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
Vvi1g461 . . . . . . . . . . . . . . . . Cpe01g01841 . . . . . . . . . . . . . . . . Cone6ag0387 Cone9ag0414 . Csa05g02013 . . . Blo11g00974 . . . . . . . . Cmo15g01004 . Cma15g00963 . Car15g00909 Cpe13g00361 . Bhi12g00920 . . . . . . Cla01g00620 Cam01g0648 Cec01g0640 Cco01g0666 Clacu01g0636 Cmu01g0609 Cre09g1892 Lsi09g00670 . Chy09g00840 Cme09g01372
Vvi1g462 . . . . . . Bma14g01896 . . . . Cma04g00066 . Car04g00063 . . . Bhi07g00363 . . . . . . . . . . . . . . Cone19ag0750 Cone6ag0386 Cone9ag0413 Lsi04g01120 . . Cme10g01593 Blo06g01008 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01147 . .
Vvi1g463 . . . . . . . . . . . . . . . . Cpe01g01840 . . . . . . . . . . . . . . Cone13ag0745 . Cone6ag0385 Cone9ag0412 . Csa05g02012 . . . . . . . . . . . . Cmo15g01006 . Cma15g00964 . Car15g00911 Cpe13g00360 . Bhi12g00922 . . . . . . Cla01g00621 Cam01g0649 Cec01g0642 Cco01g0667 Clacu01g0637 Cmu01g0611 Cre09g1891 Lsi09g00671 . Chy09g00839 Cme09g01371
Vvi1g464 . . . . . . Bma14g01897 . . . . . . . . . Cpe01g01839 . . . . . . . . . . . . . . . . Cone6ag0384 Cone9ag0411 . Csa05g02011 . . Blo06g01007 Blo11g00973 . . . . . . . Cmo04g02216 Cmo15g01007 Cma04g02117 Cma15g00965 Car04g02059 Car15g00912 Cpe13g00359 . Bhi12g00924 . . . . . . Cla01g00622 Cam01g0650 Cec01g0643 Cco01g0668 Clacu01g0638 Cmu01g0612 Cre09g1890 Lsi09g00672 . Chy09g00838 Cme09g01370
Vvi1g465 . . . . . Bpe10g00981 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g02010 . . Blo06g01006 . . . . . . . . . Cmo15g01008 . . . . Cpe13g00358 . Bhi12g00925 . . . . . . Cla01g00623 Cam01g0651 Cec01g0644 Cco01g0669 Clacu01g0639 Cmu01g0613 Cre09g1889 Lsi09g00673 . Chy09g00837 Cme09g01369
Vvi1g466 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g467 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g468 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g469 . . . . . Bpe10g00942 . . . . . Cma04g00067 . . . . . . . . . . . . . . . . . . . . . . . . . Chy10g00226 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g470 . . . . . . Bma14g01899 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa05g01138 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 16261956 16267093 - XM_039037405.1 Bhi07g00363 363
12 27684719 27688925 + XM_039050978.1 Bhi12g00920 920
12 27744257 27745296 + XM_039050792.1 Bhi12g00922 922
12 27815695 27823052 + XM_039050631.1 Bhi12g00924 924
12 27823274 27826363 - XM_039050632.1 Bhi12g00925 925
6 33299721 33301766 + BLOR17589 Blo06g01006 1006
6 33304778 33314279 - BLOR17590 Blo06g01007 1007
6 33316056 33325689 - BLOR17591 Blo06g01008 1008
11 22909796 22919903 + BLOR03849 Blo11g00973 973
11 23032594 23034953 - BLOR03850 Blo11g00974 974
14 40558616 40560983 + Bma012682.1 Bma14g01896 1896
14 40563767 40577923 - Bma012683.2 Bma14g01897 1897
14 40626929 40627403 + Bma012687.1 Bma14g01899 1899
10 14977188 14978218 - Bpe003247.1 Bpe10g00942 942
10 15252538 15254262 + Bpe003286.1 Bpe10g00981 981
1 7111615 7114709 + CaPI482276_01g006480.1 Cam01g0648 648
1 7135213 7135854 + CaPI482276_01g006490.1 Cam01g0649 649
1 7160077 7168793 + CaPI482276_01g006500.1 Cam01g0650 650
1 7169517 7171857 - CaPI482276_01g006510.1 Cam01g0651 651
4 335426 336829 + Carg22011-RA Car04g00063 63
4 16730396 16739349 - Carg26065-RA Car04g02059 2059
15 5551900 5554823 + Carg26335-RA Car15g00909 909
15 5641369 5642071 + Carg27947-RA Car15g00911 911
15 5727438 5737792 + Carg27946-RA Car15g00912 912
1 6875745 6878839 + CcPI632755_01g006660.1 Cco01g0666 666
1 6899295 6899936 + CcPI632755_01g006670.1 Cco01g0667 667
1 6931628 6940414 + CcPI632755_01g006680.1 Cco01g0668 668
1 6941135 6943588 - CcPI632755_01g006690.1 Cco01g0669 669
1 6921954 6925027 + CePI673135_01g006400.1 Cec01g0640 640
1 6950080 6950721 + CePI673135_01g006420.1 Cec01g0642 642
1 6977047 6985738 + CePI673135_01g006430.1 Cec01g0643 643
