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
Vvi5g829 . Blo12g00131 Bda03g01109 . Bpe04g01054 . Bma04g01035 . . . Cma06g01275 . Car06g01096 . . Cpe08g00372 . Bhi01g00022 . . . . . . . . . . . . . Cone14ag0202 Cone15ag0220 . . Lsi05g01798 . . Cme06g00422 . . . . . . . . . Cmo06g01284 . . . . . . . . . . . . . . Cla05g00384 Cam05g0418 Cec05g0423 Cco05g0423 Clacu05g0413 Cmu05g0396 Cre05g0458 . Csa03g01141 Chy06g00407 .
Vvi5g830 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g831 . . . . . . . . . . Cma06g01274 . Car06g01095 . . Cpe08g00373 . Bhi01g00020 . . . Hepe05g1854 . . . . . . . . . Cone14ag0204 . . . . . . Cme06g00421 . . . . . . . . . Cmo06g01282 . . . . . . . . . . . . . . Cla05g00383 Cam05g0416 Cec05g0421 Cco05g0421 Clacu05g0412 Cmu05g0395 Cre05g0457 . Csa03g01140 Chy06g00406 .
Vvi5g832 . . . . . . . . . . . Cma14g01865 . . . Cpe08g00375 Cpe03g01563 . . . . . . . . . . . . . . . . . . Lsi05g01799 . . Cme06g00420 Blo02g00636 . Bda11g00655 Bda13g00030 . . Bma02g00741 Bma06g01622 . . Cmo14g01910 . . . . . . . . . . . . . Cla05g00382 Cam05g0415 Cec05g0420 Cco05g0420 Clacu05g0411 Cmu05g0394 Cre05g0456 . Csa03g01139 Chy06g00405 .
Vvi5g833 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g834 . . . . . . . . . . Cma06g01273 . Car06g01094 . . . . Bhi01g00017 . . . . . . . . . . . . . . Cone15ag0225 . . Lsi05g01801 . . Cme06g00419 Blo02g00635 . . . . . Bma02g00740 . . Cmo06g01281 . . . . . . . . . . . . . . Cla05g00381 Cam05g0414 Cec05g0419 Cco05g0419 Clacu05g0410 Cmu05g0393 Cre05g0455 . Csa03g01138 Chy06g00404 .
Vvi5g835 . . . . Bpe04g01133 Bpe14g01292 . . . . Cma06g01272 . Car06g01093 . . Cpe08g00376 . Bhi01g00014 . . . . . . . . . . . . . . . . . Lsi05g01802 . . Cme06g00418 . . . Bda13g00029 . . Bma02g00739 . . Cmo06g01280 . . . . . . . . . . . . . . Cla05g00380 Cam05g0413 Cec05g0418 Cco05g0418 Clacu05g0409 Cmu05g0392 Cre05g0454 . Csa03g01137 Chy06g00403 .
Vvi5g836 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g837 . . . . . . . . . . Cma06g01271 . Car06g01092 . . Cpe08g00377 . Bhi01g00013 . . . . . . . . . . . . . . . . Cone4ag0380 Lsi05g01803 . . Cme06g00417 . Blo07g00293 Bda11g00656 . . . . Bma06g01304 . Cmo06g01279 . . . . . . . . . . . . . . Cla05g00379 Cam05g0412 Cec05g0417 Cco05g0417 Clacu05g0408 Cmu05g0391 Cre05g0453 . Csa03g01136 Chy06g00402 .
