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
Vvi19g274 . . . . . . . Bma13g00966 . . . . . . . . . . . . . . . . Cla10g00621 Cam10g0614 Cec10g0642 Cco10g0617 Clacu10g0644 Cmu10g1462 Cre10g0855 . . Cone14ag1081 Cone15ag1072 . Csa03g00607 . . . . . Bda12g00859 . . . . . . . . . . Car16g00809 . . . . . . . . . . . . . . . . Lsi05g00699 . Chy06g01716 .
Vvi19g275 . Blo03g01533 . Bda09g00489 . Bpe08g01039 . . . . Cma01g01192 . Car01g01016 . Sed07g2626 . Cpe02g00717 Bhi09g02013 Tan01g4437 Cmetu04g1644 . Hepe01g1363 Mch11g1102 . Cla11g01790 Cam11g1854 Cec11g1879 Cco11g1885 Clacu11g2016 Cmu11g1826 Cre11g2232 Cone6ag0122 Cone9ag0146 . . Lsi04g01295 . . . . . . . . . Bma07g01193 . . Cmo01g01245 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g276 Blo03g00637 Blo03g01532 . Bda09g00488 . Bpe08g01040 . . . . . Cma09g00888 Car01g01015 Car09g00805 Sed01g0385 Cpe06g00711 Cpe02g00718 Bhi09g02012 Tan01g5059 Cmetu11g1228 . Hepe01g1362 Mch11g1104 . Cla11g01791 Cam11g1855 Cec11g1880 Cco11g1886 Clacu11g2017 Cmu11g1827 Cre11g2233 Cone6ag0121 Cone9ag0145 . . Lsi04g01294 . . . . . . . Bpe11g00496 . Bma07g01194 . . Cmo01g01244 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g277 Blo03g00636 . Bda07g00281 . . . . . . . . Cma09g00889 Car01g01014 Car09g00806 Sed04g3152 Cpe06g00712 Cpe02g00719 Bhi09g02007 Tan01g4439 Cmetu04g1200 . Hepe01g1361 Mch11g1105 . Cla11g01794 Cam11g1859 Cec11g1883 Cco11g1890 Clacu11g2021 Cmu11g1829 Cre11g2235 Cone6ag0120 . . . Lsi04g01292 . . . . . . . Bpe11g00497 Bpe01g00390 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g278 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g279 Blo03g00634 . Bda07g00278 . . . . . . . . . Car01g01013 Car09g00807 . Cpe06g00713 Cpe02g00720 Bhi09g02004 . . . . Mch11g1106 . Cla11g01796 . . . . . . . . . . Lsi04g01289 . . . . . . . Bpe11g00498 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g280 . . . . . . . . . . . . Car01g01012 . Sed07g2622 . . Bhi09g02003 Tan01g4445 Cmetu04g2107 . Hepe01g1359 Mch11g1107 . . . . . . . . . Cone9ag0143 . . Lsi04g01288 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g281 . . . . . Bpe08g01042 . . . . . . . . . . Cpe02g00721 . . . . . . . Cla11g01797 Cam11g1863 Cec11g1887 Cco11g1893 Clacu11g2026 Cmu11g1832 Cre11g2238 Cone6ag0118 . . . . . . . . . . . . . Bma07g01197 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g282 . Blo03g01530 . Bda09g00486 . . . . . . . . Car01g01002 . . Cpe06g00714 Cpe02g00722 Bhi09g02001 . . . Hepe01g1358 Mch11g1108 . Cla11g01798 Cam11g1864 Cec11g1888 Cco11g1894 Clacu11g2027 Cmu11g1833 Cre11g2239 . Cone9ag0142 . . Lsi04g01286 . . . . . . . . . Bma07g01198 Bma14g00189 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g283 . Blo03g01527 . Bda09g00485 . Bpe08g01043 . . . . . . . . Sed04g3149 . . Bhi09g01999 Tan01g4449 Cmetu04g1129 . . . . . . . . . . . . Cone9ag0140 . . . . . . . . . . . . Bma07g01199 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 3946705 3949239 - Bda025359.1 Bda07g00278 278
