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
Vvi19g254 . . . . . . . . . . Cma01g01200 Cma09g00878 Car01g01025 Car09g00790 Sed04g3121 Cpe06g00701 Cpe02g00709 Bhi09g03398 Tan01g4413 Cmetu07g1669 . Hepe01g1374 Mch11g1085 . Cla11g01775 Cam11g1839 Cec11g1860 Cco11g1870 Clacu11g2001 Cmu11g1810 Cre11g2218 Cone6ag0134 Cone9ag0159 Cone14ag1072 Cone15ag1065 Lsi04g01322 Csa04g02358 Chy07g00087 . . . . . . . . . . Cmo01g01254 Cmo09g00867 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g255 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g256 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g257 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g258 Blo03g00646 . Bda07g00290 . . . . . . . Cma01g01199 Cma09g00879 Car01g01024 Car09g00791 Sed05g2577 Cpe06g00702 Cpe02g00710 Bhi09g03397 Tan01g4415 Cmetu07g1424 . Hepe01g1373 Mch11g1086 . Cla11g01776 Cam11g1840 Cec11g1861 Cco11g1871 Clacu11g2002 Cmu11g1811 Cre11g2219 Cone6ag0133 Cone9ag0158 . . Lsi04g01321 Csa04g02359 Chy07g00088 . . . . . Bpe11g00488 Bpe01g00417 . . . Cmo01g01253 Cmo09g00868 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g259 . Blo03g01538 . Bda09g00498 . Bpe08g01031 . . . . Cma01g01198 . Car01g01023 . Sed01g0663 . Cpe02g00711 Bhi09g03396 Tan01g4417 Cmetu07g0753 . Hepe01g1372 Mch11g1087 . Cla11g01777 Cam11g1841 Cec11g1862 Cco11g1872 Clacu11g2003 Cmu11g1812 Cre11g2220 Cone6ag0132 Cone9ag0157 . . Lsi04g01320 Csa04g02360 Chy07g00089 . . . . . . . Bma07g01188 . . Cmo01g01252 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g260 Blo03g00643 Blo03g01537 Bda07g00287 . . Bpe08g01033 . . . . Cma01g01197 . Car01g01022 Car09g00792 Sed05g2572 Cpe06g00703 Cpe02g00712 Bhi09g03395 Tan01g4418 Cmetu07g1898 . Hepe01g1371 Mch11g1088 . . . . . . . . Cone6ag0131 Cone9ag0156 Cone14ag1074 Cone15ag1067 Lsi04g01319 Csa04g02361 Chy07g00090 . . . . . Bpe11g00490 . Bma07g01189 . . Cmo01g01251 Cmo09g00869 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g261 . . Bda07g00286 . . . . . . . Cma01g01196 Cma09g00880 Car01g01021 . Sed14g0480 Cpe06g00704 Cpe02g00713 Bhi09g03394 Tan01g4420 Cmetu08g0046 . Hepe01g1370 Mch11g1089 . Cla11g01778 Cam11g1842 Cec11g1863 Cco11g1873 Clacu11g2004 Cmu11g1813 Cre11g2221 Cone6ag0130 Cone9ag0154 Cone14ag1075 Cone15ag1068 Lsi04g01318 Csa04g02363 Chy07g00092 . . . . . Bpe11g00491 . . . . Cmo01g01250 Cmo09g00870 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g262 Blo03g00641 Blo03g01536 Bda07g00285 Bda09g00492 . Bpe02g01908 . . Cmo16g00849 . . Cma09g00881 . Car09g00799 Sed01g2080 Cpe06g00705 . Bhi09g03393 Tan01g4424 Cmetu12g0009 . Hepe01g1369 Mch11g1090 . Cla11g01779 Cam11g1843 Cec11g1864 Cco11g1874 Clacu11g2005 Cmu11g1814 Cre11g2222 Cone6ag0129 Cone9ag0153 . . Lsi04g01317 Csa04g02364 Chy07g00093 . . . . . Bpe11g00492 . Bma07g01190 . . . Cmo09g00871 Cma04g00909 Cma16g00787 Car04g00854 . Cpe14g00685 . . . . . . . . . . . . . . . Lsi05g00709 . Chy06g01707 .
