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
Vvi3g666 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g667 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g668 Blo02g00939 Blo03g00081 . . Bpe07g00266 . . Bma12g00272 . Cmo11g01405 . . . . . Cpe04g00313 Cpe15g00452 . . . . . . . . . . . . . . Cone12ag1057 Cone8ag1091 . . . Csa07g00700 . Cme01g00106 . . . . . Bpe05g00483 . . . . . Cma11g01711 Cma19g00564 Car11g01130 Car19g00424 . . . . . . . . . . . . . . . . . . Chy01g00116 .
Vvi3g669 . . . . . . . . . Cmo11g01407 . . . . . Cpe04g00316 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma11g01710 . Car11g01132 . . . . . . . . . . . . . . . . . . . . .
Vvi3g670 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g671 . . . . . . . . . . . . . . . . . . . . . . . . Cla10g01009 Cam10g1032 Cec10g1063 Cco10g1027 Clacu10g1049 Cmu10g1833 Cre10g1205 . . . . . . . . . . . . . Bpe05g00482 . . Sed07g1273 Cmo04g00493 . . . . . . Cpe01g00413 Bhi11g01166 Tan01g0656 Cmetu07g2110 . Hepe07g0429 Mch10g0459 . . . . . . . . . . . .
Vvi3g672 . Blo03g00080 Bda06g01210 . Bpe07g00267 . . . Cmo19g00576 Cmo11g01409 . . . . . Cpe04g00317 . . . . . . . . Cla02g00668 Cam02g0702 Cec02g0716 Cco02g0737 Clacu02g0710 Cmu02g0705 Cre02g1020 Cone12ag1055 Cone8ag1089 Cone3ag1016 Cone10ag1033 Lsi03g00563 Csa07g00698 . Cme01g00108 . . . . . . . . . . . Cma11g01709 Cma19g00562 Car11g01133 Car19g00422 . . . . . . . . . . . . . . . . . . Chy01g00118 .
Vvi3g673 . . . . . . . . . Cmo11g01410 . . . . . Cpe04g00318 . . . . . . . . Cla02g00669 Cam02g0703 Cec02g0717 Cco02g0738 Clacu02g0711 Cmu02g0706 Cre02g1021 Cone12ag1054 . Cone3ag1017 Cone10ag1034 Lsi03g00564 Csa07g00697 . Cme01g00109 . . . . . . . . . . . Cma11g01708 . . . . . . . . . . . . . . . . . . . . . Chy01g00119 .
Vvi3g674 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g675 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 41936737 41938687 + Bda023029.1 Bda06g01210 1210
11 33974840 34001315 + XM_039047768.1 Bhi11g01166 1166
2 36379938 36393783 - BLOR10669 Blo02g00939 939
3 2712736 2714705 + BLOR11261 Blo03g00080 80
3 2715316 2717262 - BLOR11262 Blo03g00081 81
12 3645338 3646626 + Bma007168.1 Bma12g00272 272
5 19080140 19080714 + Bpe017902.1 Bpe05g00482 482
5 19081103 19081682 - Bpe017903.1 Bpe05g00483 483
7 1919505 1920799 + Bpe021078.1 Bpe07g00266 266
7 1927347 1929292 - Bpe026046 Bpe07g00267 267
2 8315160 8317257 - CaPI482276_02g007020.1 Cam02g0702 702
2 8325466 8327481 - CaPI482276_02g007030.1 Cam02g0703 703
10 22735038 22737097 + CaPI482276_10g010320.1 Cam10g1032 1032
11 9034407 9036796 + Carg26995-RA Car11g01130 1130
11 9037852 9038952 + Carg26997-RA Car11g01132 1132
11 9040311 9042214 - Carg26998-RA Car11g01133 1133
19 6051801 6054925 + Carg16344-RA Car19g00422 422
19 6060058 6061705 - Carg16346-RA Car19g00424 424
2 7610993 7613090 - CcPI632755_02g007370.1 Cco02g0737 737
2 7621212 7623205 - CcPI632755_02g007380.1 Cco02g0738 738
10 21948379 21951383 + CcPI632755_10g010270.1 Cco10g1027 1027
2 7509883 7511983 - CePI673135_02g007160.1 Cec02g0716 716
2 7520178 7522186 - CePI673135_02g007170.1 Cec02g0717 717
10 23637957 23640014 + CePI673135_10g010630.1 Cec10g1063 1063
1 755014 756626 + Chy1G001160.1 Chy01g00116 116
1 763429 765441 - Chy1G001180.1 Chy01g00118 118
1 770251 772400 - Chy1G001190.1 Chy01g00119 119
