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
Vvi16g714 . Blo15g00172 . . . Bpe07g00933 . . . . . Cma15g01088 . Car15g01000 . . . . . . . . . . Cla01g00444 Cam01g0467 Cec01g0456 Cco01g0478 Clacu01g0466 Cmu01g0444 Cre09g2068 Cone1ag1166 Cone5ag0876 . . . Csa05g00279 Chy09g01230 . . . Bda06g00688 . . . . Bma12g01117 . . Cmo15g01148 . . . . . Cpe13g00262 Bhi12g00497 . . . . . Lcy12g0037 . . . . . . . . . . Cme09g01562
Vvi16g715 Blo06g01132 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0078 Cone15ag0079 . . . . . . . Bda15g00716 . Bpe12g00436 Bma08g00297 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g716 . . . . . . . . . Cmo18g01279 . . . . . . Cpe14g00102 Bhi01g01293 . . . . . . Cla01g00450 . . . . . . . . . . Lsi05g01216 . Chy09g01031 Cme06g01014 . . . . . . . . . . . . Cma18g01253 Car16g00105 Car18g01163 Cpe09g00082 Cpe13g00095 . . . . . . . . . . . . . . . Csa03g01725 . Cme09g01573
Vvi16g717 . . . . . . . . Cmo16g00127 Cmo18g01282 . . . . . . Cpe14g00101 Bhi01g01291 . . . . . . . . . . . . . Cone1ag1169 . . . Lsi05g01215 . . Cme06g01016 . . . . . . . . . . . Cma16g00117 Cma18g01255 Car16g00104 Car18g01165 Cpe09g00080 . . . . . . . . . . . . . . . . Csa03g01726 Chy06g00956 .
Vvi16g718 Blo06g01133 . . . Bpe03g00278 . . . . . . . . . . Cpe05g00645 . . . . . . . . Cla01g00103 Cam01g0102 Cec01g0104 Cco01g0104 Clacu01g0100 Cmu01g0102 Cre09g2405 Cone1ag1170 Cone5ag0878 Cone14ag0077 Cone15ag0078 . . . . Blo07g00397 . . . . Bpe12g00437 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g719 Blo06g01134 . . . . Bpe07g00932 . . . . . Cma15g01085 . Car15g00998 . . . . . . . . . . . . . . . . . Cone1ag1171 Cone5ag0879 Cone14ag0074 Cone15ag0077 . . . . . . Bda06g00689 Bda15g00715 . Bpe12g00438 Bma08g00296 Bma12g01116 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g720 . Blo15g00173 . . . . . . . . Cma02g01074 . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g00121 . . . . . . . . . . . Cmo02g01090 Cmo15g01147 . . . . . Cpe13g00263 Bhi12g00032 . . . . . Lcy12g0040 . . . . . . . . . . .
Vvi16g721 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g722 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g723 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 9507818 9511234 - Bda023985.1 Bda06g00688 688
6 9513653 9516433 - Bda033767 Bda06g00689 689
15 10549330 10552130 + Bda012569.1 Bda15g00715 715
15 10555658 10559100 - Bda012570.1 Bda15g00716 716
1 26148660 26154130 - XM_039040814.1 Bhi01g01291 1291
1 26171890 26186348 - XM_039036864.1 Bhi01g01293 1293
12 606885 611303 + XM_039019249.1 Bhi12g00032 32
12 15687279 15700637 + XM_039050814.1 Bhi12g00497 497
6 34786067 34789564 + BLOR17715 Blo06g01132 1132
6 34790190 34790915 + BLOR17716 Blo06g01133 1133
6 34792600 34796658 - BLOR17717 Blo06g01134 1134
7 6889162 6890008 + BLOR18329 Blo07g00397 397
15 1757338 1765194 - BLOR06566 Blo15g00172 172
15 1770188 1773502 + BLOR06567 Blo15g00173 173
8 4110209 4113385 + Bma031434 Bma08g00296 296
8 4118561 4123507 - Bma027318.1 Bma08g00297 297
12 43406432 43409225 + Bma008462.1 Bma12g01116 1116
12 43411166 43415774 + Bma008463.1 Bma12g01117 1117
3 3802810 3803631 + Bpe012130.2 Bpe03g00278 278
7 15230469 15233413 + Bpe021773.1 Bpe07g00932 932
7 15234677 15239087 + Bpe021774.1 Bpe07g00933 933
12 10143940 10147512 + Bpe005696.1 Bpe12g00436 436
12 10148632 10149372 + Bpe005697.1 Bpe12g00437 437
12 10150257 10153447 - Bpe005698.1 Bpe12g00438 438
1 1331570 1334589 + CaPI482276_01g001020.1 Cam01g0102 102
1 4986676 4992520 - CaPI482276_01g004670.1 Cam01g0467 467
15 7800932 7807467 - Carg23174-RA Car15g00998 998
15 7822358 7828951 + Carg23176-RA Car15g01000 1000
16 637983 643632 - Carg15126-RA Car16g00104 104
16 644714 649284 - Carg15127-RA Car16g00105 105
18 11394110 11399582 + Carg22111-RA Car18g01163 1163
18 11403015 11408306 + Carg22113-RA Car18g01165 1165