Vvi19g263 . . . . . . . . . . . . . . . . . Bhi09g03392 Tan01g4425 . . . . . . . . . . . . . . . . Lsi04g01316 . . . . . . . . . . . . . Cmo09g00872 . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 3993997 3996138 + Bda025366.1 Bda07g00285 285
7 4007315 4013088 + Bda025367.2 Bda07g00286 286
7 4014047 4015636 + Bda025368.2 Bda07g00287 287
7 4022455 4023421 - Bda025371.2 Bda07g00290 290
9 6421408 6423179 + Bda034102 Bda09g00492 492
9 6612656 6616144 - Bda031095.1 Bda09g00498 498
9 86283370 86290094 + XM_039044090.1 Bhi09g03392 3392
9 86292053 86294165 + XM_039044340.1 Bhi09g03393 3393
9 86313913 86324452 + XM_039042368.1 Bhi09g03394 3394
9 86327257 86329247 + XM_039042369.1 Bhi09g03395 3395
9 86330355 86333160 - XM_039041234.1 Bhi09g03396 3396
9 86335621 86337183 - XM_039042620.1 Bhi09g03397 3397
9 86414245 86416270 + XM_039043071.1 Bhi09g03398 3398
3 27392906 27394800 + BLOR11822 Blo03g00641 641
3 27416956 27425218 + BLOR11824 Blo03g00643 643
3 27497911 27498491 + BLOR11827 Blo03g00646 646
3 42363385 42365086 + BLOR12717 Blo03g01536 1536
3 42530405 42538611 + BLOR12718 Blo03g01537 1537
3 42663636 42676417 + BLOR12719 Blo03g01538 1538
7 46443899 46447311 + Bma026433.1 Bma07g01188 1188
7 46472823 46474358 + Bma031401 Bma07g01189 1189
7 46668675 46671476 - Bma026440.1 Bma07g01190 1190
1 2558310 2559485 - Bpe024496 Bpe01g00417 417
2 21056085 21057520 - Bpe009734.1 Bpe02g01908 1908
8 12556494 12559967 + Bpe023155.1 Bpe08g01031 1031
8 12568801 12570344 + Bpe023157.1 Bpe08g01033 1033
11 3768776 3769731 + Bpe003859.1 Bpe11g00488 488
11 3778319 3779915 - Bpe003861.2 Bpe11g00490 490
11 3780889 3786659 - Bpe003862.1 Bpe11g00491 491
11 3795087 3796980 - Bpe003863.1 Bpe11g00492 492
11 30919811 30921416 - CaPI482276_11g018390.1 Cam11g1839 1839
11 30938845 30940312 + CaPI482276_11g018400.1 Cam11g1840 1840
11 30941467 30944066 + CaPI482276_11g018410.1 Cam11g1841 1841
11 30945056 30957476 - CaPI482276_11g018420.1 Cam11g1842 1842
11 30976214 30977790 - CaPI482276_11g018430.1 Cam11g1843 1843
1 9728856 9733252 + Carg14685-RA Car01g01021 1021
1 9734524 9736223 + Carg14686-RA Car01g01022 1022
1 9736469 9739371 - Carg14687-RA Car01g01023 1023
1 9740261 9741473 - Carg14688-RA Car01g01024 1024
1 9751913 9753588 + Carg14689-RA Car01g01025 1025
4 4946842 4947744 - Carg00029-RA Car04g00854 854
9 4652873 4654561 - Carg17112-RA Car09g00790 790
9 4658124 4660419 + Carg17113-RA Car09g00791 791
9 4661268 4663508 - Carg17114-RA Car09g00792 792
9 4831483 4834313 - Carg12753-RA Car09g00799 799
11 31352601 31354206 - CcPI632755_11g018700.1 Cco11g1870 1870
