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
Vvi2g882 . . . . . Bpe07g00056 Bma07g00965 Bma14g00112 . . . . . . . . Cpe02g00603 . . . . . . . . . . . . . . Cone8ag0527 Cone12ag0529 . . . . . . Blo03g00841 . Bda07g00138 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g883 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g884 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g885 . . . . . . . Bma14g00113 . Cmo16g01259 . . . . . Cpe14g01002 . . . . . . . . Cla10g00109 Cam10g0104 Cec10g0111 Cco10g0113 Clacu10g0108 Cmu10g0956 Cre10g0367 . . . . Lsi07g01138 . . Cme06g02414 Blo03g00842 . Bda07g00137 . . . . . . . . . Cma16g01214 . Car16g01141 . . . . . . . . . . . . . . . . . Csa03g00108 Chy06g02197 .
Vvi2g886 . . . . . Bpe07g00251 . . Cmo06g00609 Cmo16g01260 . . . . . Cpe14g01003 . . . . . . . . Cla10g00108 Cam10g0103 Cec10g0110 Cco10g0112 Clacu10g0107 Cmu10g0955 Cre10g0366 . . . . Lsi07g01137 . . Cme06g02413 . . . . . . . Bma12g00253 . . . Cma06g00602 Cma16g01216 Car06g00537 Car16g01142 . . . . . . . . . . . . . . . . . Csa03g00107 Chy06g02198 .
Vvi2g887 . . . Bda08g00652 Bpe05g00505 . . . Cmo06g00608 . . . . . . . . . . . . . . . Cla10g00106 Cam10g0102 Cec10g0109 Cco10g0111 Clacu10g0106 Cmu10g0954 Cre10g0365 . . . . Lsi07g01136 . . Cme06g02411 . . . . . . Bma05g00690 . . . . Cma06g00601 . Car06g00536 . . . . . . . . . . . . . . . . . . Csa03g00106 Chy06g02199 .
Vvi2g888 . . . . . . . . Cmo06g00607 Cmo16g01261 . . . . . Cpe14g01004 . . . . . . . . Cla10g00105 Cam10g0101 Cec10g0108 Cco10g0110 Clacu10g0105 Cmu10g0953 Cre10g0364 Cone8ag0529 . . . Lsi07g01131 . . Cme06g02410 Blo03g00843 . Bda07g00136 . . . . . . . . Cma06g00600 Cma16g01217 Car06g00535 Car16g01143 . . . . . . . . . . . . . . . . . Csa03g00105 Chy06g02200 .
Vvi2g889 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g890 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g891 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 1704851 1710492 + Bda025201.1 Bda07g00136 136
7 1711244 1712767 - Bda025202.1 Bda07g00137 137
7 1720044 1722515 + Bda025203.1 Bda07g00138 138
8 6778081 6781067 + Bda029114.1 Bda08g00652 652
3 34150508 34153551 - BLOR12022 Blo03g00841 841
3 34174193 34175738 + BLOR12023 Blo03g00842 842
3 34176895 34181591 - BLOR12024 Blo03g00843 843
5 40430735 40433748 - Bma021752.1 Bma05g00690 690
7 36976529 36979406 + Bma026104.1 Bma07g00965 965
12 3252412 3254262 - Bma007145.1 Bma12g00253 253
14 1489449 1491909 - Bma010517.1 Bma14g00112 112
14 1498994 1500544 + Bma010518.1 Bma14g00113 113
5 19239175 19242148 - Bpe017924.1 Bpe05g00505 505
7 461057 461921 + Bpe020868.1 Bpe07g00056 56
7 1791913 1795226 - Bpe021062.1 Bpe07g00251 251
10 2584940 2592050 + CaPI482276_10g001010.1 Cam10g0101 101
10 2593972 2599601 - CaPI482276_10g001020.1 Cam10g0102 102
10 2603082 2606882 + CaPI482276_10g001030.1 Cam10g0103 103
10 2608445 2610478 - CaPI482276_10g001040.1 Cam10g0104 104
6 3003021 3012260 + Carg16287-RA Car06g00535 535
6 3010459 3016807 - Carg16288-RA Car06g00536 536
6 3018858 3022916 + Carg16289-RA Car06g00537 537
16 9747761 9751742 + Carg23567-RA Car16g01141 1141
16 9754883 9757781 - Carg23566-RA Car16g01142 1142
16 9759405 9766142 - Carg23565-RA Car16g01143 1143
10 995453 1002595 + CcPI632755_10g001100.1 Cco10g0110 110
10 1004486 1010239 - CcPI632755_10g001110.1 Cco10g0111 111
10 1013816 1017622 + CcPI632755_10g001120.1 Cco10g0112 112
10 1019149 1021121 - CcPI632755_10g001130.1 Cco10g0113 113
10 1018983 1026113 + CePI673135_10g001080.1 Cec10g0108 108
