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
Vvi16g754 . . . Bda07g01901 Bpe03g00153 . . Bma14g02044 Cmo16g00108 Cmo18g01298 . . . . . . Cpe14g00086 . . . . . . . Cla01g00235 . Cec01g0233 . . . Cre09g2279 . . . . Lsi05g01196 Csa05g00252 . . . Blo09g00065 . . . . . . . . . Cma16g00100 Cma18g01268 Car16g00091 Car18g01178 Cpe09g00069 . . . . . . . . Cla05g00912 Cam05g0997 Cec05g1000 Cco05g0997 Clacu05g0985 Cmu05g0941 Cre05g1024 . Csa03g01745 Chy06g00974 Cme09g01790
Vvi16g755 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g756 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g757 . . . . . . . . . . Cma02g01080 Cma15g01076 . . . . . . . . . . . . . . . . . . . . . . . . . Chy09g01388 . . . . . . . . . . Cmo02g01097 Cmo15g01133 . . . . . Cpe13g00113 . . . . . . . . . . . . . . . . Chy06g01299 Cme09g01933
Vvi16g758 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo15g01132 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g759 . . . . . . . . . . . Cma15g01072 . . . . . . . . . . . . Cla01g00093 Cam01g0095 Cec01g0095 Cco01g0096 Clacu01g0093 Cmu01g0095 Cre09g2413 . . . . . Csa05g00107 . . . . . . . . . . . . Cmo15g01130 . . . . . . Bhi12g00779 . . . . . Lcy12g0057 . . . . . . . Lsi09g00079 . . .
Vvi16g760 . . . . . . . . . . . . . . . . Cpe14g00085 . . . . . . . . . . . . . . . . . . Lsi05g01195 . . . . . . . . . . . . . . . . Car16g00090 Car18g01179 . . . . . . . . . Cla05g00913 . . . . . . . . Chy06g00975 .
Vvi16g761 . . . . Bpe03g00154 . Bma10g01253 Bma14g02043 Cmo16g00106 Cmo18g01300 . . . . . . Cpe14g00084 . . . . . . . . . . . . . . . Cone5ag0891 Cone14ag0056 . Lsi05g01194 . . Cme06g01030 . Blo09g00064 . . . . . . . . . Cma16g00099 . Car16g00089 Car18g01180 Cpe09g00067 . . . . . . . . Cla05g00914 Cam05g1000 Cec05g1003 Cco05g0998 Clacu05g0988 Cmu05g0944 Cre05g1025 . Csa03g01747 Chy06g00976 .
Vvi16g762 Blo06g01136 Blo15g00109 . . . . . . Cmo16g00105 . . . . . . . Cpe14g00083 . . . . . . . . . . . . . . Cone1ag1191 Cone5ag0892 . . Lsi05g01193 . . . . . . Bda15g00711 . Bpe12g00442 Bma08g00293 . . . . Cma16g00098 . Car16g00088 . . . . . . . . . . . . . . . . . . Csa03g01748 Chy06g00977 .
