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
Vvi19g424 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g425 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g426 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g427 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g428 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g429 . . Bda07g00339 Bda09g00383 . Bpe08g01141 . . . . Cma01g01151 . . . Sed07g2655 . Cpe02g00750 Bhi09g01945 Tan01g4507 Cmetu04g3052 . Hepe01g1310 Mch11g1153 . . . . . . . . . . . . Lsi04g01243 . Chy04g01014 . . . . . . . Bma07g01315 Bma14g00356 . Cmo01g01204 Cmo09g00922 . . . . . . . . . . . . . Cla05g01538 Cam05g1645 Cec05g1651 Cco05g1688 Clacu05g1639 Cmu05g1534 Cre05g1644 . . . Cme04g00804
Vvi19g430 Blo03g00582 Blo03g01436 . . . . . . . . . Cma09g00926 . Car09g00841 . Cpe06g00745 . . . . . . . . . . . . . . . Cone6ag0088 Cone9ag0103 . . . . . . . . . . Bpe11g00525 . . . . . . . . . Car16g00563 . . . . . . . . . . . . . . . . . . . .
Vvi19g431 . . . . Bpe09g00192 . . Bma13g01029 . Cmo04g01004 . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1122 Cone15ag1140 . . . . . Blo10g00806 . Bda12g00890 . . . . . . . Cma04g00935 Cma16g00844 Car04g00874 . . Cpe01g00849 . . . . . . . . . . . . . . . . . .
Vvi19g432 . . . Bda09g00384 . Bpe08g01140 . . . . . . . Car09g00842 Sed04g3180 Cpe06g00746 . Bhi09g01944 Tan01g4508 Cmetu04g2640 . Hepe01g1309 . . . . . . . . . Cone6ag0087 Cone9ag0102 . . Lsi04g01241 . Chy04g01012 . . . . . . . Bma07g01314 . . . . . . . . . . . . . . . . . Cla05g01537 Cam05g1644 Cec05g1650 . Clacu05g1638 Cmu05g1533 Cre05g1643 . . . Cme04g00806
Vvi19g433 . . . . . . Bma10g00534 . . . . . . . . . . . . . . . . . . . . . . . . . Cone9ag0101 . . . . . . Blo07g00919 . Bda05g00736 . . Bpe03g00804 . . . . . . . . . . . Bhi11g00665 Tan01g1665 Cmetu06g1771 . . Mch10g1188 . . . . . . . . . . Chy06g01784 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 55741079 55741732 - Bda021880.1 Bda05g00736 736
7 4462653 4466456 - Bda025425.1 Bda07g00339 339
9 4891800 4896865 - Bda030963.1 Bda09g00383 383
9 4898875 4902310 - Bda030964.2 Bda09g00384 384
12 39614582 39624226 + Bda009423.1 Bda12g00890 890
9 54181586 54191969 + XM_039043266.1 Bhi09g01944 1944
9 54302451 54307839 + XM_039041903.1 Bhi09g01945 1945
11 15471793 15473754 + XM_039047564.1 Bhi11g00665 665
3 22835880 22839445 + BLOR11763 Blo03g00582 582
3 40928437 40950159 - BLOR12617 Blo03g01436 1436
7 28210207 28210926 - BLOR18851 Blo07g00919 919
10 25420780 25437709 + BLOR02596 Blo10g00806 806
7 48693687 48697163 + Bma026590.2 Bma07g01314 1314
7 48700524 48704390 + Bma026591.1 Bma07g01315 1315
10 6494591 6495247 + Bma004231.1 Bma10g00534 534
13 42877565 42886227 + Bma010157.1 Bma13g01029 1029
14 4351306 4354976 + Bma010777.2 Bma14g00356 356
3 27978118 27978771 - Bpe012714.1 Bpe03g00804 804
8 13265841 13269344 + Bpe026166 Bpe08g01140 1140
8 13272476 13276029 + Bpe023266.1 Bpe08g01141 1141
9 1350628 1371821 - Bpe023859.1 Bpe09g00192 192
11 4078001 4081293 - Bpe003892.1 Bpe11g00525 525
5 24192166 24196408 - CaPI482276_05g016440.1 Cam05g1644 1644
5 24226447 24230612 + CaPI482276_05g016450.1 Cam05g1645 1645
4 5037505 5049868 - Carg00049-RA Car04g00874 874
9 5129200 5134973 - Carg12795-RA Car09g00841 841
