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
Vvi19g1184 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1185 . . . . . . . . . . . . . . . . . Bhi05g01976 . . Lac12g0024 Hepe02g0006 . . . . . . . . . . . . . . Csa07g01225 . . . . . . Bpe15g00929 . Bma03g00486 . . . . . . . . Cpe15g00913 . . . . . . . . . . . . . . . . . Chy01g00837 Cme01g01492
Vvi19g1186 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1187 . . . . . . . . . . . . . . . . Cpe16g00700 . . . . . . . Cla02g01844 Cam02g1950 Cec02g1977 Cco02g2016 Clacu02g1931 Cmu02g1880 Cre02g2192 . . . . . . . Cme11g01660 . . . . . . . . Sed01g0777 . . . . . . . Cpe05g01021 Bhi10g00915 Tan05g0569 Cmetu11g0770 . Hepe08g0662 . . . . . . . . . . Csa06g01136 Chy11g01056 .
Vvi19g1188 Blo04g00452 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe15g00930 . Bma03g00485 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1189 . . . . . . . . . . . . . . . . Cpe16g00699 . . . . . . . Cla02g01845 Cam02g1952 Cec02g1980 Cco02g2018 Clacu02g1934 Cmu02g1883 Cre02g2194 . . . . . . . Cme11g01662 . . . . . . . . Sed05g3323 . . . . . . . . Bhi10g00914 Tan05g0568 Cmetu11g1408 . Hepe08g0663 . . . . . . . . . . Csa06g01135 Chy11g01057 .
Vvi19g1190 Blo04g00451 Blo13g00610 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe15g00931 . Bma03g00484 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1191 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1192 . . . . . . . . . . . . . . . . . . . . . . . . Cla02g01847 Cam02g1953 Cec02g1981 Cco02g2019 Clacu02g1935 Cmu02g1884 Cre02g2195 . . . . . . . Cme11g01667 . . . . . . . . Sed05g3325 . . . . . . . Cpe05g01020 Bhi10g00910 Tan05g0566 Cmetu11g2473 . Hepe08g0665 . . . . . . . . . . Csa06g01133 Chy11g01061 .
Vvi19g1193 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 60970062 61063144 - XM_039031771.1 Bhi05g01976 1976
10 18617704 18621972 - XM_039045721.1 Bhi10g00910 910
10 18774015 18778236 + XM_039044871.1 Bhi10g00914 914
10 18798981 18801096 + XM_039046055.1 Bhi10g00915 915
4 3721000 3722591 - BLOR13363 Blo04g00451 451
4 3723927 3768829 - BLOR13364 Blo04g00452 452
13 28531899 28533418 + BLOR19662 Blo13g00610 610
3 3773050 3774360 - Bma016768.1 Bma03g00484 484
3 3776058 3777228 - Bma016769.1 Bma03g00485 485
3 3777895 3817923 - Bma016770.1 Bma03g00486 486
15 19045251 19083647 + Bpe001850.1 Bpe15g00929 929
15 19084265 19085448 + Bpe001851.1 Bpe15g00930 930
15 19086938 19088462 + Bpe001852.2 Bpe15g00931 931
2 32630317 32632051 - CaPI482276_02g019500.1 Cam02g1950 1950
2 32647011 32649443 - CaPI482276_02g019520.1 Cam02g1952 1952
2 32655889 32659819 + CaPI482276_02g019530.1 Cam02g1953 1953
2 33141458 33143198 - CcPI632755_02g020160.1 Cco02g2016 2016
2 33152564 33160719 - CcPI632755_02g020180.1 Cco02g2018 2018
2 33167177 33171088 + CcPI632755_02g020190.1 Cco02g2019 2019
2 37640046 37641771 - CePI673135_02g019770.1 Cec02g1977 1977
2 37657236 37659668 - CePI673135_02g019800.1 Cec02g1980 1980