11 31370510 31371976 + CcPI632755_11g018710.1 Cco11g1871 1871
11 31373163 31375745 + CcPI632755_11g018720.1 Cco11g1872 1872
11 31376737 31389148 - CcPI632755_11g018730.1 Cco11g1873 1873
11 31408682 31410250 - CcPI632755_11g018740.1 Cco11g1874 1874
11 32788524 32790126 - CePI673135_11g018600.1 Cec11g1860 1860
11 32806871 32808319 + CePI673135_11g018610.1 Cec11g1861 1861
11 32809469 32812076 + CePI673135_11g018620.1 Cec11g1862 1862
11 32813063 32825521 - CePI673135_11g018630.1 Cec11g1863 1863
11 32854470 32856049 - CePI673135_11g018640.1 Cec11g1864 1864
6 19729515 19731451 - Chy6G122350.1 Chy06g01707 1707
7 789300 790848 - Chy7G129170.1 Chy07g00087 87
7 802836 804260 + Chy7G129180.1 Chy07g00088 88
7 805046 807298 + Chy7G129190.1 Chy07g00089 89
7 808808 810459 - Chy7G129200.1 Chy07g00090 90
7 814173 823183 - Chy7G129220.1 Chy07g00092 92
7 837308 838878 - Chy7G129230.1 Chy07g00093 93
11 30957591 30959196 - ClG42_11g0200100.10 Clacu11g2001 2001
11 30975702 30977169 + ClG42_11g0200200.10 Clacu11g2002 2002
11 30978341 30980937 + ClG42_11g0200300.10 Clacu11g2003 2003
11 30981930 30994285 - ClG42_11g0200400.10 Clacu11g2004 2004
11 31013643 31015219 - ClG42_11g0200500.10 Clacu11g2005 2005
11 31337148 31339098 - ClCG11G018190.1 Cla11g01775 1775
11 31356854 31358678 + ClCG11G018200.2 Cla11g01776 1776
11 31359404 31362341 + ClCG11G018210.1 Cla11g01777 1777
11 31362953 31376205 - ClCG11G018220.2 Cla11g01778 1778
11 31394677 31396843 - ClCG11G018240.1 Cla11g01779 1779
1 8686397 8692784 + CmaCh01G011960.1 Cma01g01196 1196
1 8693781 8695790 + CmaCh01G011970.1 Cma01g01197 1197
1 8695967 8698665 - CmaCh01G011980.1 Cma01g01198 1198
1 8699524 8700995 - CmaCh01G011990.1 Cma01g01199 1199
1 8711206 8713217 + CmaCh01G012000.1 Cma01g01200 1200
4 4725833 4727398 - CmaCh04G009090.1 Cma04g00909 909
9 4308805 4310508 - CmaCh09G008780.1 Cma09g00878 878
9 4314388 4316491 + CmaCh09G008790.1 Cma09g00879 879
9 4318241 4328406 - CmaCh09G008800.1 Cma09g00880 880
9 4335767 4338875 - CmaCh09G008810.1 Cma09g00881 881
16 4325952 4328446 - CmaCh16G007870.1 Cma16g00787 787
7 22135777 22138606 + PI0003115.1 Cmetu07g0753 753
7 22133882 22135572 + PI0001634.1 Cmetu07g1424 1424
7 22116657 22118682 - PI0028295.1 Cmetu07g1669 1669
7 22140513 22142793 - PI0005440.1 Cmetu07g1898 1898
8 16125711 16130780 + PI0028555.1 Cmetu08g0046 46
12 4956684 4958976 + PI0028906.1 Cmetu12g0009 9
1 10039200 10045007 + CmoCh01G012500.1 Cmo01g01250 1250
1 10046238 10047902 + CmoCh01G012510.1 Cmo01g01251 1251
1 10048330 10051037 - CmoCh01G012520.1 Cmo01g01252 1252
1 10051833 10053333 - CmoCh01G012530.1 Cmo01g01253 1253
