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
Vvi2g192 Blo02g01164 Blo03g00262 Bda06g00166 . Bpe05g00709 Bpe07g00056 . . . Cmo16g00576 Cma02g00918 . . . . Cpe14g00446 . . . . . . . . Cla07g01079 Cam07g1421 Cec07g1235 Cco07g1215 Clacu07g1140 Cmu07g1122 Cre07g1499 . . Cone6ag0871 Cone9ag0877 . . . Cme07g01522 . . . . . . . Bma12g00622 . Cmo02g00925 . . Cma16g00527 . . . . . . . . . . . . . . . . . . . Csa04g00685 Chy07g01124 .
Vvi2g193 . Blo03g00263 . Bda08g00450 Bpe05g00710 . . . . Cmo16g00575 . . . . . Cpe14g00445 . . . . . . . . Cla07g01078 Cam07g1422 Cec07g1234 Cco07g1213 Clacu07g1138 Cmu07g1121 Cre07g1498 . . . . . . . Cme07g01520 . . . . . . Bma05g00892 Bma12g00623 . . . . Cma16g00526 . . . . . . . . . . . . . . . . . . . Csa04g00686 Chy07g01123 .
Vvi2g194 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g195 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g196 . . . . . . . . . . . . . . . . . . . . . . . . Cla07g01060 Cam07g1440 Cec07g1214 Cco07g1192 Clacu07g1117 Cmu07g1100 Cre07g1477 . . . . . . . Cme07g01472 . . . . . . . . . . . . Cma16g00510 . . . . . . . . . . . . . . . . . . . Csa04g00708 Chy07g01103 .
Vvi2g197 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g198 . . . . . Bpe07g00256 . . . . Cma02g00916 . Car02g00667 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma12g00262 . Cmo02g00923 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g199 . . . . . . . . . . Cma02g00915 . Car02g00666 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo02g00922 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g200 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo19g00150 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g201 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 2367065 2367916 + Bda023368.1 Bda06g00166 166
8 4630201 4632904 + Bda024900.1 Bda08g00450 450
2 43294558 43303542 - BLOR10894 Blo02g01164 1164
3 5496179 5497854 - BLOR11443 Blo03g00262 262
3 5505614 5507936 - BLOR11444 Blo03g00263 263
19 5793683 5810608 + BLOR09493 Blo19g00150 150
5 46717305 46720266 - Bma022010.2 Bma05g00892 892
12 3458273 3460820 + Bma007156.1 Bma12g00262 262
12 27473867 27474639 - Bma007798.1 Bma12g00622 622
12 27479182 27481674 - Bma007799.1 Bma12g00623 623
5 20656851 20658259 - Bpe018122.1 Bpe05g00709 709
5 20662245 20665189 - Bpe018123.1 Bpe05g00710 710
7 461057 461921 + Bpe020868.1 Bpe07g00056 56
7 1845753 1849214 + Bpe021068.1 Bpe07g00256 256
7 28769937 28773520 - CaPI482276_07g014210.1 Cam07g1421 1421
7 28793428 28796037 - CaPI482276_07g014220.1 Cam07g1422 1422
7 28971829 28979188 + CaPI482276_07g014400.1 Cam07g1440 1440
2 4978097 4983145 + Carg08557-RA Car02g00666 666
2 4983473 4987096 - Carg08556-RA Car02g00667 667
7 25785925 25793349 - CcPI632755_07g011920.1 Cco07g1192 1192
7 25974833 25977443 + CcPI632755_07g012130.1 Cco07g1213 1213
7 25999102 26002744 + CcPI632755_07g012150.1 Cco07g1215 1215
7 27639571 27646925 - CePI673135_07g012140.1 Cec07g1214 1214
7 27833259 27835882 + CePI673135_07g012340.1 Cec07g1234 1234
7 27860498 27864119 + CePI673135_07g012350.1 Cec07g1235 1235
7 15984448 15990638 - Chy7G139330.1 Chy07g01103 1103
7 16138781 16141416 + Chy7G139530.1 Chy07g01123 1123
7 16152794 16155562 + Chy7G139540.1 Chy07g01124 1124
7 25811615 25818972 - ClG42_07g0111700.10 Clacu07g1117 1117
7 26003658 26006272 + ClG42_07g0113800.10 Clacu07g1138 1138
7 26026510 26030095 + ClG42_07g0114000.10 Clacu07g1140 1140
7 27179744 27190625 - ClCG07G011170.1 Cla07g01060 1060
7 27382234 27385841 + ClCG07G011350.1 Cla07g01078 1078
7 27406201 27410032 + ClCG07G011360.1 Cla07g01079 1079
2 5453010 5458241 + CmaCh02G009150.1 Cma02g00915 915
2 5458204 5462977 - CmaCh02G009160.1 Cma02g00916 916
2 5470667 5472496 + CmaCh02G009180.1 Cma02g00918 918
16 2617685 2626621 - CmaCh16G005100.1 Cma16g00510 510
16 2682965 2687259 + CmaCh16G005260.1 Cma16g00526 526
16 2692213 2694637 + CmaCh16G005270.1 Cma16g00527 527
7 20497400 20504140 + MELO3C016213.2.1 Cme07g01472 1472
7 21039167 21042280 + MELO3C016258.2.1 Cme07g01520 1520
7 21061594 21064530 + MELO3C016259.2.1 Cme07g01522 1522
2 5668834 5674101 + CmoCh02G009220.1 Cmo02g00922 922
2 5674154 5678674 - CmoCh02G009230.1 Cmo02g00923 923
2 5688487 5690291 + CmoCh02G009250.1 Cmo02g00925 925
16 2778554 2782871 + CmoCh16G005750.1 Cmo16g00575 575
16 2788683 2790841 + CmoCh16G005760.1 Cmo16g00576 576
7 26059880 26067237 - CmPI595203_07g011000.1 Cmu07g1100 1100
7 26251947 26254561 + CmPI595203_07g011210.1 Cmu07g1121 1121
7 26274808 26278387 + CmPI595203_07g011220.1 Cmu07g1122 1122
6 4447022 4448316 - Conep06aG0089800.1 Cone6ag0871 871
9 4270127 4271153 - Conep09aG0089900.1 Cone9ag0877 877
14 2777314 2781734 + Cp4.1LG14g02730.1 Cpe14g00445 445
14 2788064 2791722 + Cp4.1LG14g02740.1 Cpe14g00446 446
7 29997099 30011466 - CrPI670011_07g014770.1 Cre07g1477 1477
7 30208368 30210987 + CrPI670011_07g014980.1 Cre07g1498 1498
7 30234163 30237877 + CrPI670011_07g014990.1 Cre07g1499 1499
4 4651459 4654910 - CsaV3_4G006850.1 Csa04g00685 685
4 4664633 4667762 - CsaV3_4G006860.1 Csa04g00686 686
4 4795128 4801821 + CsaV3_4G007080.1 Csa04g00708 708
2 1857988 1860568 - Vvi2g192 Vvi2g192 192
2 1865269 1872643 - Vvi2g193 Vvi2g193 193
2 1877334 1878365 - Vvi2g194 Vvi2g194 194
2 1882203 1882979 - Vvi2g195 Vvi2g195 195
2 1885293 1889123 - Vvi2g196 Vvi2g196 196
2 1895466 1900156 + Vvi2g197 Vvi2g197 197
2 1900756 1904873 + Vvi2g198 Vvi2g198 198
2 1905456 1914484 - Vvi2g199 Vvi2g199 199
2 1919316 1929177 - Vvi2g200 Vvi2g200 200
2 1935458 1939794 + Vvi2g201 Vvi2g201 201
       

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