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
Vvi2g482 . Blo03g00177 Bda06g00050 . . Bpe07g00149 . . . Cmo16g01090 . . . . . Cpe14g00862 . . . . . . . . Cla10g00297 Cam10g0311 Cec10g0321 Cco10g0314 Clacu10g0308 Cmu10g1147 Cre10g0557 . . Cone6ag0710 Cone9ag0712 . . . . . . . . . . . Bma12g00143 . . . . Cma16g01042 . Car16g00993 . . . . . . . . . . . . . . . . . . Chy06g02004 .
Vvi2g483 Blo02g01061 Blo03g00176 . . . . . . Cmo06g00777 Cmo16g01091 . . . . . Cpe14g00863 . . . . . . . . Cla10g00296 . . . . . . . . Cone6ag0709 Cone9ag0711 Lsi07g01343 . . Cme06g02630 . . . . . . Bma05g00780 . . . . Cma06g00755 Cma16g01043 Car06g00674 Car16g00995 Cpe08g00760 . Bhi12g00580 . . . . . . . . . . . . . . Csa03g00318 Chy06g02006 .
Vvi2g484 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g485 Blo02g01060 . . . Bpe05g00599 . . . Cmo06g00778 Cmo16g01092 . . . . . Cpe14g00864 . . . . . . . . Cla10g00295 Cam10g0309 Cec10g0318 Cco10g0312 Clacu10g0306 Cmu10g1145 Cre10g0554 . . Cone6ag0708 Cone9ag0710 Lsi07g01342 . . Cme06g02628 . . Bda07g00020 . . Bpe11g00253 . . . . . Cma06g00756 Cma16g01044 Car06g00675 Car16g00996 Cpe08g00759 . . . . . . . . . . . . . . . . Csa03g00316 Chy06g02007 .
Vvi2g486 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g487 . . . . . . . . . . . Cma15g01162 . Car15g01050 . . . . . . . . . . . . . . . . . . . . . . Csa05g00378 Chy09g01134 . . . . . Bpe08g01448 . . . . . Cmo15g01223 . . . . . Cpe13g00211 Bhi12g00377 . . Lac11g2222 Hepe06g1638 . Lcy12g1761 Cla01g00351 Cam01g0367 Cec01g0363 Cco01g0377 Clacu01g0370 Cmu01g0350 Cre09g2160 Lsi09g00378 . . Cme09g01665
Vvi2g488 . . . . . . . . Cmo06g01166 Cmo16g01095 . . . . . Cpe14g00867 . . . . . . . . Cla10g00293 Cam10g0306 Cec10g0315 Cco10g0309 Clacu10g0303 Cmu10g1142 Cre10g0551 . . . . Lsi07g01339 . . Cme06g02624 . . . . . . . . . . . . Cma16g01046 Car06g00980 Car16g00999 Cpe08g00481 . . . . . . . . . . . . . . . . Csa03g00313 Chy06g02010 .
