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
Vvi19g1104 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1105 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1106 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1107 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1108 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1109 . . . . Bpe07g00465 . . . . . . . . . Sed04g3507 . . Bhi05g02013 Tan02g0055 Cmetu01g1246 Lac12g0052 Hepe02g0024 . . . . . . . . . . . . . . Csa07g01193 . . Blo15g00617 . . . . . . Bma12g00588 . . . . . . . Cpe15g00894 . . . . . . . . . . . . . . . . . Chy01g00870 Cme01g01521
Vvi19g1110 Blo04g00471 . . . Bpe07g00466 . . . . . . . . . Sed05g1845 Cpe04g00860 Cpe16g00715 Bhi05g02012 Tan02g0054 Cmetu01g1126 Lac12g0051 Hepe02g0023 . . Cla02g01820 Cam02g1928 Cec02g1953 Cco02g1994 Clacu02g1908 Cmu02g1856 Cre02g2171 . . . . . Csa07g01196 . Cme11g01622 Blo15g00619 . . . Bpe15g00910 . Bma03g00504 . Sed01g0757 . . . . . . Cpe15g00895 . Bhi10g00954 Tan05g0599 Cmetu11g0762 . Hepe08g0636 . . . . . . . . . . Csa06g01161 Chy11g01030 Cme01g01520
Vvi19g1111 . . . . Bpe07g00469 . Bma08g00816 . . . . . . . . . . . . . . . . . Cla02g01821 Cam02g1929 Cec02g1954 Cco02g1995 Clacu02g1910 Cmu02g1858 Cre02g2172 . . . . . . . Cme11g01623 Blo15g00626 . . . . . . Bma12g00587 Sed01g3461 . . . . . . . . Bhi10g00953 Tan05g0598 Cmetu11g0435 . Hepe08g0637 . . . . . . . . . . Csa06g01160 Chy11g01032 .
Vvi19g1112 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo15g00627 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g01159 Chy11g01033 .
Vvi19g1113 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 61787311 61788831 + XM_039031460.1 Bhi05g02012 2012
5 61876925 61885520 + XM_039032432.1 Bhi05g02013 2013
10 19408943 19411589 - XM_039044470.1 Bhi10g00953 953
10 19435961 19437215 + XM_039045900.1 Bhi10g00954 954
4 3898018 3899357 + BLOR13383 Blo04g00471 471
15 15364474 15374716 - BLOR07011 Blo15g00617 617
15 15554191 15555530 - BLOR07013 Blo15g00619 619
15 15774894 15782330 + BLOR07020 Blo15g00626 626
15 16019786 16021336 + BLOR07021 Blo15g00627 627
3 3933598 3934933 + Bma016785.1 Bma03g00504 504
8 45823120 45825156 + Bma028207.1 Bma08g00816 816
12 25763986 25766981 - Bma007755.1 Bma12g00587 587
12 25994192 26000934 + Bma007756.1 Bma12g00588 588
7 7280187 7287590 - Bpe021301.1 Bpe07g00465 465
7 7365863 7367186 - Bpe021302.1 Bpe07g00466 466
7 7472617 7475299 + Bpe021308.1 Bpe07g00469 469
15 18924211 18925505 - Bpe001832.1 Bpe15g00910 910
2 32368942 32369843 - CaPI482276_02g019280.1 Cam02g1928 1928
2 32383799 32386635 + CaPI482276_02g019290.1 Cam02g1929 1929
2 32883569 32884466 - CcPI632755_02g019940.1 Cco02g1994 1994
2 32898602 32905802 + CcPI632755_02g019950.1 Cco02g1995 1995
2 37383000 37383907 - CePI673135_02g019530.1 Cec02g1953 1953
2 37398155 37400961 + CePI673135_02g019540.1 Cec02g1954 1954
