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
Vvi16g764 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g765 Blo06g01137 . . . . Bpe07g00926 . . Cmo16g00104 Cmo18g01301 Cma02g01081 Cma15g01071 Car02g00823 Car15g00991 . Cpe05g00639 Cpe14g00081 . . . . . . . Cla01g00092 Cam01g0093 Cec01g0093 Cco01g0094 Clacu01g0091 Cmu01g0093 Cre09g2414 Cone1ag1192 Cone5ag0893 Cone14ag0055 . . Csa05g00104 Chy09g01391 . . . Bda06g00695 Bda15g00710 . Bpe12g00443 Bma08g00292 Bma12g01109 . Cmo02g01099 Cmo15g01128 Cma16g00097 Cma18g01270 Car16g00087 Car18g01182 Cpe09g00066 Cpe13g00273 Bhi12g00778 . . Lac11g0071 . . Lcy12g0058 Cla05g00915 Cam05g1001 Cec05g1005 Cco05g1002 Clacu05g0989 Cmu05g0945 . Lsi09g00078 Csa03g01749 Chy06g00978 Cme09g01935
Vvi16g766 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo09g00062 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g767 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g768 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g769 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g770 . . Bda05g00094 . Bpe03g00155 . Bma10g01254 Bma14g02042 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag0061 . Csa05g00243 . . Blo07g00373 Blo09g00061 . . . . . . . . . . . . . . . Bhi12g00777 . . . . . Lcy12g0059 . . . . . . . . . . .
Vvi16g771 . . . . Bpe03g00262 . Bma10g01255 . . . . Cma15g01070 . . . . . . . . . . . . Cla01g00091 Cam01g0092 Cec01g0092 Cco01g0093 Clacu01g0090 Cmu01g0092 Cre09g2415 . . . . . Csa05g00103 . . Blo07g00372 . . . . . . . . . Cmo15g01127 . . . . . Cpe13g00274 . . . . . . . . . . . . . . . . . Cme09g01936
Vvi16g772 . . . . Bpe03g00156 . . Bma14g02041 . Cmo18g01303 . . . . . . . . . . . . . . . . . . . . . Cone1ag1194 . . . Lsi05g01189 . . . . Blo09g00060 . . . . . . . . . . Cma18g01272 . Car18g01185 Cpe09g00064 . . . . . . . . Cla05g00918 Cam05g1006 Cec05g1010 Cco05g1006 Clacu05g0993 Cmu05g0949 Cre05g1030 . . Chy06g00979 .
Vvi16g773 . . . . Bpe03g00157 . . . Cmo16g00103 . . . . . Sed13g0543 . Cpe14g00080 Bhi01g01589 Tan01g0786 . . . Mch10g0553 . . . . . . . . Cone1ag1195 . . Cone15ag0060 Lsi05g01188 . . . . Blo09g00058 . . . . . . . . . Cma16g00096 . Car16g00086 . . . . . . . . . . Cla05g00919 Cam05g1007 Cec05g1011 Cco05g1007 Clacu05g0995 Cmu05g0950 Cre05g1031 . Csa03g01752 Chy06g00981 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 4906997 4907479 + Bda020699.1 Bda05g00094 94
6 9560526 9564404 - Bda023992.1 Bda06g00695 695
15 10515500 10518328 + Bda033309 Bda15g00710 710
1 32864861 32877059 - XM_039030876.1 Bhi01g01589 1589
12 23333257 23335015 - XM_039050555.1 Bhi12g00777 777
12 23451849 23457404 + XM_039020378.1 Bhi12g00778 778
6 34831181 34834580 - BLOR17720 Blo06g01137 1137
7 6054325 6068843 - BLOR18304 Blo07g00372 372
7 6106251 6115273 - BLOR18305 Blo07g00373 373
9 991173 995671 + BLOR20973 Blo09g00058 58
9 1039712 1040260 + BLOR20975 Blo09g00060 60
9 1069830 1077046 - BLOR20976 Blo09g00061 61
9 1085705 1099166 - BLOR20977 Blo09g00062 62