Vvi2g489 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g490 . . . Bda08g00563 Bpe05g00593 . . . . . . . . . . . . . . . . . . . Cla10g00287 Cam10g0298 Cec10g0306 Cco10g0301 Clacu10g0297 Cmu10g1136 Cre10g0544 . . Cone11ag0591 Cone18ag0916 . . . . . . Bda07g00013 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g491 . . Bda06g00040 . . Bpe07g00158 Bma07g01606 Bma14g00031 Cmo06g00783 . Cma02g01526 . Car02g01287 . . . Cpe05g00262 . . . . . . . Cla10g00286 . . . . . . . . Cone6ag0699 Cone9ag0699 . Csa05g00392 . Cme06g02615 Blo03g00403 . Bda07g00012 Bda09g00087 Bpe08g01441 Bpe11g00257 . Bma12g00151 . Cmo02g01570 . Cma06g00761 . Car06g00680 . Cpe08g00755 . Bhi12g00401 . . . . . Lcy12g1794 Cla01g00365 . . . . . . Lsi09g00392 Csa03g00305 Chy06g02017 Cme09g01650
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 417194 418322 - Bda023210.1 Bda06g00040 40
6 544613 546568 - Bda023222.1 Bda06g00050 50
7 209566 211070 - Bda025061.1 Bda07g00012 12
7 244859 245398 + Bda025064.1 Bda07g00013 13
7 341798 342241 - Bda025074.1 Bda07g00020 20
8 5714847 5715356 - Bda029022.1 Bda08g00563 563
9 1683957 1690314 + Bda030619.1 Bda09g00087 87
12 12270520 12276126 - XM_039018656.1 Bhi12g00377 377
12 13562273 13567776 + XM_039051132.1 Bhi12g00401 401
12 18223365 18226589 - XM_039020287.1 Bhi12g00580 580
2 40834724 40835252 - BLOR10790 Blo02g01060 1060
2 40839744 40842135 + BLOR10791 Blo02g01061 1061
3 4415187 4423994 + BLOR11357 Blo03g00176 176
3 4424305 4430353 - BLOR11358 Blo03g00177 177
3 10932887 10933571 + BLOR11584 Blo03g00403 403
5 44743705 44745983 + Bma021879.1 Bma05g00780 780
7 51471561 51475775 - Bma026902.1 Bma07g01606 1606
12 2063106 2064513 + Bma007021.1 Bma12g00143 143
12 2144719 2145845 + Bma007031.1 Bma12g00151 151
14 402231 403963 + Bma010438.1 Bma14g00031 31
5 19990493 19990996 + Bpe018010.1 Bpe05g00593 593
5 20012247 20012690 - Bpe018016.1 Bpe05g00599 599
7 1052810 1054738 + Bpe020959.1 Bpe07g00149 149
7 1091766 1092892 + Bpe020968.1 Bpe07g00158 158
8 15154462 15158436 - Bpe023555.1 Bpe08g01441 1441
8 15221047 15232594 + Bpe023561.1 Bpe08g01448 1448
11 1778146 1778595 + Bpe003628.1 Bpe11g00253 253
11 1851372 1855908 + Bpe003633.1 Bpe11g00257 257
1 4101156 4107393 - CaPI482276_01g003670.1 Cam01g0367 367
10 5129569 5130024 + CaPI482276_10g002980.1 Cam10g0298 298
10 5179746 5181068 + CaPI482276_10g003060.1 Cam10g0306 306
10 5191359 5193557 + CaPI482276_10g003090.1 Cam10g0309 309
10 5211904 5214071 - CaPI482276_10g003110.1 Cam10g0311 311
2 8603331 8605533 + Carg02461-RA Car02g01287 1287
6 4019850 4022354 - Carg21608-RA Car06g00674 674
6 4029104 4029547 - Carg21607-RA Car06g00675 675
6 4048243 4049261 + Carg21602-RA Car06g00680 680
6 7509821 7511119 - Carg06379-RA Car06g00980 980
15 8299306 8304417 + Carg16693-RA Car15g01050 1050
16 8421531 8424057 + Carg25277-RA Car16g00993 993
16 8424942 8428062 - Carg25275-RA Car16g00995 995
16 8438258 8438701 - Carg25274-RA Car16g00996 996
16 8446484 8447806 - Carg25271-RA Car16g00999 999