Vvi16g763 . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00233 Cam01g0239 Cec01g0231 Cco01g0246 Clacu01g0237 Cmu01g0229 Cre09g2281 . . . . . Csa05g00250 Chy09g01255 . . . . . . . . . . . . . . . . . Cpe13g00135 . . . . . . . . . . . . . . . . . Cme09g01792
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 36392314 36409909 - Bda028874.1 Bda07g01901 1901
15 10518789 10519901 - Bda012565.2 Bda15g00711 711
12 23458762 23461839 - XM_039050821.1 Bhi12g00779 779
6 34827897 34830652 + BLOR17719 Blo06g01136 1136
9 1110226 1113639 + BLOR20979 Blo09g00064 64
9 1121957 1123634 + BLOR20980 Blo09g00065 65
15 909288 910025 + BLOR06503 Blo15g00109 109
8 4009881 4012688 - Bma031433 Bma08g00293 293
10 44496980 44500431 - Bma005344.1 Bma10g01253 1253
14 43822757 43827693 + Bma012853.1 Bma14g02043 2043
14 43827818 43829481 + Bma030758 Bma14g02044 2044
3 2000028 2001680 - Bpe011997.1 Bpe03g00153 153
3 2003478 2007284 - Bpe011998.2 Bpe03g00154 154
12 10196057 10199008 + Bpe005702.1 Bpe12g00442 442
1 1242033 1243010 - CaPI482276_01g000950.1 Cam01g0095 95
1 2709826 2711263 + CaPI482276_01g002390.1 Cam01g0239 239
5 9042495 9045274 - CaPI482276_05g009970.1 Cam05g0997 997
5 9063048 9068251 - CaPI482276_05g010000.1 Cam05g1000 1000
16 549511 549922 - Carg15108-RA Car16g00088 88
16 550770 555936 + Carg15109-RA Car16g00089 89
16 557003 559210 + Carg15110-RA Car16g00090 90
16 561400 569992 + Carg15111-RA Car16g00091 91
18 11471620 11473613 - Carg22126-RA Car18g01178 1178
18 11475470 11477817 - Carg22127-RA Car18g01179 1179
18 11478517 11483354 - Carg22128-RA Car18g01180 1180
1 772414 773391 - CcPI632755_01g000960.1 Cco01g0096 96
1 2333853 2335310 + CcPI632755_01g002460.1 Cco01g0246 246
5 8798636 8801478 - CcPI632755_05g009970.1 Cco05g0997 997
5 8815113 8825364 - CcPI632755_05g009980.1 Cco05g0998 998
1 803943 806362 - CePI673135_01g000950.1 Cec01g0095 95
1 2311728 2313175 + CePI673135_01g002310.1 Cec01g0231 231
1 2323954 2326990 + CePI673135_01g002330.1 Cec01g0233 233
5 8775540 8781808 - CePI673135_05g010000.1 Cec05g1000 1000
5 8804614 8809891 - CePI673135_05g010030.1 Cec05g1003 1003
6 7188661 7196392 - Chy6G115020.1 Chy06g00974 974
6 7208470 7211673 - Chy6G115030.1 Chy06g00975 975
6 7213560 7217926 - Chy6G115040.1 Chy06g00976 976
6 7224345 7227224 + Chy6G115050.1 Chy06g00977 977
6 12143925 12149078 + Chy6G118270.1 Chy06g01299 1299
9 14576762 14578388 + Chy9G169710.1 Chy09g01255 1255
9 15623808 15626165 + Chy9G171040.1 Chy09g01388 1388
1 852688 853665 - ClG42_01g0009300.10 Clacu01g0093 93
1 2326805 2328251 + ClG42_01g0023700.10 Clacu01g0237 237
5 8754234 8757040 - ClG42_05g0098500.10 Clacu05g0985 985
5 8775218 8780398 - ClG42_05g0098800.10 Clacu05g0988 988
1 811546 821529 - ClCG01G000920.2 Cla01g00093 93
1 2366429 2368338 + ClCG01G002390.2 Cla01g00233 233
1 2378718 2386915 + ClCG01G002410.2 Cla01g00235 235
5 9041158 9044268 - ClCG05G008380.1 Cla05g00912 912
5 9057775 9060469 - ClCG05G008400.2 Cla05g00913 913
5 9061926 9067404 - ClCG05G008410.1 Cla05g00914 914
2 6429404 6432197 + CmaCh02G010800.1 Cma02g01080 1080
15 6812877 6815905 - CmaCh15G010720.1 Cma15g01072 1072
15 6839507 6841590 - CmaCh15G010760.1 Cma15g01076 1076
16 437102 440551 - CmaCh16G000980.1 Cma16g00098 98
