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
Vvi19g114 . . . . . . . . . . . . . Car09g00732 . Cpe06g00650 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g00810 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g115 . . . Bda09g00539 . . . . Cmo16g00478 . . Cma09g00816 . Car09g00733 . Cpe06g00651 . . . . . . . . . . . . . . . . . . . . . . . . . Bda05g00788 . Bpe11g00449 . . . . . Cmo09g00811 . Cma16g00443 . . Cpe14g00373 . . . . . . . . . . . . . . . . Csa04g00802 . .
Vvi19g116 Blo03g00699 . . . Bpe09g00257 Bpe08g00996 . Bma13g00930 . . Cma01g01246 Cma09g00817 Car01g01067 Car09g00734 Sed05g2521 Cpe06g00652 . Bhi09g03506 Tan01g4327 Cmetu07g1552 . . Mch11g1013 . Cla11g01713 Cam11g1782 Cec11g1803 Cco11g1808 Clacu11g1941 Cmu11g1752 Cre11g2160 . . . . Lsi04g02015 . . . . . . . Bpe11g00450 . . Bma14g00266 . Cmo01g01301 Cmo09g00812 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g117 Blo03g00690 . . . . . . . . . . Cma09g00818 . Car09g00735 . Cpe06g00653 Cpe02g00670 . . . . . . . . . . . . . . Cone6ag0191 . . . . Csa04g02288 Chy07g00025 Cme07g00539 . . . . . . . . . . Cmo09g00813 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g118 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g119 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g120 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g121 . . . . . . Bma10g00474 . Cmo16g00477 Cmo04g00613 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo07g00965 Blo10g00734 . Bda12g00818 . Bpe03g00854 . . . . . Cma04g00573 Cma16g00442 Car04g00543 . Cpe14g00372 Cpe01g00518 . . . . . . . . . . . . . . Lsi05g00796 . . .
Vvi19g122 . . . . . . . . . . Cma01g01244 Cma09g00815 Car01g01065 Car09g00731 . Cpe06g00508 Cpe02g00673 Bhi09g03502 Tan01g4331 . . . Mch11g1016 . Cla11g01716 Cam11g1785 Cec11g1806 Cco11g1811 Clacu11g1944 Cmu11g1755 Cre11g2163 Cone6ag0188 Cone9ag0214 . . Lsi04g02020 Csa04g02292 Chy07g00029 Cme07g00542 . . . . . . . . . Cmo01g01299 Cmo09g00809 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g123 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 56334546 56335313 + Bda021942.1 Bda05g00788 788
9 7066402 7076405 + Bda031142.1 Bda09g00539 539
12 37604835 37610919 - Bda009329.1 Bda12g00818 818
9 88385886 88392492 + XM_039042445.1 Bhi09g03502 3502
9 88492771 88498774 + XM_039041925.1 Bhi09g03506 3506
3 29062542 29073773 - BLOR11871 Blo03g00690 690
3 29646381 29661068 + BLOR11880 Blo03g00699 699
7 29043691 29049873 + BLOR18897 Blo07g00965 965
10 23031825 23039260 - BLOR02524 Blo10g00734 734
10 5444776 5446477 - Bma004146.1 Bma10g00474 474
13 39780582 39797477 - Bma010008.2 Bma13g00930 930
14 3133294 3137809 + Bma010679.1 Bma14g00266 266
3 28347802 28349528 + Bpe012762.1 Bpe03g00854 854
8 12293073 12297968 - Bpe023121.1 Bpe08g00996 996
9 1883106 1888375 + Bpe023928.1 Bpe09g00257 257
11 3492633 3493970 + Bpe003821.1 Bpe11g00449 449
11 3503637 3508106 + Bpe003822.1 Bpe11g00450 450
11 30298235 30303219 - CaPI482276_11g017820.1 Cam11g1782 1782
11 30333930 30336912 - CaPI482276_11g017850.1 Cam11g1785 1785
1 10000889 10004566 + Carg14729-RA Car01g01065 1065
1 10014498 10020735 + Carg14731-RA Car01g01067 1067
4 3054350 3058096 + Carg13164-RA Car04g00543 543
9 4347686 4351209 + Carg17051-RA Car09g00731 731
9 4355654 4356205 + Carg17052-RA Car09g00732 732
9 4358175 4359533 - Carg17053-RA Car09g00733 733
9 4365263 4370442 + Carg17054-RA Car09g00734 734
9 4371112 4375190 + Carg17055-RA Car09g00735 735
11 30714831 30719810 - CcPI632755_11g018080.1 Cco11g1808 1808
11 30749918 30752900 - CcPI632755_11g018110.1 Cco11g1811 1811
11 32164498 32169480 - CePI673135_11g018030.1 Cec11g1803 1803