1 3766315 3772606 - CcPI632755_01g003770.1 Cco01g0377 377
10 3583438 3583893 + CcPI632755_10g003010.1 Cco10g0301 301
10 3633789 3635111 + CcPI632755_10g003090.1 Cco10g0309 309
10 3645637 3648602 + CcPI632755_10g003120.1 Cco10g0312 312
10 3666037 3668178 - CcPI632755_10g003140.1 Cco10g0314 314
1 3779675 3786010 - CePI673135_01g003630.1 Cec01g0363 363
10 3751104 3752018 + CePI673135_10g003060.1 Cec10g0306 306
10 3803594 3804916 + CePI673135_10g003150.1 Cec10g0315 315
10 3815440 3815883 + CePI673135_10g003180.1 Cec10g0318 318
10 3854165 3856332 - CePI673135_10g003210.1 Cec10g0321 321
6 24000890 24003057 + Chy6G125320.1 Chy06g02004 2004
6 24009750 24012396 - Chy6G125340.1 Chy06g02006 2006
6 24028732 24030260 - Chy6G125350.1 Chy06g02007 2007
6 24046029 24047351 - Chy6G125380.1 Chy06g02010 2010
6 24104999 24108205 + Chy6G125450.1 Chy06g02017 2017
9 13575907 13579789 + Chy9G168500.1 Chy09g01134 1134
1 3734042 3740224 - ClG42_01g0037000.10 Clacu01g0370 370
10 3879581 3880036 + ClG42_10g0029700.10 Clacu10g0297 297
10 3930210 3931532 + ClG42_10g0030300.10 Clacu10g0303 303
10 3940633 3941076 + ClG42_10g0030600.10 Clacu10g0306 306
10 3960806 3962973 - ClG42_10g0030800.10 Clacu10g0308 308
1 3849393 3854069 - ClCG01G003660.2 Cla01g00351 351
1 4017236 4022712 + ClCG01G003780.2 Cla01g00365 365
10 3773449 3776486 - ClCG10G003010.1 Cla10g00286 286
10 3787997 3795817 + ClCG10G003020.2 Cla10g00287 287
10 3841441 3842763 + ClCG10G003090.1 Cla10g00293 293
10 3853189 3853835 + ClCG10G003120.2 Cla10g00295 295
10 3870206 3872963 + ClCG10G003130.1 Cla10g00296 296
10 3873549 3876331 - ClCG10G003140.2 Cla10g00297 297
2 8685815 8687779 + CmaCh02G015260.1 Cma02g01526 1526
6 3834180 3836693 - CmaCh06G007550.1 Cma06g00755 755
6 3842735 3843178 - CmaCh06G007560.1 Cma06g00756 756
6 3867079 3869220 + CmaCh06G007610.1 Cma06g00761 761
15 7367169 7373110 + CmaCh15G011620.1 Cma15g01162 1162
16 8008650 8011362 + CmaCh16G010420.1 Cma16g01042 1042
16 8012040 8015785 - CmaCh16G010430.1 Cma16g01043 1043
16 8024498 8024941 - CmaCh16G010440.1 Cma16g01044 1044
16 8032627 8033949 - CmaCh16G010460.1 Cma16g01046 1046
6 33401593 33405654 - MELO3C013971.2.1 Cme06g02615 2615
6 33456896 33459826 + MELO3C013979.2.1 Cme06g02624 2624
6 33476929 33478128 + MELO3C013982.2.1 Cme06g02628 2628
6 33492312 33495744 + MELO3C013983.2.1 Cme06g02630 2630
9 21231803 21236691 - MELO3C005563.2.1 Cme09g01650 1650
9 21348805 21352709 + MELO3C005579.2.1 Cme09g01665 1665
2 9068803 9071255 + CmoCh02G015700.1 Cmo02g01570 1570
6 4052804 4055752 - CmoCh06G007770.1 Cmo06g00777 777
6 4062441 4062884 - CmoCh06G007780.1 Cmo06g00778 778
6 4088334 4089352 + CmoCh06G007830.1 Cmo06g00783 783
6 8944014 8945312 - CmoCh06G011660.1 Cmo06g01166 1166
15 8442459 8447068 + CmoCh15G012230.1 Cmo15g01223 1223
16 7703806 7706517 + CmoCh16G010900.1 Cmo16g01090 1090
16 7707301 7710686 - CmoCh16G010910.1 Cmo16g01091 1091
16 7720603 7721046 - CmoCh16G010920.1 Cmo16g01092 1092
16 7727860 7729182 - CmoCh16G010950.1 Cmo16g01095 1095
