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
Vvi17g956 . . . . . . . . Cmo13g00993 . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00275 Csa01g00753 Chy12g01359 Cme12g01791 . . . . . . . . . . . . . . . Cpe09g01089 . . . . . . . . Cla01g01460 Cam01g1527 Cec01g1568 Cco01g1616 Clacu01g1552 Cmu01g1442 Cre01g1364 . . . .
Vvi17g957 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g958 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g959 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g960 . . . . Bpe12g00634 . . . Cmo13g00995 Cmo18g00076 . . . . . Cpe20g00178 . . . . . . . . . . . . . . . . . . . Lsi02g00271 Csa01g00750 Chy12g01362 Cme12g01794 Blo13g00104 . . . . . . Bma08g00126 Sed08g2797 . . Cma13g00961 Cma18g00099 Car13g00797 Car18g00089 Cpe09g01091 . Bhi08g01346 Tan05g2142 Cmetu12g0797 . Hepe07g2322 . . . . . . . . . . . . .
Vvi17g961 . . . . Bpe12g00633 . . . Cmo13g00996 Cmo18g00075 . . . . . Cpe20g00177 . . . . . . . . . . . . . . . . . . Cone19ag0306 Lsi02g00270 Csa01g00749 Chy12g01363 Cme12g01795 Blo13g00103 . . . . . . . Sed08g2796 . . Cma13g00962 . Car13g00798 Car18g00088 Cpe09g01092 . Bhi08g01345 Tan05g2143 Cmetu12g0483 Lac10g0323 . . . Cla01g01463 Cam01g1530 Cec01g1571 Cco01g1618 Clacu01g1555 Cmu01g1445 Cre01g1367 . . . .
Vvi17g962 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g963 . . . . . . . . . Cmo18g00074 . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00269 Csa01g00748 Chy12g01364 Cme12g01796 . . . . . . . . Sed08g2795 . . . Cma18g00098 . Car18g00087 Cpe09g01093 . Bhi08g01343 Tan05g2145 . Lac10g0322 . . . Cla01g01464 Cam01g1531 Cec01g1572 Cco01g1619 Clacu01g1556 Cmu01g1446 Cre01g1368 . . . .
Vvi17g964 . . . . Bpe12g00632 . . Bma12g01260 Cmo13g00999 . . . . . . Cpe20g00175 . . . . . . . . . . . . . . . . . . . . Csa01g00747 Chy12g01365 Cme12g01797 Blo13g00102 . . . Bpe07g01067 . . . . . . Cma13g00964 . . Car18g00086 Cpe09g01094 . Bhi08g01341 Tan05g2147 . Lac10g0321 . . . Cla01g01465 Cam01g1533 Cec01g1573 Cco01g1620 Clacu01g1557 Cmu01g1447 Cre01g1369 . . . .
Vvi17g965 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0364 . Lsi02g00268 Csa01g00746 Chy12g01366 Cme12g01798 . . Bda11g01566 . . . . . . . . . Cma18g00096 . Car18g00085 Cpe09g01095 . Bhi08g01339 . . . Hepe07g2325 . . Cla01g01466 . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 48750877 48751893 - Bda008432.1 Bda11g01566 1566
8 40596084 40597641 + XM_039039025.1 Bhi08g01339 1339
8 40601632 40606058 + XM_039038072.1 Bhi08g01341 1341
8 40608196 40611700 + XM_039038075.1 Bhi08g01343 1343
8 40612179 40617343 - XM_039038543.1 Bhi08g01345 1345
8 40619043 40623930 - XM_039039472.1 Bhi08g01346 1346
13 1820125 1821890 + BLOR05383 Blo13g00102 102
13 1837599 1844267 - BLOR05384 Blo13g00103 103
13 1847799 1852917 - BLOR05385 Blo13g00104 104
8 1623909 1629569 + Bma027131.1 Bma08g00126 126
12 45646726 45647835 + Bma008625.1 Bma12g01260 1260
7 16085681 16086796 + Bpe021910.1 Bpe07g01067 1067
12 11960303 11961382 + Bpe005892.1 Bpe12g00632 632
