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
Vvi4g1012 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1013 . . . . . . Bma09g00087 . . . . . . . . . . . . . . . . . Cla01g01929 Cam01g2014 Cec04g1672 Cco04g1736 Clacu01g2035 Cmu01g1910 Cre04g1587 . Cone12ag0775 . . . . . . Blo05g00805 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g03263 . .
Vvi4g1014 . . . . . . . . . . . . . . . . Cpe10g00629 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1015 . . . . . . Bma09g00088 . . . . . . . . . . . . . . . . . Cla01g01930 Cam01g2015 . Cco04g1737 Clacu01g2036 Cmu01g1911 Cre04g1588 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g03264 . .
Vvi4g1016 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi01g00659 . . . Blo05g00806 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1017 . . . . . . . . . . . . . . . . . . . . . . . . Cla01g01931 Cam01g2016 Cec04g1674 Cco04g1738 Clacu01g2037 Cmu01g1912 Cre04g1589 . . . . . . . Cme08g00868 . . . . . . . . . Cmo03g00761 . . . . . . . . . . . . . . . . . . . . . . Csa06g03265 Chy02g00627 .
Vvi4g1018 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1019 . . . . . . . . . . Cma03g00730 . . . . . . . . . . . . . . . . . . . . . . . . Lsi01g00658 . . Cme08g00869 Blo05g00807 . . . . . . . . Cmo03g00758 Cmo07g00472 . . . . . . . . . . . . . . . . . . . . . . Chy02g00625 .
Vvi4g1020 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme08g00870 . . . . . . . . . Cmo03g00757 . . . . . . . . . . . . . . . . . . . . . . Csa06g03266 Chy02g00624 .
Vvi4g1021 . . . . . . . . . . Cma03g00729 Cma07g00473 . . . . . . . . . . . . . . . . . . . . . . . Lsi01g00657 . . Cme08g00871 . . . . . Bpe06g00040 . . . Cmo03g00756 Cmo07g00471 . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 29442755 29443927 - BLOR15767 Blo05g00805 805
5 29457276 29461531 - BLOR15768 Blo05g00806 806
5 29566164 29567982 - BLOR15769 Blo05g00807 807
9 2305771 2307602 - Bma028778.1 Bma09g00087 87
9 2354875 2355857 - Bma028779.3 Bma09g00088 88
6 460823 462183 + Bpe019484.1 Bpe06g00040 40
1 33334622 33343009 - CaPI482276_01g020140.1 Cam01g2014 2014
1 33345885 33361636 - CaPI482276_01g020150.1 Cam01g2015 2015
1 33373946 33376787 + CaPI482276_01g020160.1 Cam01g2016 2016
4 32394027 32396418 - CcPI632755_04g017360.1 Cco04g1736 1736
4 32401128 32406731 - CcPI632755_04g017370.1 Cco04g1737 1737
4 32424916 32427709 + CcPI632755_04g017380.1 Cco04g1738 1738
4 35885502 35887728 - CePI673135_04g016720.1 Cec04g1672 1672
4 35900988 35903224 + CePI673135_04g016740.1 Cec04g1674 1674
2 3805480 3806977 - Chy2G028910.1 Chy02g00624 624
2 3824103 3825931 + Chy2G028920.1 Chy02g00625 625
2 3850338 3853123 + Chy2G028940.1 Chy02g00627 627
1 32185218 32201789 - ClG42_01g0203500.10 Clacu01g2035 2035
1 32210585 32213164 - ClG42_01g0203600.10 Clacu01g2036 2036
1 32226927 32229711 + ClG42_01g0203700.10 Clacu01g2037 2037
1 33967277 33969856 - ClCG01G019790.2 Cla01g01929 1929
1 33978693 33981239 - ClCG01G019800.2 Cla01g01930 1930
1 33997976 34000762 + ClCG01G019810.1 Cla01g01931 1931
3 5842990 5845158 - CmaCh03G007290.1 Cma03g00729 729
3 5846692 5848197 - CmaCh03G007300.1 Cma03g00730 730
7 2067016 2069228 - CmaCh07G004730.1 Cma07g00473 473
8 5701289 5703056 - MELO3C007846.2.1 Cme08g00868 868
8 5705296 5706983 - MELO3C007847.2.1 Cme08g00869 869
8 5714138 5715924 - MELO3C007848.2.1 Cme08g00870 870
8 5717275 5718823 - MELO3C007849.2.1 Cme08g00871 871
3 6340983 6343284 - CmoCh03G007560.1 Cmo03g00756 756
3 6347326 6348929 + CmoCh03G007570.1 Cmo03g00757 757
3 6350059 6351615 + CmoCh03G007580.1 Cmo03g00758 758
3 6357067 6359697 + CmoCh03G007610.1 Cmo03g00761 761
7 2154560 2156797 - CmoCh07G004710.1 Cmo07g00471 471
7 2158014 2160177 - CmoCh07G004720.1 Cmo07g00472 472
1 32533765 32541761 - CmPI595203_01g019100.1 Cmu01g1910 1910
1 32547785 32550348 - CmPI595203_01g019110.1 Cmu01g1911 1911
1 32564141 32566925 + CmPI595203_01g019120.1 Cmu01g1912 1912
12 7107189 7109383 - Conep12aG0079800.1 Cone12ag0775 775
10 3634408 3637699 + Cp4.1LG10g00700.1 Cpe10g00629 629
4 34389907 34392780 - CrPI670011_04g015870.1 Cre04g1587 1587
4 34406726 34408951 + CrPI670011_04g015880.1 Cre04g1588 1588
4 34411952 34412823 + CrPI670011_04g015890.1 Cre04g1589 1589
6 27459877 27461717 - CsaV3_6G046490.1 Csa06g03263 3263
6 27467723 27469134 - CsaV3_6G046500.1 Csa06g03264 3264
6 27470946 27472820 - CsaV3_6G046510.1 Csa06g03265 3265
6 27482065 27484009 + CsaV3_6G046520.1 Csa06g03266 3266
1 5292389 5295628 + Lsi01G006570.1 Lsi01g00657 657
1 5302785 5305123 + Lsi01G006580.1 Lsi01g00658 658
1 5306805 5309135 + Lsi01G006590.1 Lsi01g00659 659
4 18692506 18692990 + Vvi4g1012 Vvi4g1012 1012
4 18694253 18695869 + Vvi4g1013 Vvi4g1013 1013
4 18715798 18719071 + Vvi4g1014 Vvi4g1014 1014
4 18723062 18724798 - Vvi4g1015 Vvi4g1015 1015
4 18735668 18737405 - Vvi4g1016 Vvi4g1016 1016
4 18747648 18748758 - Vvi4g1017 Vvi4g1017 1017
4 18748768 18770419 - Vvi4g1018 Vvi4g1018 1018
4 18771261 18772949 - Vvi4g1019 Vvi4g1019 1019
4 18773455 18779766 - Vvi4g1020 Vvi4g1020 1020
4 18807502 18814040 - Vvi4g1021 Vvi4g1021 1021
       

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