1 3681052 3687274 - CmPI595203_01g003500.1 Cmu01g0350 350
10 3996613 3997068 + CmPI595203_10g011360.1 Cmu10g1136 1136
10 4047347 4048669 + CmPI595203_10g011420.1 Cmu10g1142 1142
10 4058909 4061107 + CmPI595203_10g011450.1 Cmu10g1145 1145
10 4079099 4081266 - CmPI595203_10g011470.1 Cmu10g1147 1147
6 3538753 3539400 - Conep06aG0072100.1 Cone6ag0699 699
6 3576597 3577297 - Conep06aG0073000.1 Cone6ag0708 708
6 3579306 3582128 + Conep06aG0073100.1 Cone6ag0709 709
6 3582293 3584509 - Conep06aG0073200.1 Cone6ag0710 710
9 3363497 3364131 - Conep09aG0071600.1 Cone9ag0699 699
9 3408376 3409206 - Conep09aG0072700.1 Cone9ag0710 710
9 3410708 3413366 + Conep09aG0072800.1 Cone9ag0711 711
9 3413456 3416534 - Conep09aG0072900.1 Cone9ag0712 712
11 3558397 3559618 + Conep11aG0060700.1 Cone11ag0591 591
18 6544587 6545851 - Conep18aG0094300.1 Cone18ag0916 916
5 1482343 1485065 - Cp4.1LG05g02680.1 Cpe05g00262 262
8 3084954 3086252 + Cp4.1LG08g02040.1 Cpe08g00481 481
8 6078943 6079975 - Cp4.1LG08g07540.1 Cpe08g00755 755
8 6102348 6102791 + Cp4.1LG08g07480.1 Cpe08g00759 759
8 6109344 6112176 + Cp4.1LG08g07600.1 Cpe08g00760 760
13 1598781 1605132 - Cp4.1LG13g02160.1 Cpe13g00211 211
14 7126768 7129463 + Cp4.1LG14g08530.1 Cpe14g00862 862
14 7130495 7134086 - Cp4.1LG14g08640.1 Cpe14g00863 863
14 7143419 7143862 - Cp4.1LG14g08610.1 Cpe14g00864 864
14 7151218 7153250 - Cp4.1LG14g08730.1 Cpe14g00867 867
9 40608140 40614474 + CrPI670011_09g021600.1 Cre09g2160 2160
10 4964351 4964806 + CrPI670011_10g005440.1 Cre10g0544 544
10 5022359 5023681 + CrPI670011_10g005510.1 Cre10g0551 551
10 5034240 5034683 + CrPI670011_10g005540.1 Cre10g0554 554
10 5054266 5056432 - CrPI670011_10g005570.1 Cre10g0557 557
3 2600481 2604164 - CsaV3_3G003050.1 Csa03g00305 305
3 2650470 2651989 + CsaV3_3G003130.1 Csa03g00313 313
3 2662832 2663275 + CsaV3_3G003160.1 Csa03g00316 316
3 2674310 2677811 + CsaV3_3G003180.1 Csa03g00318 318
5 2437145 2443041 - CsaV3_5G003780.1 Csa05g00378 378
5 2540628 2545728 + CsaV3_5G003920.1 Csa05g00392 392
6 67250713 67254401 - Hsped.06g16380.1 Hepe06g1638 1638
11 38264694 38270218 - Lag0032860.1 Lac11g2222 2222
12 38382486 38384857 - Maker00003025 Lcy12g1761 1761
12 38989456 38995130 + Maker00037908 Lcy12g1794 1794
7 19572709 19574031 + Lsi07G013390.1 Lsi07g01339 1339
7 19587340 19589151 + Lsi07G013420.1 Lsi07g01342 1342
7 19607203 19610300 + Lsi07G013430.1 Lsi07g01343 1343
9 3971227 3977789 - Lsi09G003780.1 Lsi09g00378 378
9 4144783 4149901 + Lsi09G003920.1 Lsi09g00392 392
2 4748584 4752156 + Vvi2g482 Vvi2g482 482
2 4752552 4755341 - Vvi2g483 Vvi2g483 483
2 4757275 4758589 - Vvi2g484 Vvi2g484 484
2 4762058 4762800 + Vvi2g485 Vvi2g485 485
2 4766575 4768165 - Vvi2g486 Vvi2g486 486
2 4768238 4782009 - Vvi2g487 Vvi2g487 487
2 4801243 4803138 - Vvi2g488 Vvi2g488 488
2 4810828 4811634 - Vvi2g489 Vvi2g489 489
2 4822702 4823194 - Vvi2g490 Vvi2g490 490
2 4836973 4839409 + Vvi2g491 Vvi2g491 491
       

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