2 37666347 37670205 + CePI673135_02g019810.1 Cec02g1981 1981
1 7210836 7232699 - Chy1G008370.1 Chy01g00837 837
11 15081016 15083591 - Chy11G196360.1 Chy11g01056 1056
11 15087359 15094875 - Chy11G196370.1 Chy11g01057 1057
11 15129643 15133465 + Chy11G196410.1 Chy11g01061 1061
2 32881974 32883711 - ClG42_02g0193100.10 Clacu02g1931 1931
2 32898783 32901215 - ClG42_02g0193400.10 Clacu02g1934 1934
2 32907736 32911666 + ClG42_02g0193500.10 Clacu02g1935 1935
2 33596883 33598815 - ClCG02G018840.2 Cla02g01844 1844
2 33611790 33617656 - ClCG02G018850.2 Cla02g01845 1845
2 33624199 33628129 + ClCG02G018880.2 Cla02g01847 1847
1 19540341 19541458 - MELO3C000424.2.1 Cme01g01492 1492
11 24514001 24516949 - MELO3C019610.2.1 Cme11g01660 1660
11 24566912 24571311 - MELO3C019608.2.1 Cme11g01662 1662
11 24635489 24639547 + MELO3C019603.2.1 Cme11g01667 1667
11 8284767 8287016 + PI0012854.1 Cmetu11g0770 770
11 8267358 8272313 + PI0009769.1 Cmetu11g1408 1408
11 8200324 8209854 - PI0001009.1 Cmetu11g2473 2473
2 32744316 32746053 - CmPI595203_02g018800.1 Cmu02g1880 1880
2 32761139 32763571 - CmPI595203_02g018830.1 Cmu02g1883 1883
2 32770116 32774046 + CmPI595203_02g018840.1 Cmu02g1884 1884
5 6653297 6657937 - Cp4.1LG05g10180.1 Cpe05g01020 1020
5 6657366 6658920 + Cp4.1LG05g10090.1 Cpe05g01021 1021
15 8722754 8765514 + Cp4.1LG15g09050.1 Cpe15g00913 913
16 7199791 7203539 + Cp4.1LG16g06880.1 Cpe16g00699 699
16 7204525 7206252 + Cp4.1LG16g06900.1 Cpe16g00700 700
2 35595933 35597667 - CrPI670011_02g021920.1 Cre02g2192 2192
2 35613589 35616021 - CrPI670011_02g021940.1 Cre02g2194 2194
2 35622555 35628392 + CrPI670011_02g021950.1 Cre02g2195 2195
6 9410941 9415460 - CsaV3_6G013310.1 Csa06g01133 1133
6 9427415 9432063 + CsaV3_6G013330.1 Csa06g01135 1135
6 9438292 9440694 + CsaV3_6G013340.1 Csa06g01136 1136
7 12058487 12119553 + CsaV3_7G023140.1 Csa07g01225 1225
2 151572 199906 - Hsped.02g00060.1 Hepe02g0006 6
8 5934431 5936186 - Hsped.08g06620.1 Hepe08g0662 662
8 5944733 5948346 - Hsped.08g06630.1 Hepe08g0663 663
8 5956377 5960125 + Hsped.08g06650.1 Hepe08g0665 665
12 360165 369046 - Lag0014396.1 Lac12g0024 24
1 5804527 5807193 - Sed0012612.1 Sed01g0777 777
5 42577390 42581321 - Sed0001463.1 Sed05g3323 3323
5 42589311 42592944 + Sed0004446.1 Sed05g3325 3325
5 4021387 4025280 - Tan0011938.1 Tan05g0566 566
5 4041932 4045486 + Tan0010510.1 Tan05g0568 568
5 4047800 4050721 + Tan0006219.1 Tan05g0569 569
19 23634532 23683391 + Vvi19g1184 Vvi19g1184 1184
19 23701985 23776140 + Vvi19g1185 Vvi19g1185 1185
19 23780411 23784906 - Vvi19g1186 Vvi19g1186 1186
19 23803973 23806961 - Vvi19g1187 Vvi19g1187 1187
19 23817846 23823394 + Vvi19g1188 Vvi19g1188 1188
19 23824656 23827974 - Vvi19g1189 Vvi19g1189 1189
19 23829723 23831896 + Vvi19g1190 Vvi19g1190 1190
19 23832464 23836195 + Vvi19g1191 Vvi19g1191 1191
19 23841501 23845561 + Vvi19g1192 Vvi19g1192 1192
19 23845781 23846168 + Vvi19g1193 Vvi19g1193 1193
       

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