1 867408 870567 + CcPI632755_01g001040.1 Cco01g0104 104
1 4685900 4691742 - CcPI632755_01g004780.1 Cco01g0478 478
1 898002 900949 + CePI673135_01g001040.1 Cec01g0104 104
1 4707290 4713106 - CePI673135_01g004560.1 Cec01g0456 456
6 7043558 7047701 + Chy6G114840.1 Chy06g00956 956
9 12833155 12838842 - Chy9G167470.1 Chy09g01031 1031
9 14379765 14388609 - Chy9G169460.1 Chy09g01230 1230
1 941927 944824 + ClG42_01g0010000.10 Clacu01g0100 100
1 4630509 4636332 - ClG42_01g0046600.10 Clacu01g0466 466
1 912854 915937 + ClCG01G001060.1 Cla01g00103 103
1 4814853 4820676 - ClCG01G004510.2 Cla01g00444 444
1 4878826 4885245 + ClCG01G004570.1 Cla01g00450 450
2 6392968 6395774 - CmaCh02G010740.1 Cma02g01074 1074
15 6905389 6909804 - CmaCh15G010850.1 Cma15g01085 1085
15 6927633 6934342 + CmaCh15G010880.1 Cma15g01088 1088
16 529363 546475 - CmaCh16G001170.1 Cma16g00117 117
18 9779557 9784506 + CmaCh18G012530.1 Cma18g01253 1253
18 9789182 9793558 + CmaCh18G012550.1 Cma18g01255 1255
6 7297120 7310751 + MELO3C006923.2.1 Cme06g01014 1014
6 7312624 7318028 + MELO3C006924.2.1 Cme06g01016 1016
9 20594822 20600346 - MELO3C005479.2.1 Cme09g01562 1562
9 20662260 20668426 + MELO3C005490.2.1 Cme09g01573 1573
2 6620441 6623371 - CmoCh02G010900.1 Cmo02g01090 1090
15 8008905 8015361 + CmoCh15G011470.1 Cmo15g01147 1147
15 8015837 8022421 + CmoCh15G011480.1 Cmo15g01148 1148
16 572977 603973 - CmoCh16G001270.1 Cmo16g00127 127
18 12396337 12402249 + CmoCh18G012790.1 Cmo18g01279 1279
18 12406382 12410698 + CmoCh18G012820.1 Cmo18g01282 1282
1 886745 889633 + CmPI595203_01g001020.1 Cmu01g0102 102
1 4587402 4593223 - CmPI595203_01g004440.1 Cmu01g0444 444
1 55753201 55757291 + Conep01aG0121500.1 Cone1ag1166 1166
1 55762429 55767939 + Conep01aG0121800.1 Cone1ag1169 1169
1 55768825 55769555 + Conep01aG0121900.1 Cone1ag1170 1170
1 55769733 55773662 - Conep01aG0122000.1 Cone1ag1171 1171
5 3743178 3747306 + Conep05aG0090200.1 Cone5ag0876 876
5 3760884 3761813 + Conep05aG0090400.1 Cone5ag0878 878
5 3761916 3765865 - Conep05aG0090500.1 Cone5ag0879 879
14 396164 399271 + Conep14aG0007700.1 Cone14ag0074 74
14 403312 404058 - Conep14aG0008000.1 Cone14ag0077 77
14 404700 407110 - Conep14aG0008100.1 Cone14ag0078 78
15 420408 423330 + Conep15aG0007900.1 Cone15ag0077 77
15 424038 427101 - Conep15aG0008000.1 Cone15ag0078 78
15 427257 429669 - Conep15aG0008100.1 Cone15ag0079 79
5 3943996 3946820 + Cp4.1LG05g06410.1 Cpe05g00645 645
9 475069 480346 - Cp4.1LG09g00790.1 Cpe09g00080 80
9 483132 489324 - Cp4.1LG09g01000.1 Cpe09g00082 82
13 682750 693003 - Cp4.1LG13g00880.1 Cpe13g00095 95
13 2028434 2035029 - Cp4.1LG13g02620.1 Cpe13g00262 262
13 2035885 2048756 - Cp4.1LG13g02660.1 Cpe13g00263 263
14 547642 554471 - Cp4.1LG14g06160.1 Cpe14g00101 101
14 555543 560421 - Cp4.1LG14g06210.1 Cpe14g00102 102
9 39737164 39743016 + CrPI670011_09g020680.1 Cre09g2068 2068
9 43411595 43414663 - CrPI670011_09g024050.1 Cre09g2405 2405
3 12921325 12934331 + CsaV3_3G017250.1 Csa03g01725 1725
3 12936395 12941988 + CsaV3_3G017260.1 Csa03g01726 1726
5 613328 617102 + CsaV3_5G001210.1 Csa05g00121 121
5 1714005 1724614 + CsaV3_5G002790.1 Csa05g00279 279
12 633926 639937 - Maker00038690 Lcy12g0037 37
12 658925 662128 - Maker00038454 Lcy12g0040 40
5 20018140 20023900 - Lsi05G012150.1 Lsi05g01215 1215
5 20026351 20069699 - Lsi05G012160.1 Lsi05g01216 1216
16 17625000 17630168 + Vvi16g714 Vvi16g714 714
16 17630577 17633330 - Vvi16g715 Vvi16g715 715
16 17636564 17646586 + Vvi16g716 Vvi16g716 716
16 17649999 17657367 + Vvi16g717 Vvi16g717 717
16 17658141 17659121 + Vvi16g718 Vvi16g718 718
16 17659515 17670931 - Vvi16g719 Vvi16g719 719
16 17674546 17676106 + Vvi16g720 Vvi16g720 720
16 17676107 17676678 + Vvi16g721 Vvi16g721 721
16 17676677 17678461 + Vvi16g722 Vvi16g722 722
16 17678463 17678918 + Vvi16g723 Vvi16g723 723
       

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