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
Vvi19g174 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g175 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g176 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe01g00439 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g177 . . . . . . . . . . . Cma09g00841 . Car09g00754 . . . Bhi09g03466 . . . Hepe01g1411 . . Cla11g01733 Cam11g1803 Cec11g1823 Cco11g1829 Clacu11g1962 Cmu11g1772 Cre11g2179 . Cone9ag0197 . . Lsi04g02043 Csa04g02315 Chy07g00050 Cme07g00568 Blo07g00954 . Bda05g00775 . . Bpe03g00842 . . . . Cmo09g00834 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g178 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g179 . . Bda07g00312 . . . . . . . Cma01g01229 . Car01g01050 Car09g00755 Sed04g2424 Cpe06g00670 Cpe02g00687 Bhi09g03464 Tan01g4364 Cmetu07g0974 . Hepe01g1410 Mch11g1040 . Cla11g01734 Cam11g1804 Cec11g1824 Cco11g1830 Clacu11g1963 Cmu11g1773 Cre11g2180 Cone6ag0170 Cone9ag0196 Cone14ag1052 Cone15ag1044 Lsi04g02044 Csa04g02316 . Cme07g00569 . . . . . . . Bma14g00251 . Cmo01g01282 Cmo09g00835 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g180 . . . Bda09g00528 Bpe09g00242 . Bma10g00494 . Cmo16g00438 Cmo04g00587 Cma01g01227 Cma09g00843 Car01g01048 Car09g00756 . Cpe06g00671 Cpe02g00688 Bhi09g03463 . . . . Mch11g1041 . Cla11g01735 . . . . . . Cone6ag0169 Cone9ag0195 . . Lsi04g02045 Csa04g02317 . Cme07g00570 . Blo10g00750 . Bda12g00830 . . . . . Cmo01g01281 Cmo09g00836 Cma04g00554 Cma16g00405 Car04g00522 . . Cpe01g00495 . . . . . . . Cla05g01000 . . . . . . . . . .
Vvi19g181 . . . Bda09g00526 . . . . . . Cma01g01224 . Car01g01046 . . . Cpe02g00690 Bhi09g03461 . . . Hepe01g1407 . . Cla11g01737 Cam11g1807 Cec11g1827 . Clacu11g1967 Cmu11g1777 Cre11g2183 . . Cone14ag1055 Cone15ag1048 Lsi04g02047 Csa04g02319 Chy07g00053 Cme07g00572 . . . . . . . . . Cmo01g01277 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g182 . Blo03g01555 . . . Bpe08g01011 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone9ag0193 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g183 Blo03g00670 . . Bda09g00525 . Bpe08g01012 . . . . Cma01g01223 Cma09g00845 Car01g01045 Car09g00758 Sed05g2552 Cpe06g00673 Cpe02g00691 Bhi09g03459 Tan01g4369 Cmetu07g0293 . Hepe01g1406 Mch11g1044 . Cla11g01738 Cam11g1808 Cec11g1828 Cco11g1834 Clacu11g1968 Cmu11g1778 Cre11g2184 Cone6ag0168 Cone9ag0192 . . Lsi04g02048 Csa04g02320 Chy07g00054 Cme07g00573 . . . . . . . . . Cmo01g01276 Cmo09g00839 . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 56209954 56211169 - Bda021926.1 Bda05g00775 775
7 4189091 4191795 - Bda025395.1 Bda07g00312 312
9 6934055 6935374 - Bda031127.1 Bda09g00525 525
9 6936332 6941582 - Bda031128.1 Bda09g00526 526
9 6949993 6951353 - Bda031130.1 Bda09g00528 528
12 37885036 37887382 + Bda009347.1 Bda12g00830 830
9 87445486 87449367 - XM_039043793.1 Bhi09g03459 3459
9 87456247 87472163 - XM_039042307.1 Bhi09g03461 3461
9 87538819 87541541 - XM_039043718.1 Bhi09g03463 3463
9 87616385 87620288 + XM_039043902.1 Bhi09g03464 3464
9 87622123 87625767 + XM_039044324.1 Bhi09g03466 3466
3 28270125 28271668 + BLOR11851 Blo03g00670 670
3 43261360 43262934 - BLOR12736 Blo03g01555 1555
7 28835730 28836998 - BLOR18886 Blo07g00954 954
10 23602509 23605047 - BLOR02540 Blo10g00750 750
10 5847001 5849002 - Bma004185.1 Bma10g00494 494