2 7326003 7328101 - ClG42_02g0071000.10 Clacu02g0710 710
2 7336144 7338149 - ClG42_02g0071100.10 Clacu02g0711 711
10 22378864 22381845 + ClG42_10g0104900.10 Clacu10g1049 1049
2 7668762 7671185 - ClCG02G006660.1 Cla02g00668 668
2 7678802 7681288 - ClCG02G006670.1 Cla02g00669 669
10 23412997 23416023 + ClCG10G010580.2 Cla10g01009 1009
11 11309826 11312318 + CmaCh11G017080.1 Cma11g01708 1708
11 11316431 11318485 + CmaCh11G017090.1 Cma11g01709 1709
11 11319149 11321669 - CmaCh11G017100.1 Cma11g01710 1710
11 11321973 11324120 - CmaCh11G017110.1 Cma11g01711 1711
19 6383319 6386345 + CmaCh19G005620.1 Cma19g00562 562
19 6390924 6393241 - CmaCh19G005640.1 Cma19g00564 564
1 737095 739155 + MELO3C018505.2.1 Cme01g00106 106
1 745087 747635 - MELO3C018507.2.1 Cme01g00108 108
1 751367 753887 - MELO3C018508.2.1 Cme01g00109 109
7 536505 538875 + PI0022152.1 Cmetu07g2110 2110
4 2454995 2457348 + CmoCh04G004930.1 Cmo04g00493 493
11 9890467 9893881 + CmoCh11G014050.1 Cmo11g01405 1405
11 9895617 9896645 + CmoCh11G014070.1 Cmo11g01407 1407
11 9897645 9899584 - CmoCh11G014090.1 Cmo11g01409 1409
11 9904024 9906584 - CmoCh11G014100.1 Cmo11g01410 1410
19 6559825 6563424 + CmoCh19G005760.1 Cmo19g00576 576
2 7231205 7233303 - CmPI595203_02g007050.1 Cmu02g0705 705
2 7241363 7243368 - CmPI595203_02g007060.1 Cmu02g0706 706
10 22993633 22995721 + CmPI595203_10g018330.1 Cmu10g1833 1833
3 28992709 28995153 - Conep03aG0151500.1 Cone3ag1016 1016
3 28996159 28996918 - Conep03aG0151600.1 Cone3ag1017 1017
8 9794240 9797381 + Conep08aG0112000.1 Cone8ag1089 1089
8 9800589 9802140 - Conep08aG0112200.1 Cone8ag1091 1091
10 7202376 7205362 - Conep10aG0106000.1 Cone10ag1033 1033
10 7206922 7208977 - Conep10aG0106100.1 Cone10ag1034 1034
12 8755420 8756895 + Conep12aG0108800.1 Cone12ag1054 1054
12 8757750 8760212 + Conep12aG0108900.1 Cone12ag1055 1055
12 8763736 8765335 - Conep12aG0109100.1 Cone12ag1057 1057
1 2384511 2388047 + Cp4.1LG01g02610.1 Cpe01g00413 413
4 3917138 3919709 + Cp4.1LG04g07720.1 Cpe04g00313 313
4 3921315 3922256 + Cp4.1LG04g07730.1 Cpe04g00316 316
4 3923949 3925007 - Cp4.1LG04g07670.1 Cpe04g00317 317
4 3929986 3932512 - Cp4.1LG04g07640.1 Cpe04g00318 318
15 5612241 5614534 - Cp4.1LG15g04530.1 Cpe15g00452 452
2 7854427 7856531 - CrPI670011_02g010200.1 Cre02g1020 1020
2 7864777 7866794 - CrPI670011_02g010210.1 Cre02g1021 1021
10 24692986 24695046 + CrPI670011_10g012050.1 Cre10g1205 1205
7 4987024 4989843 + CsaV3_7G007960.1 Csa07g00697 697
7 4993281 4996177 + CsaV3_7G007970.1 Csa07g00698 698
7 5001905 5003954 - CsaV3_7G007990.1 Csa07g00700 700
7 4429343 4433189 + Hsped.07g04290.1 Hepe07g0429 429
3 6806984 6809623 - Lsi03G005630.1 Lsi03g00563 563
3 6818230 6821081 - Lsi03G005640.1 Lsi03g00564 564
10 2989466 2990799 + MC10g0375 Mch10g0459 459
7 9562756 9567279 + Sed0024111.2 Sed07g1273 1273
1 6217075 6220705 + Tan0003926.2 Tan01g0656 656
3 6775423 6776620 - Vvi3g666 Vvi3g666 666
3 6785296 6787059 - Vvi3g667 Vvi3g667 667
3 6798198 6802367 + Vvi3g668 Vvi3g668 668
3 6804576 6807417 + Vvi3g669 Vvi3g669 669
3 6811802 6813183 + Vvi3g670 Vvi3g670 670
3 6815260 6818599 - Vvi3g671 Vvi3g671 671
3 6846057 6849868 - Vvi3g672 Vvi3g672 672
3 6851537 6855077 - Vvi3g673 Vvi3g673 673
3 6859780 6860409 - Vvi3g674 Vvi3g674 674
3 6871680 6872380 - Vvi3g675 Vvi3g675 675
       

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