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
Vvi16g704 . . . . . . . . Cmo16g00130 Cmo18g01274 . . . . . . Cpe14g00105 Bhi01g01308 Tan01g0243 . . . Mch10g0149 . . . . . . . . Cone1ag1161 . . . Lsi05g01217 . . Cme06g01008 Blo07g00404 . . . . . . . . . . Cma16g00121 Cma18g01251 Car16g00111 Car18g01158 Cpe09g00086 . . . . . . . . Cla05g00888 Cam05g0975 Cec05g0979 Cco05g0978 Clacu05g0962 Cmu05g0919 Cre05g1004 . Csa03g01720 Chy06g00952 .
Vvi16g705 . . Bda05g00079 . Bpe03g00282 . Bma10g01228 . . Cmo18g01275 . . . . . . Cpe14g00104 Bhi01g01307 Tan01g0241 . . Hepe07g0148 . . Cla01g00256 Cam01g0262 Cec01g0254 Cco01g0267 Clacu01g0260 Cmu01g0249 Cre09g2260 Cone1ag1162 Cone5ag0872 . . . . . Cme06g01009 Blo07g00402 . . . . . . . . . . . Cma18g01252 Car16g00109 Car18g01159 Cpe09g00085 . . . . . . . . Cla05g00889 Cam05g0976 Cec05g0980 Cco05g0979 Clacu05g0963 Cmu05g0920 Cre05g1005 . Csa03g01721 Chy06g00953 .
Vvi16g706 . . . . . . . . . . . . . . Sed07g1024 . . Bhi01g01305 Tan01g0239 Cmetu06g0283 . Hepe07g0147 . . . . . . . . . . . . . . . . Cme06g01010 . . . . . . . . . . . Cma16g00118 . Car16g00108 . . . . . . . . . . . . . . . . . . Csa03g01722 Chy06g00954 .
Vvi16g707 . . . . . . . Bma14g02074 . Cmo18g01276 . . . . . . Cpe14g00103 Bhi01g01302 Tan01g0237 . . . Mch10g0147 . . . . . . . . Cone1ag1163 Cone5ag0873 . . . . . Cme06g01012 . . . . . . . . . . . . . Car16g00107 Car18g01161 Cpe09g00084 . . . . . . . . Cla05g00890 . Cec05g0981 . . Cmu05g0921 . . Csa03g01723 . .
Vvi16g708 Blo06g01130 Blo15g00170 Bda05g00080 . Bpe03g00281 Bpe07g00935 Bma10g01229 . . Cmo18g01278 Cma02g01070 Cma15g01095 Car02g00813 Car15g01006 Sed05g0499 Cpe05g00649 . Bhi01g01300 Tan01g0235 Cmetu09g0361 . . Mch10g0146 . Cla01g00437 Cam01g0459 Cec01g0448 Cco01g0471 Clacu01g0458 Cmu01g0437 . Cone1ag1164 Cone5ag0874 . . . . . Cme06g01013 Blo07g00401 Blo09g00102 Bda06g00686 . . . Bma08g00300 . . Cmo02g01088 Cmo15g01153 . . Car16g00106 Car18g01162 Cpe09g00083 Cpe13g00256 . . . . . . . Cla05g00891 . . . . . . . Csa03g01724 Chy06g00955 Cme09g01555
Vvi16g709 Blo06g01131 Blo15g00171 . . . Bpe07g00934 . . . . Cma02g01071 . Car02g00815 Car15g01002 . Cpe05g00648 . . . . . . . . . . . . . . . . . Cone14ag0079 Cone15ag0080 . . . . . . Bda06g00687 Bda15g00718 . . Bma08g00298 Bma12g01118 . Cmo02g01089 . . . . . . Cpe13g00260 Bhi12g00499 . . . Hepe06g0690 . Lcy12g0035 . . . . . . . . . . Cme09g01560
Vvi16g710 . . . . . . . . . . . Cma15g01089 . Car15g01001 . . . . . . . . . . Cla01g00443 Cam01g0466 Cec01g0455 Cco01g0477 Clacu01g0465 Cmu01g0443 Cre09g2070 Cone1ag1165 Cone5ag0875 . . . . . . . . . . . . . . . . Cmo15g01149 . . . . . Cpe13g00261 Bhi12g00498 . . . . . Lcy12g0036 . . . . . . . . . . Cme09g01561
Vvi16g711 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe13g00058 . . . . . . . . . . . . . . . . . .