14 2983508 2986224 - Bma010664.1 Bma14g00251 251
1 2694153 2695866 - Bpe000424.2 Bpe01g00439 439
3 28269837 28271670 - Bpe012750.1 Bpe03g00842 842
8 12409519 12414336 + Bpe026161 Bpe08g01011 1011
8 12411185 12412502 - Bpe023136.1 Bpe08g01012 1012
9 1764994 1767343 + Bpe023912.1 Bpe09g00242 242
11 30540030 30543695 - CaPI482276_11g018030.1 Cam11g1803 1803
11 30545224 30548316 - CaPI482276_11g018040.1 Cam11g1804 1804
11 30581323 30592419 + CaPI482276_11g018070.1 Cam11g1807 1807
11 30593950 30597883 + CaPI482276_11g018080.1 Cam11g1808 1808
1 9877915 9880450 - Carg14709-RA Car01g01045 1045
1 9880930 9892821 - Carg14710-RA Car01g01046 1046
1 9900557 9902555 - Carg14712-RA Car01g01048 1048
1 9910414 9913559 + Carg14714-RA Car01g01050 1050
4 2934681 2936899 - Carg13185-RA Car04g00522 522
9 4464796 4469231 - Carg17076-RA Car09g00754 754
9 4468749 4471113 - Carg17077-RA Car09g00755 755
9 4475168 4476931 + Carg17078-RA Car09g00756 756
9 4483722 4486619 + Carg17080-RA Car09g00758 758
11 30950011 30951453 - CcPI632755_11g018290.1 Cco11g1829 1829
11 30953532 30961396 - CcPI632755_11g018300.1 Cco11g1830 1830
11 30996979 31011746 + CcPI632755_11g018340.1 Cco11g1834 1834
11 32402707 32404149 - CePI673135_11g018230.1 Cec11g1823 1823
11 32406179 32413824 - CePI673135_11g018240.1 Cec11g1824 1824
11 32446635 32457623 + CePI673135_11g018270.1 Cec11g1827 1827
11 32459121 32463002 + CePI673135_11g018280.1 Cec11g1828 1828
7 443093 449129 - Chy7G128800.1 Chy07g00050 50
7 475820 485073 + Chy7G128830.1 Chy07g00053 53
7 486035 488716 + Chy7G128840.1 Chy07g00054 54
11 30576089 30578621 - ClG42_11g0196200.10 Clacu11g1962 1962
11 30580711 30583800 - ClG42_11g0196300.10 Clacu11g1963 1963
11 30618895 30628370 + ClG42_11g0196700.10 Clacu11g1967 1967
11 30629811 30633552 + ClG42_11g0196800.10 Clacu11g1968 1968
5 10068842 10072188 + ClCG05G009250.1 Cla05g01000 1000
11 30931645 30938394 - ClCG11G017760.2 Cla11g01733 1733
11 30939898 30943347 - ClCG11G017780.1 Cla11g01734 1734
11 30964447 30966810 + ClCG11G017790.2 Cla11g01735 1735
11 30982233 30992119 + ClCG11G017810.1 Cla11g01737 1737
11 30993219 30997660 + ClCG11G017820.1 Cla11g01738 1738
1 8839857 8842813 - CmaCh01G012230.1 Cma01g01223 1223
1 8843641 8855556 - CmaCh01G012240.1 Cma01g01224 1224
1 8863199 8864071 - CmaCh01G012270.1 Cma01g01227 1227
1 8871906 8874892 + CmaCh01G012290.1 Cma01g01229 1229
4 2803152 2805052 - CmaCh04G005540.1 Cma04g00554 554
9 4127785 4129647 - CmaCh09G008410.1 Cma09g00841 841
9 4137423 4139255 + CmaCh09G008430.1 Cma09g00843 843
9 4145125 4147473 + CmaCh09G008450.1 Cma09g00845 845
16 2011953 2014074 - CmaCh16G004050.1 Cma16g00405 405
7 4862240 4864893 - MELO3C025614.2.1 Cme07g00568 568
7 4865261 4868843 - MELO3C025613.2.1 Cme07g00569 569
7 4892727 4895543 + MELO3C025611.2.1 Cme07g00570 570
7 4907345 4916858 + MELO3C025610.2.1 Cme07g00572 572
7 4919860 4923454 + MELO3C025609.2.1 Cme07g00573 573
7 21830416 21833411 + PI0028239.1 Cmetu07g0293 293
7 21788667 21792093 - PI0003113.1 Cmetu07g0974 974
1 10193587 10196469 - CmoCh01G012760.1 Cmo01g01276 1276
1 10197644 10209631 - CmoCh01G012770.1 Cmo01g01277 1277
1 10218239 10218789 - CmoCh01G012810.1 Cmo01g01281 1281
1 10226696 10229971 + CmoCh01G012820.1 Cmo01g01282 1282
4 2928153 2930382 - CmoCh04G005870.1 Cmo04g00587 587
9 4279155 4281016 - CmoCh09G008340.1 Cmo09g00834 834
9 4282674 4285186 - CmoCh09G008350.1 Cmo09g00835 835