8 4000269 4009249 + Bma027314.1 Bma08g00292 292
10 44535085 44535571 + Bma005346.1 Bma10g01254 1254
10 44559064 44559550 + Bma005348.1 Bma10g01255 1255
12 43367239 43372134 + Bma008454.1 Bma12g01109 1109
14 43817101 43817646 + Bma012851.1 Bma14g02041 2041
14 43820434 43820853 - Bma012852.2 Bma14g02042 2042
3 2009331 2009806 + Bpe011999.1 Bpe03g00155 155
3 2020932 2021297 - Bpe012000.1 Bpe03g00156 156
3 2027785 2030896 - Bpe012001.1 Bpe03g00157 157
3 3581257 3581651 - Bpe012115.1 Bpe03g00262 262
7 15194305 15202365 + Bpe021767.1 Bpe07g00926 926
12 10199438 10201981 - Bpe024893 Bpe12g00443 443
1 1213101 1214341 - CaPI482276_01g000920.1 Cam01g0092 92
1 1226092 1231692 + CaPI482276_01g000930.1 Cam01g0093 93
5 9072226 9076037 - CaPI482276_05g010010.1 Cam05g1001 1001
5 9088292 9088855 - CaPI482276_05g010060.1 Cam05g1006 1006
5 9090682 9100098 - CaPI482276_05g010070.1 Cam05g1007 1007
2 5944384 5949072 - Carg08398-RA Car02g00823 823
15 7604220 7608506 + Carg27024-RA Car15g00991 991
16 539729 543542 + Carg15105-RA Car16g00086 86
16 544302 547266 + Carg15106-RA Car16g00087 87
18 11485491 11486277 - Carg22130-RA Car18g01182 1182
18 11491076 11491645 - Carg22133-RA Car18g01185 1185
1 737011 738253 - CcPI632755_01g000930.1 Cco01g0093 93
1 755985 761462 + CcPI632755_01g000940.1 Cco01g0094 94
5 8837940 8840170 - CcPI632755_05g010020.1 Cco05g1002 1002
5 8853127 8853690 - CcPI632755_05g010060.1 Cco05g1006 1006
5 8854223 8863163 - CcPI632755_05g010070.1 Cco05g1007 1007
1 776134 777357 - CePI673135_01g000920.1 Cec01g0092 92
1 789290 794468 + CePI673135_01g000930.1 Cec01g0093 93
5 8815778 8820977 - CePI673135_05g010050.1 Cec05g1005 1005
5 8833179 8833739 - CePI673135_05g010100.1 Cec05g1010 1010
5 8834274 8845533 - CePI673135_05g010110.1 Cec05g1011 1011
6 7227934 7233827 - Chy6G115060.1 Chy06g00978 978
6 7241101 7241578 - Chy6G115070.1 Chy06g00979 979
6 7253509 7263319 - Chy6G115090.1 Chy06g00981 981
9 15629230 15633244 - Chy9G171070.1 Chy09g01391 1391
1 823757 824988 - ClG42_01g0009000.10 Clacu01g0090 90
1 836817 841999 + ClG42_01g0009100.10 Clacu01g0091 91
5 8784791 8788048 - ClG42_05g0098900.10 Clacu05g0989 989
5 8800338 8800901 - ClG42_05g0099300.10 Clacu05g0993 993
5 8810901 8812378 - ClG42_05g0099500.10 Clacu05g0995 995
1 791064 792774 - ClCG01G000900.2 Cla01g00091 91
1 804475 810581 + ClCG01G000910.2 Cla01g00092 92
5 9071384 9075033 - ClCG05G008420.2 Cla05g00915 915
5 9088439 9089002 - ClCG05G008430.1 Cla05g00918 918
5 9089522 9100477 - ClCG05G008440.2 Cla05g00919 919
2 6432597 6437328 - CmaCh02G010810.1 Cma02g01081 1081
15 6781069 6782824 - CmaCh15G010700.1 Cma15g01070 1070
15 6787085 6791475 + CmaCh15G010710.1 Cma15g01071 1071
16 430111 434131 + CmaCh16G000960.1 Cma16g00096 96
16 434759 437408 + CmaCh16G000970.1 Cma16g00097 97
18 9873783 9874836 - CmaCh18G012700.1 Cma18g01270 1270
18 9877833 9878399 - CmaCh18G012720.1 Cma18g01272 1272
9 23387161 23392195 - MELO3C005840.2.1 Cme09g01935 1935