1 7736151 7745130 + Chy1G008700.1 Chy01g00870 870
11 14728083 14728964 - Chy11G196100.1 Chy11g01030 1030
11 14741608 14743786 + Chy11G196120.1 Chy11g01032 1032
11 14758767 14762088 + Chy11G196130.1 Chy11g01033 1033
2 32627976 32628884 - ClG42_02g0190800.10 Clacu02g1908 1908
2 32642899 32646318 + ClG42_02g0191000.10 Clacu02g1910 1910
2 33327496 33328461 - ClCG02G018610.1 Cla02g01820 1820
2 33344186 33347019 + ClCG02G018615.1 Cla02g01821 1821
1 20075783 20077504 + MELO3C012614.2.1 Cme01g01520 1520
1 20160230 20169040 + MELO3C012616.2.1 Cme01g01521 1521
11 23984994 23986178 - MELO3C019643.2.1 Cme11g01622 1622
11 24006351 24009051 + MELO3C019642.2.1 Cme11g01623 1623
1 7320671 7321884 + PI0006033.1 Cmetu01g1126 1126
1 7345297 7345791 + PI0026091.1 Cmetu01g1246 1246
11 8733952 8736781 - PI0018756.1 Cmetu11g0435 435
11 8757010 8758308 + PI0008356.1 Cmetu11g0762 762
2 32490158 32491068 - CmPI595203_02g018560.1 Cmu02g1856 1856
2 32505108 32508518 + CmPI595203_02g018580.1 Cmu02g1858 1858
4 7918265 7919693 + Cp4.1LG04g02250.1 Cpe04g00860 860
15 8607377 8611352 - Cp4.1LG15g09000.1 Cpe15g00894 894
15 8613048 8614562 - Cp4.1LG15g08960.1 Cpe15g00895 895
16 7288796 7290166 + Cp4.1LG16g07020.1 Cpe16g00715 715
2 35329418 35330314 - CrPI670011_02g021710.1 Cre02g2171 2171
2 35344359 35351652 + CrPI670011_02g021720.1 Cre02g2172 2172
6 9676821 9681165 - CsaV3_6G013570.1 Csa06g01159 1159
6 9695970 9699438 - CsaV3_6G013580.1 Csa06g01160 1160
6 9710134 9711388 + CsaV3_6G013590.1 Csa06g01161 1161
7 11715753 11725817 - CsaV3_7G022820.1 Csa07g01193 1193
7 11749863 11751828 - CsaV3_7G022850.1 Csa07g01196 1196
2 361134 362611 + Hsped.02g00230.1 Hepe02g0023 23
2 375842 383855 + Hsped.02g00240.1 Hepe02g0024 24
8 5685039 5686428 - Hsped.08g06360.1 Hepe08g0636 636
8 5696928 5700716 + Hsped.08g06370.1 Hepe08g0637 637
12 608393 609207 + Lag0014423.1 Lac12g0051 51
12 620281 629408 + Lag0014424.1 Lac12g0052 52
1 5639941 5641015 - Sed0011738.1 Sed01g0757 757
1 63739491 63741553 + Sed0025557.1 Sed01g3461 3461
4 44546346 44556014 - Sed0009567.1 Sed04g3507 3507
5 31904864 31905719 + Sed0022394.1 Sed05g1845 1845
2 710478 712006 + Tan0022745.1 Tan02g0054 54
2 732502 739807 + Tan0004390.1 Tan02g0055 55
5 4340292 4343410 - Tan0017124.1 Tan05g0598 598
5 4354127 4355577 + Tan0007571.1 Tan05g0599 599
19 22233244 22235162 - Vvi19g1104 Vvi19g1104 1104
19 22237213 22253133 + Vvi19g1105 Vvi19g1105 1105
19 22256469 22257340 + Vvi19g1106 Vvi19g1106 1106
19 22260501 22262536 - Vvi19g1107 Vvi19g1107 1107
19 22279114 22279775 + Vvi19g1108 Vvi19g1108 1108
19 22290728 22301684 - Vvi19g1109 Vvi19g1109 1109
19 22323045 22329438 - Vvi19g1110 Vvi19g1110 1110
19 22340451 22349741 + Vvi19g1111 Vvi19g1111 1111
19 22358834 22361459 + Vvi19g1112 Vvi19g1112 1112
19 22379271 22383673 - Vvi19g1113 Vvi19g1113 1113
       

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