9 5137972 5146734 - Carg12796-RA Car09g00842 842
16 3566404 3570463 + Carg05648-RA Car16g00563 563
5 24698670 24702816 + CcPI632755_05g016880.1 Cco05g1688 1688
5 27078195 27082403 - CePI673135_05g016500.1 Cec05g1650 1650
5 27108602 27112744 + CePI673135_05g016510.1 Cec05g1651 1651
4 14896435 14900585 - Chy4G077300.1 Chy04g01012 1012
4 14952725 14956875 + Chy4G077320.1 Chy04g01014 1014
6 21268771 21270424 - Chy6G123120.1 Chy06g01784 1784
5 24267409 24271664 - ClG42_05g0163800.10 Clacu05g1638 1638
5 24303081 24307229 + ClG42_05g0163900.10 Clacu05g1639 1639
5 25631053 25638924 - ClCG05G014780.1 Cla05g01537 1537
5 25669340 25674697 + ClCG05G014790.2 Cla05g01538 1538
1 8418264 8423933 + CmaCh01G011510.1 Cma01g01151 1151
4 4813426 4826279 - CmaCh04G009350.1 Cma04g00935 935
9 4616438 4632757 - CmaCh09G009260.1 Cma09g00926 926
16 4946461 4962306 - CmaCh16G008440.1 Cma16g00844 844
4 9994971 10000208 + MELO3C018126.2.1 Cme04g00804 804
4 10021721 10026267 + MELO3C018124.2.1 Cme04g00806 806
4 24786006 24790906 + PI0009871.1 Cmetu04g2640 2640
4 24872133 24877507 + PI0016641.1 Cmetu04g3052 3052
6 25612745 25613789 - PI0006094.1 Cmetu06g1771 1771
1 9750385 9754721 + CmoCh01G012040.1 Cmo01g01204 1204
4 5053222 5066211 - CmoCh04G010040.1 Cmo04g01004 1004
9 4817447 4832989 - CmoCh09G009220.1 Cmo09g00922 922
5 23989663 23993935 - CmPI595203_05g015330.1 Cmu05g1533 1533
5 24025211 24029359 + CmPI595203_05g015340.1 Cmu05g1534 1534
6 423485 426187 + Conep06aG0008700.1 Cone6ag0087 87
6 427189 432520 + Conep06aG0008800.1 Cone6ag0088 88
9 440979 442389 - Conep09aG0010100.1 Cone9ag0101 101
9 442567 445786 + Conep09aG0010200.1 Cone9ag0102 102
9 446159 451354 + Conep09aG0010300.1 Cone9ag0103 103
14 9344122 9350853 - Conep14aG0114500.1 Cone14ag1122 1122
15 9259052 9266132 - Conep15aG0116700.1 Cone15ag1140 1140
1 5024557 5037372 - Cp4.1LG01g08350.1 Cpe01g00849 849
2 4768555 4773393 - Cp4.1LG02g01190.1 Cpe02g00750 750
6 4670718 4677232 - Cp4.1LG06g08960.1 Cpe06g00745 745
6 4679531 4688156 - Cp4.1LG06g09010.1 Cpe06g00746 746
5 27111972 27116207 - CrPI670011_05g016430.1 Cre05g1643 1643
5 27149717 27153914 + CrPI670011_05g016440.1 Cre05g1644 1644
1 78297378 78302362 + Hsped.01g13090.1 Hepe01g1309 1309
1 78321077 78326796 + Hsped.01g13100.1 Hepe01g1310 1310
4 19327709 19332971 + Lsi04G012410.1 Lsi04g01241 1241
4 19389339 19394747 + Lsi04G012430.1 Lsi04g01243 1243
10 9271141 9271773 - MC10g1002 Mch10g1188 1188
11 8092196 8097851 - MC11g0952 Mch11g1153 1153
4 42528984 42535786 - Sed0007148.1 Sed04g3180 3180
7 41980469 41985766 - Sed0016223.1 Sed07g2655 2655
1 17692891 17709892 - Tan0017660.1 Tan01g1665 1665
1 110709549 110715071 - Tan0018981.1 Tan01g4507 4507
1 110728996 110734377 - Tan0005494.1 Tan01g4508 4508
19 5422993 5430258 + Vvi19g424 Vvi19g424 424
19 5430840 5434734 - Vvi19g425 Vvi19g425 425
19 5439379 5442644 + Vvi19g426 Vvi19g426 426
19 5459287 5477423 - Vvi19g427 Vvi19g427 427
19 5477936 5482499 + Vvi19g428 Vvi19g428 428
19 5485498 5486468 - Vvi19g429 Vvi19g429 429
19 5486470 5495533 - Vvi19g430 Vvi19g430 430
19 5530862 5545741 + Vvi19g431 Vvi19g431 431
19 5547676 5560992 - Vvi19g432 Vvi19g432 432
19 5561705 5563074 + Vvi19g433 Vvi19g433 433
       

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