12 11964730 11969810 - Bpe005893.1 Bpe12g00633 633
12 11970948 11976670 - Bpe005894.1 Bpe12g00634 634
1 28823439 28827850 + CaPI482276_01g015270.1 Cam01g1527 1527
1 28881763 28893788 + CaPI482276_01g015300.1 Cam01g1530 1530
1 28894491 28897271 - CaPI482276_01g015310.1 Cam01g1531 1531
1 28902655 28903788 - CaPI482276_01g015330.1 Cam01g1533 1533
13 8811132 8815776 + Carg04875-RA Car13g00797 797
13 8816660 8820442 + Carg04874-RA Car13g00798 798
18 452748 454517 + Carg06650-RA Car18g00085 85
18 456093 457226 + Carg06651-RA Car18g00086 86
18 462693 465940 + Carg06652-RA Car18g00087 87
18 467096 471687 - Carg06653-RA Car18g00088 88
18 473102 477731 - Carg06654-RA Car18g00089 89
1 28848156 28852278 + CcPI632755_01g016160.1 Cco01g1616 1616
1 28882813 28895082 + CcPI632755_01g016180.1 Cco01g1618 1618
1 28895802 28903245 - CcPI632755_01g016190.1 Cco01g1619 1619
1 28903923 28905056 - CcPI632755_01g016200.1 Cco01g1620 1620
1 30261017 30265769 + CePI673135_01g015680.1 Cec01g1568 1568
1 30300239 30312642 + CePI673135_01g015710.1 Cec01g1571 1571
1 30313333 30316123 - CePI673135_01g015720.1 Cec01g1572 1572
1 30316205 30322742 - CePI673135_01g015730.1 Cec01g1573 1573
12 17838551 17842195 + Chy12G219590.1 Chy12g01359 1359
12 17860318 17864566 + Chy12G219620.1 Chy12g01362 1362
12 17866442 17870997 + Chy12G219630.1 Chy12g01363 1363
12 17871668 17873982 - Chy12G219640.1 Chy12g01364 1364
12 17880222 17881355 - Chy12G219650.1 Chy12g01365 1365
12 17884348 17886147 - Chy12G219660.1 Chy12g01366 1366
1 27606542 27610653 + ClG42_01g0155200.10 Clacu01g1552 1552
1 27667770 27679886 + ClG42_01g0155500.10 Clacu01g1555 1555
1 27680574 27683366 - ClG42_01g0155600.10 Clacu01g1556 1556
1 27688635 27689765 - ClG42_01g0155700.10 Clacu01g1557 1557
1 29111711 29116506 + ClCG01G014800.1 Cla01g01460 1460
1 29173135 29185433 + ClCG01G014830.2 Cla01g01463 1463
1 29185852 29189183 - ClCG01G014850.1 Cla01g01464 1464
1 29194182 29195312 - ClCG01G014860.1 Cla01g01465 1465
1 29202880 29204655 - ClCG01G014870.1 Cla01g01466 1466
13 7521882 7526272 + CmaCh13G009610.1 Cma13g00961 961
13 7527314 7531175 + CmaCh13G009620.1 Cma13g00962 962
13 7534565 7535704 - CmaCh13G009640.1 Cma13g00964 964
18 442584 446803 + CmaCh18G000960.1 Cma18g00096 96
18 452059 455953 + CmaCh18G000980.1 Cma18g00098 98
18 456561 466720 - CmaCh18G000990.1 Cma18g00099 99
12 24434127 24438509 + MELO3C002171.2.1 Cme12g01791 1791
12 24455864 24460661 + MELO3C002167.2.1 Cme12g01794 1794
12 24461710 24466783 + MELO3C002165.2.1 Cme12g01795 1795
12 24465422 24469966 - MELO3C002164.2.1 Cme12g01796 1796
12 24472027 24476895 - MELO3C002163.2.1 Cme12g01797 1797
12 24479833 24481632 - MELO3C035754.2.1 Cme12g01798 1798
12 1794729 1799307 - PI0021052.1 Cmetu12g0483 483
12 1803207 1807482 - PI0017697.1 Cmetu12g0797 797
13 8495819 8500285 + CmoCh13G009930.1 Cmo13g00993 993
13 8507753 8512122 + CmoCh13G009950.1 Cmo13g00995 995
13 8513500 8517293 + CmoCh13G009960.1 Cmo13g00996 996
13 8520524 8521651 - CmoCh13G009990.1 Cmo13g00999 999