1 10061910 10063821 + CmoCh01G012540.1 Cmo01g01254 1254
9 4473651 4475736 - CmoCh09G008670.1 Cmo09g00867 867
9 4479137 4481478 + CmoCh09G008680.1 Cmo09g00868 868
9 4481952 4485878 - CmoCh09G008690.1 Cmo09g00869 869
9 4485990 4492798 - CmoCh09G008700.1 Cmo09g00870 870
9 4500357 4503386 - CmoCh09G008710.1 Cmo09g00871 871
9 4506319 4523249 - CmoCh09G008720.1 Cmo09g00872 872
16 4491070 4493613 - CmoCh16G008490.1 Cmo16g00849 849
11 30213092 30214697 - CmPI595203_11g018100.1 Cmu11g1810 1810
11 30231182 30232649 + CmPI595203_11g018110.1 Cmu11g1811 1811
11 30233814 30236409 + CmPI595203_11g018120.1 Cmu11g1812 1812
11 30237402 30249760 - CmPI595203_11g018130.1 Cmu11g1813 1813
11 30269128 30270704 - CmPI595203_11g018140.1 Cmu11g1814 1814
6 632693 634719 + Conep06aG0013000.1 Cone6ag0129 129
6 637844 642841 + Conep06aG0013100.1 Cone6ag0130 130
6 644040 646135 + Conep06aG0013200.1 Cone6ag0131 131
6 645891 647763 - Conep06aG0013300.1 Cone6ag0132 132
6 648007 649325 - Conep06aG0013400.1 Cone6ag0133 133
6 656735 658571 + Conep06aG0013500.1 Cone6ag0134 134
9 677873 679886 + Conep09aG0015500.1 Cone9ag0153 153
9 685015 689855 + Conep09aG0015600.1 Cone9ag0154 154
9 691074 691944 + Conep09aG0015800.1 Cone9ag0156 156
9 691831 693510 - Conep09aG0015900.1 Cone9ag0157 157
9 694081 695349 - Conep09aG0016000.1 Cone9ag0158 158
9 701789 703240 + Conep09aG0016100.1 Cone9ag0159 159
14 9004527 9006438 - Conep14aG0109300.1 Cone14ag1072 1072
14 9013256 9015130 - Conep14aG0109500.1 Cone14ag1074 1074
14 9015738 9019612 - Conep14aG0109600.1 Cone14ag1075 1075
15 8802183 8804222 - Conep15aG0108800.1 Cone15ag1065 1065
15 8813642 8815631 - Conep15aG0109000.1 Cone15ag1067 1067
15 8821622 8825337 - Conep15aG0109100.1 Cone15ag1068 1068
2 4479845 4481902 - Cp4.1LG02g01560.1 Cpe02g00709 709
2 4492391 4493824 + Cp4.1LG02g01630.1 Cpe02g00710 710
2 4494688 4498976 + Cp4.1LG02g01700.1 Cpe02g00711 711
2 4497055 4499755 - Cp4.1LG02g01580.1 Cpe02g00712 712
2 4500503 4506183 - Cp4.1LG02g01610.1 Cpe02g00713 713
6 4354000 4356394 - Cp4.1LG06g06990.1 Cpe06g00701 701
6 4358642 4361385 + Cp4.1LG06g06890.1 Cpe06g00702 702
6 4362040 4364351 - Cp4.1LG06g07030.1 Cpe06g00703 703
6 4365356 4373808 - Cp4.1LG06g07010.1 Cpe06g00704 704
6 4381123 4384194 - Cp4.1LG06g07000.1 Cpe06g00705 705
14 4501822 4504223 - Cp4.1LG14g00250.1 Cpe14g00685 685
11 33888725 33890330 - CrPI670011_11g022180.1 Cre11g2218 2218
11 33907217 33908655 + CrPI670011_11g022190.1 Cre11g2219 2219
11 33909745 33912381 + CrPI670011_11g022200.1 Cre11g2220 2220
11 33913364 33925823 - CrPI670011_11g022210.1 Cre11g2221 2221
11 33944512 33946092 - CrPI670011_11g022220.1 Cre11g2222 2222
