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
Vvi4g1032 . . . . Bpe15g00323 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma20g00819 . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1033 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1034 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1035 . . . . . . . . . Cmo16g00690 . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy07g01258 . . . . . . . Bma03g00979 . . . . Cma16g00633 . . . . Cpe14g00540 . . . . . . . Cla07g00830 . . . . . . Lsi07g00239 . . .
Vvi4g1036 . . . Bda10g00147 . . . Bma15g00988 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy07g01259 . . . . . Bpe10g00128 . . . . . . . . . . . . . . . . . . . Cla07g00831 Cam07g0901 Cec07g0951 Cco07g0942 Clacu07g0874 Cmu07g0875 Cre07g1235 . Csa04g00544 . .
Vvi4g1037 . . Bda04g00038 Bda10g00148 . . Bma09g00090 Bma15g00987 . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0827 Cone12ag0778 . . . . . . Blo05g00809 Blo06g00144 . . Bpe10g00129 Bpe06g00038 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1038 . . . . Bpe15g00416 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1039 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1040 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1041 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 652270 655061 + Bda033560 Bda04g00038 38
10 4373927 4374418 + Bda006618.1 Bda10g00147 147
10 4375600 4378433 - Bda006619.1 Bda10g00148 148
5 29625984 29628808 - BLOR15771 Blo05g00809 809
6 5634611 5637630 - BLOR16727 Blo06g00144 144
3 10415463 10417019 + Bma017319.1 Bma03g00979 979
9 2428857 2431707 - Bma028781.1 Bma09g00090 90
15 38329103 38331936 + Bma014267.1 Bma15g00987 987
15 38332972 38333438 - Bma030839 Bma15g00988 988
6 440514 443293 + Bpe019482.1 Bpe06g00038 38
10 2405197 2405688 + Bpe002431.1 Bpe10g00128 128
10 2406843 2409680 - Bpe024644 Bpe10g00129 129
15 14770096 14772216 - Bpe024558 Bpe15g00323 323
15 15670568 15681470 + Bpe001354.3 Bpe15g00416 416
7 22094889 22097004 + CaPI482276_07g009010.1 Cam07g0901 901
7 21574720 21576839 + CcPI632755_07g009420.1 Cco07g0942 942
7 23388637 23389991 + CePI673135_07g009510.1 Cec07g0951 951
7 17283472 17285424 - Chy7G140880.1 Chy07g01258 1258
7 17297656 17298977 + Chy7G140890.1 Chy07g01259 1259
7 21825342 21826654 + ClG42_07g0087400.10 Clacu07g0874 874
7 22974479 22979594 - ClCG07G008710.1 Cla07g00830 830
7 22998880 23000866 + ClCG07G008720.1 Cla07g00831 831
16 3265872 3267824 - CmaCh16G006330.1 Cma16g00633 633
20 3876090 3878486 - CmaCh20G008190.1 Cma20g00819 819
16 3412918 3414870 - CmoCh16G006900.1 Cmo16g00690 690
7 22046364 22048487 + CmPI595203_07g008750.1 Cmu07g0875 875
8 8247239 8250369 + Conep08aG0085300.1 Cone8ag0827 827
12 7124452 7128726 + Conep12aG0080100.1 Cone12ag0778 778
14 3403281 3407259 - Cp4.1LG14g01760.1 Cpe14g00540 540
7 25834377 25836522 + CrPI670011_07g012350.1 Cre07g1235 1235
4 3621333 3624265 - CsaV3_4G005440.1 Csa04g00544 544
7 2644023 2645975 + Lsi07G002390.1 Lsi07g00239 239
4 19007045 19009917 - Vvi4g1032 Vvi4g1032 1032
4 19011765 19024677 - Vvi4g1033 Vvi4g1033 1033
4 19034477 19035506 + Vvi4g1034 Vvi4g1034 1034
4 19037258 19039810 - Vvi4g1035 Vvi4g1035 1035
4 19040069 19040849 + Vvi4g1036 Vvi4g1036 1036
4 19042211 19049128 - Vvi4g1037 Vvi4g1037 1037
4 19062451 19064462 + Vvi4g1038 Vvi4g1038 1038
4 19065536 19067983 + Vvi4g1039 Vvi4g1039 1039
4 19069128 19069734 + Vvi4g1040 Vvi4g1040 1040
4 19071627 19073234 + Vvi4g1041 Vvi4g1041 1041
       

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