Vvi16g712 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g713 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 3852091 3854779 + Bda020670.1 Bda05g00079 79
5 3881540 3881994 - Bda033623 Bda05g00080 80
6 9499576 9501462 - Bda023983.1 Bda06g00686 686
6 9503644 9506633 + Bda023984.1 Bda06g00687 687
15 10566641 10571109 - Bda033310 Bda15g00718 718
1 26203338 26204197 - XM_039030330.1 Bhi01g01300 1300
1 26206160 26211478 - XM_039036544.1 Bhi01g01302 1302
1 26228034 26236490 - XM_039043854.1 Bhi01g01305 1305
1 26238492 26243857 - XM_039040046.1 Bhi01g01307 1307
1 26316892 26330953 + XM_039020703.1 Bhi01g01308 1308
12 15702747 15705778 - XM_039050569.1 Bhi12g00498 498
12 15713269 15717525 - XM_039020111.1 Bhi12g00499 499
6 34777053 34777733 - BLOR17713 Blo06g01130 1130
6 34782061 34784913 + BLOR17714 Blo06g01131 1131
7 7172927 7173380 + BLOR18333 Blo07g00401 401
7 7174875 7177482 - BLOR18334 Blo07g00402 402
7 7197143 7200259 + BLOR18336 Blo07g00404 404
9 1912910 1913837 - BLOR21017 Blo09g00102 102
15 1737711 1745489 - BLOR06564 Blo15g00170 170
15 1748832 1752411 + BLOR06565 Blo15g00171 171
8 4133633 4137118 - Bma027319.1 Bma08g00298 298
8 4167495 4168081 + Bma027323.1 Bma08g00300 300
10 43677388 43680151 + Bma005308.1 Bma10g01228 1228
10 43683738 43684384 - Bma005309.1 Bma10g01229 1229
12 43416675 43419589 - Bma008464.2 Bma12g01118 1118
14 44104270 44109690 + Bma012883.1 Bma14g02074 2074
3 3870385 3870892 + Bpe025367 Bpe03g00281 281
3 3874278 3877033 - Bpe012133.1 Bpe03g00282 282
7 15240022 15242901 - Bpe021775.1 Bpe07g00934 934
7 15245460 15246027 + Bpe021776.1 Bpe07g00935 935
1 2923747 2936221 - CaPI482276_01g002620.1 Cam01g0262 262
1 4888975 4918483 - CaPI482276_01g004590.1 Cam01g0459 459
1 4982766 4985325 + CaPI482276_01g004660.1 Cam01g0466 466
5 8766283 8781598 - CaPI482276_05g009750.1 Cam05g0975 975
5 8792148 8811754 + CaPI482276_05g009760.1 Cam05g0976 976
2 5889279 5890440 - Carg08408-RA Car02g00813 813
2 5894371 5898118 + Carg08406-RA Car02g00815 815
15 7830641 7833224 - Carg23177-RA Car15g01001 1001
15 7834644 7839610 - Carg23178-RA Car15g01002 1002
15 7854822 7856488 + Carg23182-RA Car15g01006 1006
16 649859 651309 - Carg15128-RA Car16g00106 106
16 651982 656852 - Carg15129-RA Car16g00107 107
16 657251 665658 - Carg15130-RA Car16g00108 108
16 666132 667819 - Carg15131-RA Car16g00109 109
16 670951 674183 + Carg15133-RA Car16g00111 111
18 11375645 11379543 - Carg22106-RA Car18g01158 1158
18 11384096 11385415 + Carg22107-RA Car18g01159 1159
18 11386714 11390907 + Carg22109-RA Car18g01161 1161
18 11392064 11393714 + Carg22110-RA Car18g01162 1162
1 2552844 2565337 - CcPI632755_01g002670.1 Cco01g0267 267
1 4612736 4614949 - CcPI632755_01g004710.1 Cco01g0471 471
1 4681957 4684531 + CcPI632755_01g004770.1 Cco01g0477 477
5 8536849 8549683 - CcPI632755_05g009780.1 Cco05g0978 978
5 8558627 8579265 + CcPI632755_05g009790.1 Cco05g0979 979
1 2529611 2542124 - CePI673135_01g002540.1 Cec01g0254 254
1 4614020 4642261 - CePI673135_01g004480.1 Cec01g0448 448