4 23968658 23970718 - CsaV3_4G033840.1 Csa04g02358 2358
4 23984077 23985521 + CsaV3_4G033850.1 Csa04g02359 2359
4 23986278 23988534 + CsaV3_4G033860.1 Csa04g02360 2360
4 23990373 23992959 - CsaV3_4G033870.1 Csa04g02361 2361
4 23994726 24005626 - CsaV3_4G033890.1 Csa04g02363 2363
4 24018510 24020869 - CsaV3_4G033900.1 Csa04g02364 2364
1 78909168 78910937 + Hsped.01g13690.1 Hepe01g1369 1369
1 78935406 78943610 + Hsped.01g13700.1 Hepe01g1370 1370
1 78946279 78948168 + Hsped.01g13710.1 Hepe01g1371 1371
1 78949012 78951537 - Hsped.01g13720.1 Hepe01g1372 1372
1 78954191 78955947 - Hsped.01g13730.1 Hepe01g1373 1373
1 78976387 78978291 + Hsped.01g13740.1 Hepe01g1374 1374
4 20924820 20931587 + Lsi04G013160.1 Lsi04g01316 1316
4 20936166 20938492 + Lsi04G013170.1 Lsi04g01317 1317
4 20966338 20976954 + Lsi04G013180.1 Lsi04g01318 1318
4 20982359 20984639 + Lsi04G013190.1 Lsi04g01319 1319
4 20986446 20989660 - Lsi04G013200.1 Lsi04g01320 1320
4 20997635 20999605 - Lsi04G013210.1 Lsi04g01321 1321
4 21023441 21025454 + Lsi04G013220.1 Lsi04g01322 1322
5 9561977 9563938 + Lsi05G007090.1 Lsi05g00709 709
11 7536865 7539171 - MC11g0890 Mch11g1085 1085
11 7568028 7569683 + MC11g0891 Mch11g1086 1086
11 7569803 7572186 + MC11g0892 Mch11g1087 1087
11 7575202 7577273 - MC11g0893 Mch11g1088 1088
11 7578442 7587483 - MC11g0894 Mch11g1089 1089
11 7600079 7602225 - MC11g0895 Mch11g1090 1090
1 4871215 4874129 + Sed0018738.1 Sed01g0663 663
1 15569861 15572657 + Sed0006898.2 Sed01g2080 2080
4 42042970 42044867 - Sed0008533.1 Sed04g3121 3121
5 37540848 37543306 + Sed0001792.1 Sed05g2572 2572
5 37547156 37548965 - Sed0021321.2 Sed05g2577 2577
14 4774950 4782162 - Sed0015562.1 Sed14g0480 480
1 109265375 109267085 - Tan0017764.1 Tan01g4413 4413
1 109315217 109316841 + Tan0010360.2 Tan01g4415 4415
1 109319780 109322352 + Tan0012857.2 Tan01g4417 4417
1 109322978 109324956 - Tan0005134.1 Tan01g4418 4418
1 109327347 109338387 - Tan0009921.2 Tan01g4420 4420
1 109405527 109408062 - Tan0018244.1 Tan01g4424 4424
1 109411737 109418595 - Tan0001169.1 Tan01g4425 4425
19 3265468 3267267 - Vvi19g254 Vvi19g254 254
19 3276227 3277109 - Vvi19g255 Vvi19g255 255
19 3277108 3279574 - Vvi19g256 Vvi19g256 256
19 3279598 3284011 - Vvi19g257 Vvi19g257 257
19 3286082 3287727 + Vvi19g258 Vvi19g258 258
19 3289701 3292924 + Vvi19g259 Vvi19g259 259
19 3298277 3300519 - Vvi19g260 Vvi19g260 260
19 3302031 3310746 - Vvi19g261 Vvi19g261 261
19 3331336 3333335 - Vvi19g262 Vvi19g262 262
19 3337835 3339870 - Vvi19g263 Vvi19g263 263
       

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