9 4289036 4290703 + CmoCh09G008360.1 Cmo09g00836 836
9 4297970 4300769 + CmoCh09G008390.1 Cmo09g00839 839
16 2083507 2086104 - CmoCh16G004380.1 Cmo16g00438 438
11 29831445 29833977 - CmPI595203_11g017720.1 Cmu11g1772 1772
11 29836067 29839157 - CmPI595203_11g017730.1 Cmu11g1773 1773
11 29874469 29883929 + CmPI595203_11g017770.1 Cmu11g1777 1777
11 29885370 29889097 + CmPI595203_11g017780.1 Cmu11g1778 1778
6 815341 817121 - Conep06aG0016900.1 Cone6ag0168 168
6 818644 820634 - Conep06aG0017000.1 Cone6ag0169 169
6 826133 828279 + Conep06aG0017100.1 Cone6ag0170 170
9 831348 834469 - Conep09aG0019400.1 Cone9ag0192 192
9 831920 832546 + Conep09aG0019500.1 Cone9ag0193 193
9 836125 837587 - Conep09aG0019700.1 Cone9ag0195 195
9 842530 845001 + Conep09aG0019800.1 Cone9ag0196 196
9 845400 846699 + Conep09aG0019900.1 Cone9ag0197 197
14 8871687 8890102 - Conep14aG0107300.1 Cone14ag1052 1052
14 8906300 8907419 + Conep14aG0107600.1 Cone14ag1055 1055
15 8663399 8665306 - Conep15aG0106600.1 Cone15ag1044 1044
15 8682534 8686683 + Conep15aG0107000.1 Cone15ag1048 1048
1 2862334 2864493 - Cp4.1LG01g01680.1 Cpe01g00495 495
2 4320144 4323244 - Cp4.1LG02g01920.1 Cpe02g00687 687
2 4330009 4332517 + Cp4.1LG02g01950.1 Cpe02g00688 688
2 4340715 4352776 + Cp4.1LG02g01820.1 Cpe02g00690 690
2 4353027 4355699 + Cp4.1LG02g01830.1 Cpe02g00691 691
6 4156834 4162013 - Cp4.1LG06g06710.1 Cpe06g00670 670
6 4167350 4169351 + Cp4.1LG06g06610.1 Cpe06g00671 671
6 4175602 4178888 + Cp4.1LG06g06600.1 Cpe06g00673 673
11 33495841 33498375 - CrPI670011_11g021790.1 Cre11g2179 2179
11 33500655 33503728 - CrPI670011_11g021800.1 Cre11g2180 2180
11 33536828 33547966 + CrPI670011_11g021830.1 Cre11g2183 2183
11 33549518 33553469 + CrPI670011_11g021840.1 Cre11g2184 2184
4 23649764 23651713 - CsaV3_4G033410.1 Csa04g02315 2315
4 23652836 23655737 - CsaV3_4G033420.1 Csa04g02316 2316
4 23667312 23669928 + CsaV3_4G033430.1 Csa04g02317 2317
4 23682142 23691781 + CsaV3_4G033450.1 Csa04g02319 2319
4 23692715 23695881 + CsaV3_4G033460.1 Csa04g02320 2320
1 79295325 79298310 - Hsped.01g14060.1 Hepe01g1406 1406
1 79300214 79312237 - Hsped.01g14070.1 Hepe01g1407 1407
1 79346647 79349421 + Hsped.01g14100.1 Hepe01g1410 1410
1 79350596 79352924 + Hsped.01g14110.1 Hepe01g1411 1411
4 27514150 27519524 - Lsi04G020430.1 Lsi04g02043 2043
4 27524052 27530788 - Lsi04G020440.1 Lsi04g02044 2044
4 27551472 27554233 + Lsi04G020450.1 Lsi04g02045 2045
4 27577473 27588716 + Lsi04G020470.1 Lsi04g02047 2047
4 27590097 27594274 + Lsi04G020480.1 Lsi04g02048 2048
11 7230214 7239877 - MC11g0851 Mch11g1040 1040
11 7249030 7251180 + MC11g0852 Mch11g1041 1041
11 7274003 7278857 + MC11g0855 Mch11g1044 1044
4 37519472 37523224 + Sed0016625.1 Sed04g2424 2424
5 37440411 37443056 + Sed0026173.1 Sed05g2552 2552
1 108540526 108543854 - Tan0020726.1 Tan01g4364 4364
1 108634114 108637182 + Tan0021483.1 Tan01g4369 4369
19 2290388 2291418 - Vvi19g174 Vvi19g174 174
19 2291818 2293513 - Vvi19g175 Vvi19g175 175
19 2297283 2302164 + Vvi19g176 Vvi19g176 176
19 2304392 2306969 - Vvi19g177 Vvi19g177 177
19 2307789 2308877 - Vvi19g178 Vvi19g178 178
19 2309055 2317229 - Vvi19g179 Vvi19g179 179
19 2325684 2327321 + Vvi19g180 Vvi19g180 180
19 2328735 2354460 + Vvi19g181 Vvi19g181 181
19 2356591 2358344 - Vvi19g182 Vvi19g182 182
19 2359667 2364324 + Vvi19g183 Vvi19g183 183
       

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