1 4703358 4706532 + CePI673135_01g004550.1 Cec01g0455 455
5 8521432 8538278 - CePI673135_05g009790.1 Cec05g0979 979
5 8548511 8551728 + CePI673135_05g009800.1 Cec05g0980 980
5 8562608 8567744 + CePI673135_05g009810.1 Cec05g0981 981
6 6988965 6997185 - Chy6G114800.1 Chy06g00952 952
6 7006617 7010364 + Chy6G114810.1 Chy06g00953 953
6 7011336 7019919 + Chy6G114820.1 Chy06g00954 954
6 7021445 7040472 + Chy6G114830.1 Chy06g00955 955
1 2542867 2555447 - ClG42_01g0026000.10 Clacu01g0260 260
1 4535914 4563511 - ClG42_01g0045800.10 Clacu01g0458 458
1 4626673 4629137 + ClG42_01g0046500.10 Clacu01g0465 465
5 8482553 8498035 - ClG42_05g0096200.10 Clacu05g0962 962
5 8506793 8527950 + ClG42_05g0096300.10 Clacu05g0963 963
1 2598063 2610990 - ClCG01G002620.2 Cla01g00256 256
1 4738154 4739868 - ClCG01G004450.2 Cla01g00437 437
1 4805089 4813855 + ClCG01G004500.1 Cla01g00443 443
5 8744604 8763504 - ClCG05G008120.2 Cla05g00888 888
5 8773639 8778250 + ClCG05G008130.1 Cla05g00889 889
5 8779340 8794717 + ClCG05G008140.1 Cla05g00890 890
5 8805629 8825071 + ClCG05G008150.2 Cla05g00891 891
2 6369886 6371077 - CmaCh02G010700.1 Cma02g01070 1070
2 6378437 6392694 + CmaCh02G010710.1 Cma02g01071 1071
15 6935813 6944558 - CmaCh15G010890.1 Cma15g01089 1089
15 6959433 6961293 + CmaCh15G010950.1 Cma15g01095 1095
16 546752 559499 - CmaCh16G001180.1 Cma16g00118 118
16 561081 565050 + CmaCh16G001210.1 Cma16g00121 121
18 9760140 9764162 - CmaCh18G012510.1 Cma18g01251 1251
18 9766061 9779309 + CmaCh18G012520.1 Cma18g01252 1252
6 7237982 7246131 - MELO3C006917.2.1 Cme06g01008 1008
6 7252114 7257602 + MELO3C006918.2.1 Cme06g01009 1009
6 7258371 7267469 + MELO3C006919.2.1 Cme06g01010 1010
6 7277133 7287322 + MELO3C031643.2.1 Cme06g01012 1012
6 7294368 7296618 + MELO3C006922.2.1 Cme06g01013 1013
9 20561469 20563475 - MELO3C005472.2.1 Cme09g01555 1555
9 20586105 20590364 + MELO3C005477.2.1 Cme09g01560 1560
9 20590991 20593735 + MELO3C005478.2.1 Cme09g01561 1561
6 7222039 7230898 + PI0027943.1 Cmetu06g0283 283
9 3442265 3444142 - PI0023707.1 Cmetu09g0361 361
2 6601623 6603354 - CmoCh02G010880.1 Cmo02g01088 1088
2 6606331 6620496 + CmoCh02G010890.1 Cmo02g01089 1089
15 8023707 8032693 - CmoCh15G011490.1 Cmo15g01149 1149
15 8048500 8050027 + CmoCh15G011530.1 Cmo15g01153 1153
16 605501 609441 + CmoCh16G001300.1 Cmo16g00130 130
18 12377830 12382128 - CmoCh18G012740.1 Cmo18g01274 1274
18 12384021 12388239 + CmoCh18G012750.1 Cmo18g01275 1275
18 12388723 12393746 + CmoCh18G012760.1 Cmo18g01276 1276
18 12394479 12395432 + CmoCh18G012780.1 Cmo18g01278 1278
1 2495775 2508382 - CmPI595203_01g002490.1 Cmu01g0249 249
1 4500251 4520340 - CmPI595203_01g004370.1 Cmu01g0437 437
1 4583569 4586033 + CmPI595203_01g004430.1 Cmu01g0443 443
5 8329309 8344684 - CmPI595203_05g009190.1 Cmu05g0919 919
5 8353443 8367940 + CmPI595203_05g009200.1 Cmu05g0920 920
5 8369453 8374608 + CmPI595203_05g009210.1 Cmu05g0921 921
1 55733883 55737721 - Conep01aG0121000.1 Cone1ag1161 1161
1 55739070 55742148 + Conep01aG0121100.1 Cone1ag1162 1162