18 497158 500896 + CmoCh18G000740.1 Cmo18g00074 74
18 501455 505989 - CmoCh18G000750.1 Cmo18g00075 75
18 507364 512092 - CmoCh18G000760.1 Cmo18g00076 76
1 27949514 27953626 + CmPI595203_01g014420.1 Cmu01g1442 1442
1 28011085 28023219 + CmPI595203_01g014450.1 Cmu01g1445 1445
1 28023907 28026699 - CmPI595203_01g014460.1 Cmu01g1446 1446
1 28028448 28033102 - CmPI595203_01g014470.1 Cmu01g1447 1447
13 3316335 3327878 - Conep13aG0038400.1 Cone13ag0364 364
19 2321505 2334426 - Conep19aG0031700.1 Cone19ag0306 306
9 9425975 9431088 + Cp4.1LG09g10840.1 Cpe09g01089 1089
9 9440611 9445646 + Cp4.1LG09g10820.1 Cpe09g01091 1091
9 9447074 9451479 + Cp4.1LG09g10830.1 Cpe09g01092 1092
9 9452605 9455822 - Cp4.1LG09g11070.1 Cpe09g01093 1093
9 9462056 9463189 - Cp4.1LG09g11060.1 Cpe09g01094 1094
9 9464618 9466910 - Cp4.1LG09g11050.1 Cpe09g01095 1095
20 1001030 1002169 + Cp4.1LG20g01760.1 Cpe20g00175 175
20 1005251 1009101 - Cp4.1LG20g01810.1 Cpe20g00177 177
20 1010439 1014889 - Cp4.1LG20g01790.1 Cpe20g00178 178
1 26823261 26827400 + CrPI670011_01g013640.1 Cre01g1364 1364
1 26871519 26883646 + CrPI670011_01g013670.1 Cre01g1367 1367
1 26884350 26891942 - CrPI670011_01g013680.1 Cre01g1368 1368
1 26892599 26893732 - CrPI670011_01g013690.1 Cre01g1369 1369
1 4741195 4743844 + CsaV3_1G007460.1 Csa01g00746 746
1 4746270 4750299 + CsaV3_1G007470.1 Csa01g00747 747
1 4752862 4761422 + CsaV3_1G007480.1 Csa01g00748 748
1 4756263 4761422 - CsaV3_1G007490.1 Csa01g00749 749
1 4762129 4767431 - CsaV3_1G007500.1 Csa01g00750 750
1 4785934 4790360 - CsaV3_1G007530.1 Csa01g00753 753
7 67549422 67565496 + Hsped.07g23220.1 Hepe07g2322 2322
7 67583264 67585119 - Hsped.07g23250.1 Hepe07g2325 2325
10 2490345 2491478 + Lag0024366.1 Lac10g0321 321
10 2497081 2499899 + Lag0024367.1 Lac10g0322 322
10 2500513 2504870 - Lag0024368.1 Lac10g0323 323
2 2266246 2278037 + Lsi02G002680.1 Lsi02g00268 268
2 2284082 2287606 + Lsi02G002690.1 Lsi02g00269 269
2 2288131 2293374 - Lsi02G002700.1 Lsi02g00270 270
2 2295794 2301129 - Lsi02G002710.1 Lsi02g00271 271
2 2330830 2335543 - Lsi02G002750.1 Lsi02g00275 275
8 39419744 39424522 + Sed0026870.2 Sed08g2795 2795
8 39425296 39430815 - Sed0009023.1 Sed08g2796 2796
8 39432057 39437072 - Sed0019851.1 Sed08g2797 2797
5 72194832 72199904 + Tan0010242.1 Tan05g2142 2142
5 72203159 72208456 + Tan0003569.1 Tan05g2143 2143
5 72209517 72213861 - Tan0017048.2 Tan05g2145 2145
5 72215411 72220560 - Tan0020653.2 Tan05g2147 2147
17 14475339 14480298 + Vvi17g956 Vvi17g956 956
17 14484811 14486185 + Vvi17g957 Vvi17g957 957
17 14509291 14517801 - Vvi17g958 Vvi17g958 958
17 14575745 14577071 + Vvi17g959 Vvi17g959 959
17 14593392 14610766 + Vvi17g960 Vvi17g960 960
17 14646145 14654828 + Vvi17g961 Vvi17g961 961
17 14668240 14673945 + Vvi17g962 Vvi17g962 962
17 14688579 14720793 - Vvi17g963 Vvi17g963 963
17 14857050 14870612 - Vvi17g964 Vvi17g964 964
17 14953742 14955539 - Vvi17g965 Vvi17g965 965
       

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