7 3962148 3963040 + Bda025362.1 Bda07g00281 281
9 6342142 6346010 - Bda031081.1 Bda09g00485 485
9 6346664 6349637 - Bda031082.1 Bda09g00486 486
9 6385777 6386661 + Bda031084.1 Bda09g00488 488
9 6388863 6398658 - Bda031085.1 Bda09g00489 489
12 38863798 38868561 + Bda033186 Bda12g00859 859
9 55846469 55852253 - XM_039041139.1 Bhi09g01999 1999
9 55874862 55878591 - XM_039042262.1 Bhi09g02001 2001
9 55883102 55884489 + XM_039041950.1 Bhi09g02003 2003
9 55884622 55888375 - XM_039041949.1 Bhi09g02004 2004
9 56094662 56098660 + XM_039041181.1 Bhi09g02007 2007
9 56290530 56292222 + XM_039040548.1 Bhi09g02012 2012
9 56300504 56315870 - XM_039042070.1 Bhi09g02013 2013
3 27162630 27165164 - BLOR11815 Blo03g00634 634
3 27200682 27202585 + BLOR11817 Blo03g00636 636
3 27244313 27245200 + BLOR11818 Blo03g00637 637
3 42206286 42211832 - BLOR12708 Blo03g01527 1527
3 42264869 42267797 - BLOR12711 Blo03g01530 1530
3 42319835 42320719 + BLOR12713 Blo03g01532 1532
3 42324402 42340951 - BLOR12714 Blo03g01533 1533
7 46735663 46745137 + Bma026443.1 Bma07g01193 1193
7 46750072 46750956 - Bma026444.1 Bma07g01194 1194
7 46774579 46775728 - Bma026447.1 Bma07g01197 1197
7 46780025 46783007 + Bma031402 Bma07g01198 1198
7 46783564 46787180 + Bma031403 Bma07g01199 1199
13 41322183 41325956 + Bma010073.1 Bma13g00966 966
14 2426906 2440385 + Bma010601.1 Bma14g00189 189
1 2420989 2429648 - Bpe000378.1 Bpe01g00390 390
8 12605511 12620894 + Bpe023163.1 Bpe08g01039 1039
8 12622526 12623410 - Bpe023164.1 Bpe08g01040 1040
8 12634191 12635353 - Bpe023166.1 Bpe08g01042 1042
8 12638513 12641352 + Bpe023167.1 Bpe08g01043 1043
11 3822582 3823466 - Bpe003867.1 Bpe11g00496 496
11 3831520 3833413 - Bpe003868.1 Bpe11g00497 497
11 3842006 3844540 + Bpe003869.1 Bpe11g00498 498
10 9388711 9393570 + CaPI482276_10g006140.1 Cam10g0614 614
11 31113396 31128426 + CaPI482276_11g018540.1 Cam11g1854 1854
11 31135530 31136750 - CaPI482276_11g018550.1 Cam11g1855 1855
11 31159972 31163226 - CaPI482276_11g018590.1 Cam11g1859 1859
11 31192635 31193744 - CaPI482276_11g018630.1 Cam11g1863 1863
11 31199261 31201529 + CaPI482276_11g018640.1 Cam11g1864 1864
1 9486751 9489290 - Carg27978-RA Car01g01002 1002
1 9660210 9661738 + Carg14676-RA Car01g01012 1012
1 9662947 9665475 - Carg14677-RA Car01g01013 1013
1 9671580 9675411 + Carg14678-RA Car01g01014 1014
1 9681265 9682387 + Carg14679-RA Car01g01015 1015
1 9685004 9696801 - Carg14680-RA Car01g01016 1016
9 4867577 4868861 - Carg12759-RA Car09g00805 805
9 4877322 4880531 - Carg12760-RA Car09g00806 806
9 4886675 4889194 + Carg12761-RA Car09g00807 807
16 5323777 5330519 + Carg24065-RA Car16g00809 809
10 8235422 8240284 + CcPI632755_10g006170.1 Cco10g0617 617
11 31554798 31570591 + CcPI632755_11g018850.1 Cco11g1885 1885
11 31577653 31578868 - CcPI632755_11g018860.1 Cco11g1886 1886