1 55742407 55747642 + Conep01aG0121200.1 Cone1ag1163 1163
1 55747896 55749313 - Conep01aG0121300.1 Cone1ag1164 1164
1 55749540 55752319 + Conep01aG0121400.1 Cone1ag1165 1165
5 3728580 3731385 + Conep05aG0089800.1 Cone5ag0872 872
5 3732340 3737652 + Conep05aG0089900.1 Cone5ag0873 873
5 3738172 3739716 - Conep05aG0090000.1 Cone5ag0874 874
5 3739961 3742096 + Conep05aG0090100.1 Cone5ag0875 875
14 407326 409894 - Conep14aG0008200.1 Cone14ag0079 79
15 430040 432608 - Conep15aG0008200.1 Cone15ag0080 80
5 3960340 3964555 - Cp4.1LG05g06550.1 Cpe05g00648 648
5 3966564 3968265 + Cp4.1LG05g06470.1 Cpe05g00649 649
9 489633 491357 - Cp4.1LG09g01030.1 Cpe09g00083 83
9 492145 497400 - Cp4.1LG09g01010.1 Cpe09g00084 84
9 497687 501705 - Cp4.1LG09g01020.1 Cpe09g00085 85
9 503678 507793 + Cp4.1LG09g00870.1 Cpe09g00086 86
13 457012 460025 + Cp4.1LG13g00530.1 Cpe13g00058 58
13 2002436 2004178 - Cp4.1LG13g02600.1 Cpe13g00256 256
13 2018719 2023341 + Cp4.1LG13g02550.1 Cpe13g00260 260
13 2024438 2027211 + Cp4.1LG13g02580.1 Cpe13g00261 261
14 560647 576144 - Cp4.1LG14g06200.1 Cpe14g00103 103
14 577031 580706 - Cp4.1LG14g06170.1 Cpe14g00104 104
14 581138 585266 + Cp4.1LG14g06080.1 Cpe14g00105 105
5 9217181 9233375 - CrPI670011_05g010040.1 Cre05g1004 1004
5 9241898 9262894 + CrPI670011_05g010050.1 Cre05g1005 1005
9 39749127 39752015 - CrPI670011_09g020700.1 Cre09g2070 2070
9 41776089 41788682 + CrPI670011_09g022600.1 Cre09g2260 2260
3 12880358 12888911 - CsaV3_3G017200.1 Csa03g01720 1720
3 12896278 12901671 + CsaV3_3G017210.1 Csa03g01721 1721
3 12901918 12911169 + CsaV3_3G017220.1 Csa03g01722 1722
3 12911598 12917812 + CsaV3_3G017230.1 Csa03g01723 1723
3 12918773 12920314 + CsaV3_3G017240.1 Csa03g01724 1724
6 51004428 51007469 - Hsped.06g06900.1 Hepe06g0690 690
7 1343794 1353348 - Hsped.07g01470.1 Hepe07g0147 147
7 1354298 1366017 - Hsped.07g01480.1 Hepe07g0148 148
12 625292 629683 + Maker00038402 Lcy12g0035 35
12 630936 634190 + Maker00038713 Lcy12g0036 36
5 20072517 20084762 + Lsi05G012170.1 Lsi05g01217 1217
10 879760 880749 - MC10g0123 Mch10g0146 146
10 882072 897470 - MC10g0124 Mch10g0147 147
10 904610 911443 + MC10g0126 Mch10g0149 149
5 3421038 3423408 + Sed0016277.2 Sed05g0499 499
7 7420038 7432061 - Sed0009742.1 Sed07g1024 1024
1 2054700 2056699 - Tan0003316.2 Tan01g0235 235
1 2057659 2063260 - Tan0002130.2 Tan01g0237 237
1 2064335 2075093 - Tan0006274.1 Tan01g0239 239
1 2077145 2081541 - Tan0016625.2 Tan01g0241 241
1 2086313 2097418 + Tan0007285.2 Tan01g0243 243
16 17512818 17521780 - Vvi16g704 Vvi16g704 704
16 17534537 17540449 + Vvi16g705 Vvi16g705 705
16 17546562 17566153 + Vvi16g706 Vvi16g706 706
16 17566980 17576243 + Vvi16g707 Vvi16g707 707
16 17577186 17578280 - Vvi16g708 Vvi16g708 708
16 17582058 17587160 + Vvi16g709 Vvi16g709 709
16 17587950 17591587 + Vvi16g710 Vvi16g710 710
16 17593252 17594524 - Vvi16g711 Vvi16g711 711
16 17596767 17598908 - Vvi16g712 Vvi16g712 712
16 17604160 17614162 + Vvi16g713 Vvi16g713 713
       

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