Vvi5g838 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag0226 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 11277656 11286716 - Bda033515 Bda03g01109 1109
11 6475117 6477767 + Bda005401.2 Bda11g00655 655
11 6497434 6500760 - Bda005402.1 Bda11g00656 656
13 498607 500729 - Bda000871.1 Bda13g00029 29
13 503012 503779 - Bda000872.1 Bda13g00030 30
1 220914 225139 + XM_039044354.1 Bhi01g00013 13
1 226118 228762 - XM_039025169.1 Bhi01g00014 14
1 273210 274803 + XM_039026206.1 Bhi01g00017 17
1 284761 291768 - XM_039026194.1 Bhi01g00020 20
1 293401 296680 + XM_039019441.1 Bhi01g00022 22
2 14312644 14313881 + BLOR10365 Blo02g00635 635
2 14314729 14315486 - BLOR10366 Blo02g00636 636
7 3401441 3410503 - BLOR18225 Blo07g00293 293
12 9244751 9247467 + BLOR04150 Blo12g00131 131
2 38373646 38375758 - Bma015441.1 Bma02g00739 739
2 38376132 38377601 + Bma030899 Bma02g00740 740
2 38378319 38379086 - Bma015442.1 Bma02g00741 741
4 18252247 18255857 - Bma019655.1 Bma04g01035 1035
6 50065003 50066504 - Bma024413.1 Bma06g01304 1304
6 52352684 52353583 + Bma024736.2 Bma06g01622 1622
4 7740613 7747101 - Bpe015723.1 Bpe04g01054 1054
4 9940261 9941809 - Bpe015814.1 Bpe04g01133 1133
14 9839393 9841484 + Bpe025552 Bpe14g01292 1292
5 3806388 3810076 + CaPI482276_05g004120.1 Cam05g0412 412
5 3811489 3814104 - CaPI482276_05g004130.1 Cam05g0413 413
5 3815299 3817098 + CaPI482276_05g004140.1 Cam05g0414 414
5 3817584 3818336 - CaPI482276_05g004150.1 Cam05g0415 415
5 3819894 3825145 - CaPI482276_05g004160.1 Cam05g0416 416
5 3831855 3833645 + CaPI482276_05g004180.1 Cam05g0418 418
6 8210794 8215475 + Carg06267-RA Car06g01092 1092
6 8216546 8219635 - Carg06266-RA Car06g01093 1093
6 8220385 8222262 + Carg06265-RA Car06g01094 1094
6 8224094 8230554 - Carg06264-RA Car06g01095 1095
6 8233100 8236818 + Carg06263-RA Car06g01096 1096
5 3460264 3463945 + CcPI632755_05g004170.1 Cco05g0417 417
5 3465408 3467900 - CcPI632755_05g004180.1 Cco05g0418 418
5 3469195 3470971 + CcPI632755_05g004190.1 Cco05g0419 419
5 3471458 3472210 - CcPI632755_05g004200.1 Cco05g0420 420
5 3473852 3479088 - CcPI632755_05g004210.1 Cco05g0421 421
5 3486011 3487951 + CcPI632755_05g004230.1 Cco05g0423 423
5 3457017 3460699 + CePI673135_05g004170.1 Cec05g0417 417
5 3462117 3464723 - CePI673135_05g004180.1 Cec05g0418 418
5 3465825 3467616 + CePI673135_05g004190.1 Cec05g0419 419
5 3468103 3468855 - CePI673135_05g004200.1 Cec05g0420 420
5 3470473 3475586 - CePI673135_05g004210.1 Cec05g0421 421
5 3482639 3484173 + CePI673135_05g004230.1 Cec05g0423 423
6 2731654 2735106 + Chy6G109300.1 Chy06g00402 402
6 2735977 2738808 - Chy6G109310.1 Chy06g00403 403
6 2738954 2740443 + Chy6G109320.1 Chy06g00404 404
6 2740926 2741675 - Chy6G109330.1 Chy06g00405 405
6 2743732 2747833 - Chy6G109340.1 Chy06g00406 406
6 2751244 2756428 + Chy6G109350.1 Chy06g00407 407
5 3518707 3522680 + ClG42_05g0040800.10 Clacu05g0408 408
5 3524094 3526680 - ClG42_05g0040900.10 Clacu05g0409 409
5 3527869 3529662 + ClG42_05g0041000.10 Clacu05g0410 410
5 3530149 3530901 - ClG42_05g0041100.10 Clacu05g0411 411
5 3532504 3538152 - ClG42_05g0041200.10 Clacu05g0412 412
5 3540146 3544687 + ClG42_05g0041300.10 Clacu05g0413 413
5 3479764 3483946 + ClCG05G003650.1 Cla05g00379 379
5 3484887 3487667 - ClCG05G003660.2 Cla05g00380 380
5 3488794 3490649 + ClCG05G003670.2 Cla05g00381 381
5 3491136 3491888 - ClCG05G003675.1 Cla05g00382 382
5 3494152 3498811 - ClCG05G003680.1 Cla05g00383 383
5 3501840 3507964 + ClCG05G003690.2 Cla05g00384 384