11 31602252 31605367 - CcPI632755_11g018900.1 Cco11g1890 1890
11 31634945 31637438 - CcPI632755_11g018930.1 Cco11g1893 1893
11 31641522 31644047 + CcPI632755_11g018940.1 Cco11g1894 1894
10 8606855 8611703 + CePI673135_10g006420.1 Cec10g0642 642
11 33016502 33031459 + CePI673135_11g018790.1 Cec11g1879 1879
11 33038646 33039857 - CePI673135_11g018800.1 Cec11g1880 1880
11 33062113 33065950 - CePI673135_11g018830.1 Cec11g1883 1883
11 33095517 33098016 - CePI673135_11g018870.1 Cec11g1887 1887
11 33102087 33104355 + CePI673135_11g018880.1 Cec11g1888 1888
6 20007420 20025849 - Chy6G122440.1 Chy06g01716 1716
10 8729349 8734211 + ClG42_10g0064400.10 Clacu10g0644 644
11 31156400 31171403 + ClG42_11g0201600.10 Clacu11g2016 2016
11 31178549 31179774 - ClG42_11g0201700.10 Clacu11g2017 2017
11 31201685 31205566 - ClG42_11g0202100.10 Clacu11g2021 2021
11 31234852 31235967 - ClG42_11g0202600.10 Clacu11g2026 2026
11 31241307 31244156 + ClG42_11g0202700.10 Clacu11g2027 2027
10 9236402 9241264 + ClCG10G006680.2 Cla10g00621 621
11 31553275 31568862 + ClCG11G018320.1 Cla11g01790 1790
11 31575745 31577793 - ClCG11G018340.1 Cla11g01791 1791
11 31602220 31605351 - ClCG11G018360.1 Cla11g01794 1794
11 31629607 31634418 + ClCG11G018380.2 Cla11g01796 1796
11 31635165 31636280 - ClCG11G018390.1 Cla11g01797 1797
11 31641299 31644786 + ClCG11G018400.1 Cla11g01798 1798
1 8635353 8647176 - CmaCh01G011920.1 Cma01g01192 1192
9 4369642 4371443 - CmaCh09G008880.1 Cma09g00888 888
9 4376296 4379854 - CmaCh09G008890.1 Cma09g00889 889
4 26270708 26282466 - PI0017149.1 Cmetu04g1129 1129
4 26447276 26449321 + PI0024443.1 Cmetu04g1200 1200
4 26521502 26540486 - PI0024690.1 Cmetu04g1644 1644
4 26369777 26370889 + PI0004760.1 Cmetu04g2107 2107
11 25137325 25140909 + PI0024356.1 Cmetu11g1228 1228
1 9990982 9992533 + CmoCh01G012440.1 Cmo01g01244 1244
1 9994837 10006488 - CmoCh01G012450.1 Cmo01g01245 1245
10 9303307 9308168 + CmPI595203_10g014620.1 Cmu10g1462 1462
11 30405805 30420819 + CmPI595203_11g018260.1 Cmu11g1826 1826
11 30427973 30429198 - CmPI595203_11g018270.1 Cmu11g1827 1827
11 30451920 30455053 - CmPI595203_11g018290.1 Cmu11g1829 1829
11 30484344 30485459 - CmPI595203_11g018320.1 Cmu11g1832 1832
11 30490811 30493660 + CmPI595203_11g018330.1 Cmu11g1833 1833
6 570519 571629 + Conep06aG0011800.1 Cone6ag0118 118
6 577174 580209 + Conep06aG0012000.1 Cone6ag0120 120
6 582006 583738 + Conep06aG0012100.1 Cone6ag0121 121
6 585137 593678 - Conep06aG0012300.1 Cone6ag0122 122
9 604870 608226 - Conep09aG0014100.1 Cone9ag0140 140
9 613544 616436 - Conep09aG0014300.1 Cone9ag0142 142
9 623100 623801 + Conep09aG0014400.1 Cone9ag0143 143
9 632630 634989 + Conep09aG0014600.1 Cone9ag0145 145
9 635817 645380 - Conep09aG0014800.1 Cone9ag0146 146
14 9055239 9058766 - Conep14aG0110200.1 Cone14ag1081 1081
15 8860423 8863570 - Conep15aG0109500.1 Cone15ag1072 1072
2 4537609 4549615 + Cp4.1LG02g01680.1 Cpe02g00717 717
