 7840098 7843830 + CePI673135_01g007020.1 Cec01g0702 702
5 38721541 38737940 - CePI673135_05g028510.1 Cec05g2851 2851
5 38751665 38754545 + CePI673135_05g028540.1 Cec05g2854 2854
9 4040046 4042972 - Chy9G161710.1 Chy09g00455 455
1 7641746 7645371 + ClG42_01g0069600.10 Clacu01g0696 696
5 35471358 35475824 - ClG42_05g0281900.10 Clacu05g2819 2819
5 35501289 35504209 + ClG42_05g0282200.10 Clacu05g2822 2822
1 8047913 8052278 + ClCG01G006940.1 Cla01g00678 678
5 37443255 37463367 - ClCG05G026170.2 Cla05g02625 2625
5 37465029 37475105 - ClCG05G026200.2 Cla05g02627 2627
5 37476556 37478569 + ClCG05G026220.1 Cla05g02628 2628
4 9082342 9086935 - CmaCh04G018010.1 Cma04g01801 1801
4 9092997 9095079 - CmaCh04G018030.1 Cma04g01803 1803
4 9099762 9111196 - CmaCh04G018050.1 Cma04g01805 1805
4 9113831 9115039 + CmaCh04G018070.1 Cma04g01807 1807
4 15155856 15159231 + CmaCh04G021610.1 Cma04g02161 2161
15 4396373 4411778 - CmaCh15G008710.1 Cma15g00871 871
18 6549239 6556776 + CmaCh18G007240.1 Cma18g00724 724
18 6558630 6560651 + CmaCh18G007250.1 Cma18g00725 725
18 6563412 6574511 + CmaCh18G007260.1 Cma18g00726 726
9 17494761 17498564 - MELO3C005218.2.1 Cme09g01261 1261
10 3747539 3751313 - MELO3C011939.2.1 Cme10g00583 583
10 3941780 3944298 - MELO3C011907.2.1 Cme10g00618 618
10 3947099 3953235 + MELO3C011906.2.1 Cme10g00619 619
10 3955647 3957786 + MELO3C011905.2.1 Cme10g00620 620
10 17993725 17998756 + PI0000533.1 Cmetu10g0423 423
10 17983325 17990212 + PI0026234.1 Cmetu10g1236 1236
4 9684342 9691377 - CmoCh04G019010.1 Cmo04g01901 1901
4 9691913 9698393 - CmoCh04G019020.1 Cmo04g01902 1902
4 9700720 9711690 - CmoCh04G019030.1 Cmo04g01903 1903
4 16895850 16899451 + CmoCh04G022600.1 Cmo04g02260 2260
15 4584076 4587431 - CmoCh15G009060.1 Cmo15g00906 906
18 8942293 8949847 + CmoCh18G007110.1 Cmo18g00711 711
18 8951379 8953965 + CmoCh18G007120.1 Cmo18g00712 712
18 8955919 8963199 + CmoCh18G007130.1 Cmo18g00713 713
1 7615105 7620209 + CmPI595203_01g006710.1 Cmu01g0671 671
5 35209649 35214115 - CmPI595203_05g026670.1 Cmu05g2667 2667
5 35239592 35242836 + CmPI595203_05g026700.1 Cmu05g2670 2670
8 7153202 7155881 - Conep08aG0073600.1 Cone8ag0713 713
8 7168428 7176752 - Conep08aG0073700.1 Cone8ag0714 714
8 7185843 7188652 - Conep08aG0073800.1 Cone8ag0715 715
8 7215291 7218834 + Conep08aG0073900.1 Cone8ag0716 716
13 8809752 8811939 - Conep13aG0111400.1 Cone13ag1083 1083
13 8910793 8912438 + Conep13aG0113900.1 Cone13ag1107 1107
13 8915265 8917358 + Conep13aG0114000.1 Cone13ag1108 1108
13 8917487 8919813 - Conep13aG0114100.1 Cone13ag1109 1109
19 7839857 7841781 - Conep19aG0110300.1 Cone19ag1071 1071
19 7940086 7944400 - Conep19aG0112800.1 Cone19ag1094 1094
19 7945802 7946879 + Conep19aG0112900.1 Cone19ag1095 1095
19 7950857 7953104 + Conep19aG0113000.1 Cone19ag1096 1096
19 7953234 7955327 - Conep19aG0113100.1 Cone19ag1097 1097
1 9689958 9697808 - Cp4.1LG01g15940.1 Cpe01g01586 1586
1 9698787 9707157 - Cp4.1LG01g15870.1 Cpe01g01587 1587
1 9709064 9711741 - Cp4.1LG01g15900.1 Cpe01g01588 1588
1 9713540 9720676 - Cp4.1LG01g15930.1 Cpe01g01589 1589
1 9724403 9727438 + Cp4.1LG01g15820.1 Cpe01g01591 1591
1 16081061 16089588 + Cp4.1LG01g18710.1 Cpe01g01874 1874
9 3884015 3893949 - Cp4.1LG09g06200.1 Cpe09g00563 563
9 3895568 3897737 - Cp4.1LG09g06220.1 Cpe09g00564 564
9 3899379 3907016 - Cp4.1LG09g06080.1 Cpe09g00565 565
5 38574241 38578839 - CrPI670011_05g027830.1 Cre05g2783 2783
5 38604228 38606884 + CrPI670011_05g027870.1 Cre05g2787 2787
9 36713347 36716966 - CrPI670011_09g018340.1 Cre09g1834 1834
5 13926275 13929197 + CsaV3_5G017360.1 Csa05g01313 1313
10 52274179 52282718 + Hsped.10g15550.1 Hepe10g1555 1555
10 52291260 52296657 + Hsped.10g15560.1 Hepe10g1556 1556
13 700668 707566 + Lag0039896.1 Lac13g0100 100
4 5869847 5885985 - Lsi04G006400.1 Lsi04g00640 640
4 5887730 5890457 - Lsi04G006410.1 Lsi04g00641 641
4 5893697 5899104 - Lsi04G006420.1 Lsi04g00642 642
4 5901527 5903519 + Lsi04G006430.1 Lsi04g00643 643
9 8475976 8480281 + Lsi09G007350.1 Lsi09g00735 735
4 4039284 4046755 + Sed0010682.1 Sed04g0545 545
6 41893999 41902896 - Sed0018065.2 Sed06g1718 1718
4 757533 765269 + Tan0013758.5 Tan04g0116 116
4 769086 773843 + Tan0012452.1 Tan04g0120 120
1 19129616 19145392 - Vvi1g1111 Vvi1g1111 1111
1 19145957 19153266 - Vvi1g1112 Vvi1g1112 1112
1 19156178 19163419 - Vvi1g1113 Vvi1g1113 1113
1 19163418 19172097 - Vvi1g1114 Vvi1g1114 1114
1 19178778 19180228 + Vvi1g1115 Vvi1g1115 1115
1 19181575 19184139 - Vvi1g1116 Vvi1g1116 1116
1 19185328 19190687 - Vvi1g1117 Vvi1g1117 1117
1 19198277 19200334 + Vvi1g1118 Vvi1g1118 1118
1 19206464 19214664 + Vvi1g1119 Vvi1g1119 1119
1 19214736 19218992 - Vvi1g1120 Vvi1g1120 1120
       

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