16 440870 446062 + CmaCh16G000990.1 Cma16g00099 99
16 447168 454066 + CmaCh16G001000.1 Cma16g00100 100
18 9855086 9866453 - CmaCh18G012680.1 Cma18g01268 1268
6 7456120 7465255 + MELO3C006936.2.1 Cme06g01030 1030
9 22323835 22327134 - MELO3C005704.2.1 Cme09g01790 1790
9 22334035 22335823 - MELO3C005706.2.1 Cme09g01792 1792
9 23381564 23383919 + MELO3C005839.2.1 Cme09g01933 1933
2 6654766 6657837 + CmoCh02G010970.1 Cmo02g01097 1097
15 7852838 7853741 - CmoCh15G011300.1 Cmo15g01130 1130
15 7859006 7860805 - CmoCh15G011320.1 Cmo15g01132 1132
15 7864669 7866469 - CmoCh15G011330.1 Cmo15g01133 1133
16 480853 483672 - CmoCh16G001050.1 Cmo16g00105 105
16 484010 489771 + CmoCh16G001060.1 Cmo16g00106 106
16 494904 497541 + CmoCh16G001080.1 Cmo16g00108 108
18 12476386 12479058 - CmoCh18G012980.1 Cmo18g01298 1298
18 12483687 12488318 - CmoCh18G013000.1 Cmo18g01300 1300
1 797069 798046 - CmPI595203_01g000950.1 Cmu01g0095 95
1 2279834 2281280 + CmPI595203_01g002290.1 Cmu01g0229 229
5 8600835 8603641 - CmPI595203_05g009410.1 Cmu05g0941 941
5 8620401 8625603 - CmPI595203_05g009440.1 Cmu05g0944 944
1 55855561 55858401 + Conep01aG0124000.1 Cone1ag1191 1191
5 3831241 3835093 - Conep05aG0091700.1 Cone5ag0891 891
5 3835454 3838400 + Conep05aG0091800.1 Cone5ag0892 892
14 332064 334872 + Conep14aG0005800.1 Cone14ag0056 56
9 395869 400629 + Cp4.1LG09g00730.1 Cpe09g00067 67
9 405399 407869 + Cp4.1LG09g00740.1 Cpe09g00069 69
13 817498 821080 + Cp4.1LG13g01100.1 Cpe13g00113 113
13 980603 982387 + Cp4.1LG13g01260.1 Cpe13g00135 135
14 453666 456551 - Cp4.1LG14g06400.1 Cpe14g00083 83
14 456973 463475 + Cp4.1LG14g06440.1 Cpe14g00084 84
14 464296 466343 + Cp4.1LG14g06290.1 Cpe14g00085 85
14 468453 471329 + Cp4.1LG14g06240.1 Cpe14g00086 86
5 9482647 9488988 - CrPI670011_05g010240.1 Cre05g1024 1024
5 9502154 9512368 - CrPI670011_05g010250.1 Cre05g1025 1025
9 41993938 41998196 - CrPI670011_09g022790.1 Cre09g2279 2279
9 42008932 42010381 - CrPI670011_09g022810.1 Cre09g2281 2281
9 43520099 43523223 + CrPI670011_09g024130.1 Cre09g2413 2413
3 13069657 13072982 - CsaV3_3G017450.1 Csa03g01745 1745
3 13087932 13093051 - CsaV3_3G017470.1 Csa03g01747 1747
3 13094503 13098153 + CsaV3_3G017480.1 Csa03g01748 1748
5 535469 537821 - CsaV3_5G001070.1 Csa05g00107 107
5 1519517 1521503 + CsaV3_5G002500.1 Csa05g00250 250
5 1528968 1532711 + CsaV3_5G002520.1 Csa05g00252 252
12 830255 834210 + Maker00038451 Lcy12g0057 57
5 19805911 19807370 - Lsi05G011930.1 Lsi05g01193 1193
5 19809017 19814038 + Lsi05G011940.1 Lsi05g01194 1194
5 19815987 19818795 + Lsi05G011950.1 Lsi05g01195 1195
5 19829087 19832862 + Lsi05G011960.1 Lsi05g01196 1196
9 687019 690388 - Lsi09G000790.1 Lsi09g00079 79
16 18017014 18018914 - Vvi16g754 Vvi16g754 754
16 18020281 18021197 - Vvi16g755 Vvi16g755 755
16 18021205 18021998 - Vvi16g756 Vvi16g756 756
16 18026547 18029340 + Vvi16g757 Vvi16g757 757
16 18030386 18039463 + Vvi16g758 Vvi16g758 758
16 18039843 18041713 + Vvi16g759 Vvi16g759 759
16 18042201 18045399 - Vvi16g760 Vvi16g760 760
16 18045534 18052668 - Vvi16g761 Vvi16g761 761
16 18054146 18057038 + Vvi16g762 Vvi16g762 762
16 18058679 18062107 - Vvi16g763 Vvi16g763 763
       

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