11 32200644 32203625 - CePI673135_11g018060.1 Cec11g1806 1806
7 217774 222352 - Chy7G128550.1 Chy07g00025 25
7 253701 256671 - Chy7G128590.1 Chy07g00029 29
11 30335480 30340462 - ClG42_11g0194100.10 Clacu11g1941 1941
11 30370163 30373145 - ClG42_11g0194400.10 Clacu11g1944 1944
11 30674021 30689406 - ClCG11G017480.2 Cla11g01713 1713
11 30720599 30723581 - ClCG11G017520.2 Cla11g01716 1716
1 8963556 8966867 + CmaCh01G012440.1 Cma01g01244 1244
1 8976735 8987741 + CmaCh01G012460.1 Cma01g01246 1246
4 2920426 2923112 + CmaCh04G005730.1 Cma04g00573 573
9 4002602 4006468 + CmaCh09G008150.1 Cma09g00815 815
9 4013502 4014860 - CmaCh09G008160.1 Cma09g00816 816
9 4019523 4024693 + CmaCh09G008170.1 Cma09g00817 817
9 4025738 4029921 + CmaCh09G008180.1 Cma09g00818 818
16 2204068 2208159 - CmaCh16G004420.1 Cma16g00442 442
16 2211987 2213303 + CmaCh16G004430.1 Cma16g00443 443
7 4470125 4475050 - MELO3C025637.2.1 Cme07g00539 539
7 4501766 4506135 - MELO3C025634.2.1 Cme07g00542 542
7 21564540 21570411 - PI0029107.1 Cmetu07g1552 1552
1 10325223 10328850 + CmoCh01G012990.1 Cmo01g01299 1299
1 10339801 10346256 + CmoCh01G013010.1 Cmo01g01301 1301
4 3052828 3056382 + CmoCh04G006130.1 Cmo04g00613 613
9 4160541 4164672 + CmoCh09G008090.1 Cmo09g00809 809
9 4168535 4170049 + CmoCh09G008100.1 Cmo09g00810 810
9 4171305 4172663 - CmoCh09G008110.1 Cmo09g00811 811
9 4179053 4183696 + CmoCh09G008120.1 Cmo09g00812 812
9 4184584 4188859 + CmoCh09G008130.1 Cmo09g00813 813
16 2280928 2287411 - CmoCh16G004770.1 Cmo16g00477 477
16 2288991 2290307 + CmoCh16G004780.1 Cmo16g00478 478
11 29588601 29593583 - CmPI595203_11g017520.1 Cmu11g1752 1752
11 29623279 29626261 - CmPI595203_11g017550.1 Cmu11g1755 1755
6 904741 908719 + Conep06aG0019000.1 Cone6ag0188 188
6 920142 923159 + Conep06aG0019300.1 Cone6ag0191 191
9 917068 921187 + Conep09aG0021700.1 Cone9ag0214 214
1 2980992 2984609 + Cp4.1LG01g01580.1 Cpe01g00518 518
2 4205963 4209918 - Cp4.1LG02g02070.1 Cpe02g00670 670
2 4227564 4231240 - Cp4.1LG02g02040.1 Cpe02g00673 673
6 3027491 3030540 + Cp4.1LG06g05020.1 Cpe06g00508 508
6 4046703 4047447 + Cp4.1LG06g06460.1 Cpe06g00650 650
6 4049263 4050621 - Cp4.1LG06g06550.1 Cpe06g00651 651
6 4056565 4061699 + Cp4.1LG06g06500.1 Cpe06g00652 652
6 4062919 4067004 + Cp4.1LG06g06540.1 Cpe06g00653 653
14 2274107 2278660 - Cp4.1LG14g03380.1 Cpe14g00372 372
14 2283825 2289159 + Cp4.1LG14g03470.1 Cpe14g00373 373
11 33242018 33246992 - CrPI670011_11g021600.1 Cre11g2160 2160
11 33276681 33279662 - CrPI670011_11g021630.1 Cre11g2163 2163
4 5619575 5626101 - CsaV3_4G008020.1 Csa04g00802 802
4 23433930 23439249 - CsaV3_4G033140.1 Csa04g02288 2288
4 23465791 23470303 - CsaV3_4G033180.1 Csa04g02292 2292
4 27219586 27233478 - Lsi04G020150.1 Lsi04g02015 2015
4 27268432 27272475 - Lsi04G020200.1 Lsi04g02020 2020
5 11636923 11639446 - Lsi05G007960.1 Lsi05g00796 796
11 7015709 7021694 - MC11g_new0184 Mch11g1013 1013
11 7040334 7047236 - MC11g0832 Mch11g1016 1016
5 37254259 37260506 - Sed0024627.1 Sed05g2521 2521
1 108084091 108090210 - Tan0004302.2 Tan01g4327 4327
1 108145997 108149969 - Tan0014097.2 Tan01g4331 4331
19 1427251 1429656 - Vvi19g114 Vvi19g114 114
19 1451416 1452775 + Vvi19g115 Vvi19g115 115
19 1470023 1477163 + Vvi19g116 Vvi19g116 116
19 1480081 1486910 + Vvi19g117 Vvi19g117 117
19 1489144 1494170 + Vvi19g118 Vvi19g118 118
19 1494736 1500193 - Vvi19g119 Vvi19g119 119
19 1509613 1511168 + Vvi19g120 Vvi19g120 120
19 1528686 1547441 + Vvi19g121 Vvi19g121 121
19 1566159 1570486 - Vvi19g122 Vvi19g122 122
19 1570518 1570851 + Vvi19g123 Vvi19g123 123
       

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