6 8469631 8474191 + CmaCh06G012710.1 Cma06g01271 1271
6 8475230 8478559 - CmaCh06G012720.1 Cma06g01272 1272
6 8479400 8480848 + CmaCh06G012730.1 Cma06g01273 1273
6 8481326 8490644 - CmaCh06G012740.1 Cma06g01274 1274
6 8491777 8495281 + CmaCh06G012750.1 Cma06g01275 1275
14 13223759 13224499 + CmaCh14G018650.1 Cma14g01865 1865
6 2686558 2690483 + MELO3C006344.2.1 Cme06g00417 417
6 2690930 2693727 - MELO3C006345.2.1 Cme06g00418 418
6 2695077 2696982 + MELO3C006346.2.1 Cme06g00419 419
6 2696586 2697632 - MELO3C006347.2.1 Cme06g00420 420
6 2698986 2704481 - MELO3C031654.2.1 Cme06g00421 421
6 2706551 2709626 + MELO3C006348.2.1 Cme06g00422 422
6 9660025 9663753 + CmoCh06G012790.1 Cmo06g01279 1279
6 9664786 9667944 - CmoCh06G012800.1 Cmo06g01280 1280
6 9668614 9670019 + CmoCh06G012810.1 Cmo06g01281 1281
6 9670497 9680679 - CmoCh06G012820.1 Cmo06g01282 1282
6 9681169 9685368 + CmoCh06G012840.1 Cmo06g01284 1284
14 14210942 14211682 + CmoCh14G019100.1 Cmo14g01910 1910
5 3356730 3360705 + CmPI595203_05g003910.1 Cmu05g0391 391
5 3362119 3364705 - CmPI595203_05g003920.1 Cmu05g0392 392
5 3365897 3367698 + CmPI595203_05g003930.1 Cmu05g0393 393
5 3368185 3368937 - CmPI595203_05g003940.1 Cmu05g0394 394
5 3370538 3377095 - CmPI595203_05g003950.1 Cmu05g0395 395
5 3378415 3384068 + CmPI595203_05g003960.1 Cmu05g0396 396
4 1727802 1730741 - Conep04aG0039300.1 Cone4ag0380 380
14 920845 922379 - Conep14aG0020600.1 Cone14ag0202 202
14 938499 940672 + Conep14aG0020800.1 Cone14ag0204 204
15 1039889 1041776 - Conep15aG0022400.1 Cone15ag0220 220
15 1056960 1057710 - Conep15aG0022900.1 Cone15ag0225 225
15 1059434 1061025 + Conep15aG0023000.1 Cone15ag0226 226
3 12108423 12109163 + Cp4.1LG03g18290.1 Cpe03g01563 1563
8 2314474 2316850 - Cp4.1LG08g02990.1 Cpe08g00372 372
8 2320647 2329252 + Cp4.1LG08g03090.1 Cpe08g00373 373
8 2330347 2331183 + Cp4.1LG08g03040.1 Cpe08g00375 375
8 2333780 2336959 + Cp4.1LG08g03060.1 Cpe08g00376 376
8 2338053 2341747 - Cp4.1LG08g03010.1 Cpe08g00377 377
5 4142085 4145780 + CrPI670011_05g004530.1 Cre05g0453 453
5 4147196 4149774 - CrPI670011_05g004540.1 Cre05g0454 454
5 4150962 4152744 + CrPI670011_05g004550.1 Cre05g0455 455
5 4153231 4153983 - CrPI670011_05g004560.1 Cre05g0456 456
5 4155557 4162109 - CrPI670011_05g004570.1 Cre05g0457 457
5 4163463 4169492 + CrPI670011_05g004580.1 Cre05g0458 458
3 8951274 8954887 + CsaV3_3G011360.1 Csa03g01136 1136
3 8955925 8958720 - CsaV3_3G011370.1 Csa03g01137 1137
3 8958554 8961795 + CsaV3_3G011380.1 Csa03g01138 1138
3 8960830 8961579 - CsaV3_3G011390.1 Csa03g01139 1139
3 8963019 8968489 - CsaV3_3G011400.1 Csa03g01140 1140
3 8970219 8973321 + CsaV3_3G011410.1 Csa03g01141 1141
5 68844978 68849816 - Hsped.05g18540.1 Hepe05g1854 1854
5 25268105 25270795 - Lsi05G017980.1 Lsi05g01798 1798
5 25272019 25283464 + Lsi05G017990.1 Lsi05g01799 1799
5 25282270 25283817 - Lsi05G018010.1 Lsi05g01801 1801
5 25284876 25287663 + Lsi05G018020.1 Lsi05g01802 1802
5 25289051 25295890 - Lsi05G018030.1 Lsi05g01803 1803
5 10902339 10909796 - Vvi5g829 Vvi5g829 829
5 10923364 10923571 - Vvi5g830 Vvi5g830 830
5 10933220 10936995 + Vvi5g831 Vvi5g831 831
5 10938187 10941512 + Vvi5g832 Vvi5g832 832
5 10941512 10941653 + Vvi5g833 Vvi5g833 833
5 10944034 10946420 - Vvi5g834 Vvi5g834 834
5 10988735 10994229 + Vvi5g835 Vvi5g835 835
5 11007057 11011480 + Vvi5g836 Vvi5g836 836
5 11020639 11049781 - Vvi5g837 Vvi5g837 837
5 11066379 11068652 + Vvi5g838 Vvi5g838 838
       

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