2 4551873 4553518 - Cp4.1LG02g01470.1 Cpe02g00718 718
2 4558719 4563204 - Cp4.1LG02g01480.1 Cpe02g00719 719
2 4569646 4572174 + Cp4.1LG02g01550.1 Cpe02g00720 720
2 4573464 4574972 - Cp4.1LG02g01460.1 Cpe02g00721 721
2 4577905 4581695 + Cp4.1LG02g01540.1 Cpe02g00722 722
6 4416769 4418757 - Cp4.1LG06g07130.1 Cpe06g00711 711
6 4423492 4426887 - Cp4.1LG06g07140.1 Cpe06g00712 712
6 4432208 4435281 + Cp4.1LG06g07110.1 Cpe06g00713 713
6 4437134 4440231 + Cp4.1LG06g07080.1 Cpe06g00714 714
10 9381053 9385958 + CrPI670011_10g008550.1 Cre10g0855 855
11 34072975 34087974 + CrPI670011_11g022320.1 Cre11g2232 2232
11 34095413 34096629 - CrPI670011_11g022330.1 Cre11g2233 2233
11 34121767 34124865 - CrPI670011_11g022350.1 Cre11g2235 2235
11 34154484 34156980 - CrPI670011_11g022380.1 Cre11g2238 2238
11 34160992 34163559 + CrPI670011_11g022390.1 Cre11g2239 2239
3 5223603 5229643 + CsaV3_3G006070.1 Csa03g00607 607
1 78758184 78761782 - Hsped.01g13580.1 Hepe01g1358 1358
1 78765112 78766437 + Hsped.01g13590.1 Hepe01g1359 1359
1 78786154 78790258 + Hsped.01g13610.1 Hepe01g1361 1361
1 78799451 78801107 + Hsped.01g13620.1 Hepe01g1362 1362
1 78806938 78823707 - Hsped.01g13630.1 Hepe01g1363 1363
4 20294340 20297074 - Lsi04G012860.1 Lsi04g01286 1286
4 20303266 20304690 + Lsi04G012880.1 Lsi04g01288 1288
4 20305282 20308062 - Lsi04G012890.1 Lsi04g01289 1289
4 20363351 20367041 + Lsi04G012920.1 Lsi04g01292 1292
4 20416525 20418540 + Lsi04G012940.1 Lsi04g01294 1294
4 20442275 20458531 - Lsi04G012950.1 Lsi04g01295 1295
5 9319519 9324870 + Lsi05G006990.1 Lsi05g00699 699
11 7685918 7701081 + MC11g0905 Mch11g1102 1102
11 7704881 7706253 - MC11g0907 Mch11g1104 1104
11 7713724 7717803 - MC11g0908 Mch11g1105 1105
11 7731521 7733968 + MC11g0909 Mch11g1106 1106
11 7734664 7735762 - MC11g0910 Mch11g1107 1107
11 7739870 7743000 + MC11g0911 Mch11g1108 1108
1 2933620 2938701 - Sed0025175.1 Sed01g0385 385
4 42279253 42284466 - Sed0023337.2 Sed04g3149 3149
4 42309205 42313369 + Sed0023425.1 Sed04g3152 3152
7 41683642 41684888 + Sed0005473.1 Sed07g2622 2622
7 41716271 41733396 - Sed0019496.2 Sed07g2626 2626
1 109713526 109728129 + Tan0006285.1 Tan01g4437 4437
1 109754504 109758680 - Tan0001869.1 Tan01g4439 4439
1 109804130 109805240 - Tan0003144.1 Tan01g4445 4445
1 109832010 109839778 + Tan0004681.2 Tan01g4449 4449
1 116132828 116134363 - Tan0015221.1 Tan01g5059 5059
19 3443315 3474846 - Vvi19g274 Vvi19g274 274
19 3475727 3513246 + Vvi19g275 Vvi19g275 275
19 3520520 3522543 - Vvi19g276 Vvi19g276 276
19 3531546 3536479 - Vvi19g277 Vvi19g277 277
19 3543605 3544316 + Vvi19g278 Vvi19g278 278
19 3557788 3561705 + Vvi19g279 Vvi19g279 279
19 3562144 3563502 - Vvi19g280 Vvi19g280 280
19 3567925 3574374 - Vvi19g281 Vvi19g281 281
19 3579038 3581410 + Vvi19g282 Vvi19g282 282
19 3604726 3606157 + Vvi19g283 Vvi19g283 283
       

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