9 23397027 23398549 + MELO3C005841.2.1 Cme09g01936 1936
2 6658410 6662730 - CmoCh02G010990.1 Cmo02g01099 1099
15 7830368 7832201 - CmoCh15G011270.1 Cmo15g01127 1127
15 7838545 7842866 + CmoCh15G011280.1 Cmo15g01128 1128
16 472196 477157 + CmoCh16G001030.1 Cmo16g00103 103
16 477515 480617 + CmoCh16G001040.1 Cmo16g00104 104
18 12488869 12491606 - CmoCh18G013010.1 Cmo18g01301 1301
18 12496259 12496828 - CmoCh18G013030.1 Cmo18g01303 1303
1 768155 769385 - CmPI595203_01g000920.1 Cmu01g0092 92
1 781262 786815 + CmPI595203_01g000930.1 Cmu01g0093 93
5 8629603 8633252 - CmPI595203_05g009450.1 Cmu05g0945 945
5 8645496 8646059 - CmPI595203_05g009490.1 Cmu05g0949 949
5 8646580 8654677 - CmPI595203_05g009500.1 Cmu05g0950 950
1 55858539 55861849 - Conep01aG0124100.1 Cone1ag1192 1192
1 55863268 55863966 - Conep01aG0124300.1 Cone1ag1194 1194
1 55864263 55867096 - Conep01aG0124400.1 Cone1ag1195 1195
5 3838499 3841830 - Conep05aG0091900.1 Cone5ag0893 893
14 329012 331703 + Conep14aG0005700.1 Cone14ag0055 55
15 349849 351875 + Conep15aG0006200.1 Cone15ag0060 60
15 352631 353517 - Conep15aG0006300.1 Cone15ag0061 61
5 3909914 3914811 + Cp4.1LG05g06290.1 Cpe05g00639 639
9 387409 387981 + Cp4.1LG09g00490.1 Cpe09g00064 64
9 392549 395376 + Cp4.1LG09g00710.1 Cpe09g00066 66
13 2173206 2177680 - Cp4.1LG13g02710.1 Cpe13g00273 273
13 2180576 2182780 + Cp4.1LG13g02690.1 Cpe13g00274 274
14 443820 446999 + Cp4.1LG14g06510.1 Cpe14g00080 80
14 448709 450418 + Cp4.1LG14g06520.1 Cpe14g00081 81
5 9534746 9535309 - CrPI670011_05g010300.1 Cre05g1030 1030
5 9535790 9546720 - CrPI670011_05g010310.1 Cre05g1031 1031
9 43525101 43530327 - CrPI670011_09g024140.1 Cre09g2414 2414
9 43547165 43548411 + CrPI670011_09g024150.1 Cre09g2415 2415
3 13095764 13102124 - CsaV3_3G017490.1 Csa03g01749 1749
3 13117461 13125388 - CsaV3_3G017520.1 Csa03g01752 1752
5 521724 523679 - CsaV3_5G001030.1 Csa05g00103 103
5 528092 533031 + CsaV3_5G001040.1 Csa05g00104 104
5 1483491 1484881 - CsaV3_5G002430.1 Csa05g00243 243
11 623634 628777 - Lag0030709.1 Lac11g0071 71
12 859829 865783 - Maker00038855 Lcy12g0058 58
12 875171 878826 + Maker00038496 Lcy12g0059 59
5 19785605 19791523 + Lsi05G011880.1 Lsi05g01188 1188
5 19794640 19795194 + Lsi05G011890.1 Lsi05g01189 1189
9 678849 685684 + Lsi09G000780.1 Lsi09g00078 78
10 3644332 3645371 + MC10g0450 Mch10g0553 553
13 3748283 3753125 - Sed0018121.1 Sed13g0543 543
1 7496048 7500773 + Tan0007360.2 Tan01g0786 786
16 18064704 18071828 + Vvi16g764 Vvi16g764 764
16 18073808 18081913 - Vvi16g765 Vvi16g765 765
16 18083404 18086266 + Vvi16g766 Vvi16g766 766
16 18105330 18107713 + Vvi16g767 Vvi16g767 767
16 18108244 18110229 + Vvi16g768 Vvi16g768 768
16 18110666 18124050 + Vvi16g769 Vvi16g769 769
16 18124528 18126065 + Vvi16g770 Vvi16g770 770
16 18132220 18133994 + Vvi16g771 Vvi16g771 771
16 18138627 18139532 - Vvi16g772 Vvi16g772 772
16 18150125 18152952 - Vvi16g773 Vvi16g773 773
       

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