10 1028046 1033692 - CePI673135_10g001090.1 Cec10g0109 109
10 1036803 1040597 + CePI673135_10g001100.1 Cec10g0110 110
10 1042191 1044167 - CePI673135_10g001110.1 Cec10g0111 111
6 26206797 26208699 + Chy6G127250.1 Chy06g02197 2197
6 26210363 26214141 - Chy6G127260.1 Chy06g02198 2198
6 26215969 26220477 + Chy6G127270.1 Chy06g02199 2199
6 26221976 26227931 - Chy6G127280.1 Chy06g02200 2200
10 1312383 1319658 + ClG42_10g0010500.10 Clacu10g0105 105
10 1321302 1326716 - ClG42_10g0010600.10 Clacu10g0106 106
10 1330248 1334033 + ClG42_10g0010700.10 Clacu10g0107 107
10 1335545 1337578 - ClG42_10g0010800.10 Clacu10g0108 108
10 1035873 1045946 + ClCG10G001020.2 Cla10g00105 105
10 1047870 1053313 - ClCG10G001030.2 Cla10g00106 106
10 1056657 1060918 + ClCG10G001050.1 Cla10g00108 108
10 1060513 1064167 - ClCG10G001060.2 Cla10g00109 109
6 2891334 2906852 + CmaCh06G006000.1 Cma06g00600 600
6 2903971 2910447 - CmaCh06G006010.1 Cma06g00601 601
6 2913219 2917840 + CmaCh06G006020.1 Cma06g00602 602
16 9197433 9201566 + CmaCh16G012140.1 Cma16g01214 1214
16 9204013 9206444 - CmaCh16G012160.1 Cma16g01216 1216
16 9207691 9215810 - CmaCh16G012170.1 Cma16g01217 1217
6 31247371 31252018 + MELO3C013794.2.1 Cme06g02410 2410
6 31252826 31258005 - MELO3C013795.2.1 Cme06g02411 2411
6 31259518 31263651 + MELO3C013797.2.1 Cme06g02413 2413
6 31264843 31267466 - MELO3C013798.2.1 Cme06g02414 2414
6 2988239 2996174 + CmoCh06G006070.1 Cmo06g00607 607
6 2995897 3002034 - CmoCh06G006080.1 Cmo06g00608 608
6 3004021 3008680 + CmoCh06G006090.1 Cmo06g00609 609
16 8979524 8983616 + CmoCh16G012590.1 Cmo16g01259 1259
16 8986534 8989711 - CmoCh16G012600.1 Cmo16g01260 1260
16 8991073 9001003 - CmoCh16G012610.1 Cmo16g01261 1261
10 1464982 1470822 + CmPI595203_10g009530.1 Cmu10g0953 953
10 1472798 1478189 - CmPI595203_10g009540.1 Cmu10g0954 954
10 1481715 1485510 + CmPI595203_10g009550.1 Cmu10g0955 955
10 1487028 1489061 - CmPI595203_10g009560.1 Cmu10g0956 956
8 3827092 3832645 - Conep08aG0054800.1 Cone8ag0527 527
8 3871273 3876280 - Conep08aG0055000.1 Cone8ag0529 529
12 3678684 3683900 - Conep12aG0055000.1 Cone12ag0529 529
2 3635048 3640510 - Cp4.1LG02g02690.1 Cpe02g00603 603
14 8454502 8459063 + Cp4.1LG14g10070.1 Cpe14g01002 1002
14 8460607 8463788 - Cp4.1LG14g10080.1 Cpe14g01003 1003
14 8465046 8472093 - Cp4.1LG14g10130.1 Cpe14g01004 1004
10 2423838 2430985 + CrPI670011_10g003640.1 Cre10g0364 364
10 2432934 2438574 - CrPI670011_10g003650.1 Cre10g0365 365
10 2441668 2445456 + CrPI670011_10g003660.1 Cre10g0366 366
10 2446959 2448991 - CrPI670011_10g003670.1 Cre10g0367 367
3 821250 828311 + CsaV3_3G001050.1 Csa03g00105 105
3 828939 834202 - CsaV3_3G001060.1 Csa03g00106 106
3 835283 839951 + CsaV3_3G001070.1 Csa03g00107 107
3 840579 843985 - CsaV3_3G001080.1 Csa03g00108 108
7 16747609 16755857 + Lsi07G011310.1 Lsi07g01131 1131
7 16788891 16794551 - Lsi07G011360.1 Lsi07g01136 1136
7 16797318 16801650 + Lsi07G011370.1 Lsi07g01137 1137
7 16802861 16806424 - Lsi07G011380.1 Lsi07g01138 1138
2 16404253 16408500 + Vvi2g882 Vvi2g882 882
2 16442784 16443042 + Vvi2g883 Vvi2g883 883
2 16490274 16499446 - Vvi2g884 Vvi2g884 884
2 16537603 16542457 + Vvi2g885 Vvi2g885 885
2 16542490 16552676 - Vvi2g886 Vvi2g886 886
2 16565461 16578129 - Vvi2g887 Vvi2g887 887
2 16617283 16628864 - Vvi2g888 Vvi2g888 888
2 16648892 16649144 + Vvi2g889 Vvi2g889 889
2 16649839 16650046 + Vvi2g890 Vvi2g890 890
2 16654145 16656614 - Vvi2g891 Vvi2g891 891
       

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