1 6986460 6988844 - CePI673135_01g006440.1 Cec01g0644 644
9 11150722 11152979 + Chy9G165530.1 Chy09g00837 837
9 11154113 11163559 - Chy9G165540.1 Chy09g00838 838
9 11177931 11178579 - Chy9G165550.1 Chy09g00839 839
9 11191864 11195066 - Chy9G165560.1 Chy09g00840 840
10 5738833 5741128 - Chy10G174200.1 Chy10g00226 226
1 6745698 6748792 + ClG42_01g0063600.10 Clacu01g0636 636
1 6769049 6769690 + ClG42_01g0063700.10 Clacu01g0637 637
1 6805207 6813851 + ClG42_01g0063800.10 Clacu01g0638 638
1 6814566 6816902 - ClG42_01g0063900.10 Clacu01g0639 639
1 7111442 7119316 + ClCG01G006360.2 Cla01g00620 620
1 7135142 7136125 + ClCG01G006370.1 Cla01g00621 621
1 7172773 7181655 + ClCG01G006380.1 Cla01g00622 622
1 7182132 7184540 - ClCG01G006390.1 Cla01g00623 623
4 312376 320021 + CmaCh04G000660.1 Cma04g00066 66
4 320782 326960 + CmaCh04G000670.1 Cma04g00067 67
4 14795299 14807050 - CmaCh04G021170.1 Cma04g02117 2117
15 5226154 5229983 + CmaCh15G009630.1 Cma15g00963 963
15 5270576 5271896 + CmaCh15G009640.1 Cma15g00964 964
15 5359067 5368120 + CmaCh15G009650.1 Cma15g00965 965
9 18920596 18923294 + MELO3C005292.2.1 Cme09g01369 1369
9 18923642 18933781 - MELO3C005293.2.1 Cme09g01370 1370
9 18944938 18945771 - MELO3C000609.2.1 Cme09g01371 1371
9 18962244 18966527 - MELO3C005294.2.1 Cme09g01372 1372
10 21059568 21064417 - MELO3C026424.2.1 Cme10g01593 1593
4 16520595 16531292 - CmoCh04G022160.1 Cmo04g02216 2216
15 5438704 5441784 + CmoCh15G010040.1 Cmo15g01004 1004
15 5483347 5484456 + CmoCh15G010060.1 Cmo15g01006 1006
15 5565856 5577340 + CmoCh15G010070.1 Cmo15g01007 1007
15 5577017 5579857 - CmoCh15G010080.1 Cmo15g01008 1008
1 6706551 6709645 + CmPI595203_01g006090.1 Cmu01g0609 609
1 6739124 6739765 + CmPI595203_01g006110.1 Cmu01g0611 611
1 6767524 6776169 + CmPI595203_01g006120.1 Cmu01g0612 612
1 6776884 6779220 - CmPI595203_01g006130.1 Cmu01g0613 613
6 1868313 1875219 - Conep06aG0039200.1 Cone6ag0384 384
6 1877082 1877937 + Conep06aG0039300.1 Cone6ag0385 385
6 1878713 1880526 - Conep06aG0039400.1 Cone6ag0386 386
6 1882507 1884506 - Conep06aG0039500.1 Cone6ag0387 387
9 1899470 1906315 - Conep09aG0042100.1 Cone9ag0411 411
9 1910825 1911747 + Conep09aG0042200.1 Cone9ag0412 412
9 1912445 1914378 - Conep09aG0042300.1 Cone9ag0413 413
9 1915582 1916359 - Conep09aG0042400.1 Cone9ag0414 414
13 7097210 7098136 + Conep13aG0076900.1 Cone13ag0745 745
19 6126358 6128895 + Conep19aG0077100.1 Cone19ag0750 750
1 15636496 15646056 - Cp4.1LG01g18420.1 Cpe01g01839 1839
1 15647726 15648365 - Cp4.1LG01g18390.1 Cpe01g01840 1840
1 15665425 15670092 + Cp4.1LG01g18370.1 Cpe01g01841 1841
13 3683843 3686090 + Cp4.1LG13g03580.1 Cpe13g00358 358
13 3686568 3696358 - Cp4.1LG13g03590.1 Cpe13g00359 359
13 3795720 3796899 - Cp4.1LG13g03600.1 Cpe13g00360 360
13 3893792 3897960 - Cp4.1LG13g03620.1 Cpe13g00361 361
9 37538322 37540748 + CrPI670011_09g018890.1 Cre09g1889 1889
9 37541474 37550172 - CrPI670011_09g018900.1 Cre09g1890 1890
9 37574174 37574842 - CrPI670011_09g018910.1 Cre09g1891 1891
9 37596947 37600356 - CrPI670011_09g018920.1 Cre09g1892 1892
5 11658345 11660812 - CsaV3_5G014620.1 Csa05g01138 1138
5 11773292 11778374 - CsaV3_5G014710.1 Csa05g01147 1147
5 23451164 23454584 + CsaV3_5G028290.1 Csa05g02010 2010
5 23455292 23465358 - CsaV3_5G028300.1 Csa05g02011 2011
5 23478238 23480492 - CsaV3_5G028310.1 Csa05g02012 2012
5 23491256 23495690 - CsaV3_5G028320.1 Csa05g02013 2013
4 14621727 14626835 + Lsi04G011200.1 Lsi04g01120 1120
9 7556365 7560942 + Lsi09G006700.1 Lsi09g00670 670
9 7578047 7579271 + Lsi09G006710.1 Lsi09g00671 671
9 7593052 7603485 + Lsi09G006720.1 Lsi09g00672 672
9 7603919 7606881 - Lsi09G006730.1 Lsi09g00673 673
1 4953885 4958333 + Vvi1g461 Vvi1g461 461
1 4966028 4973928 + Vvi1g462 Vvi1g462 462
1 4981756 4983176 + Vvi1g463 Vvi1g463 463
1 4989640 5011798 + Vvi1g464 Vvi1g464 464
1 5011823 5018047 - Vvi1g465 Vvi1g465 465
1 5018049 5026418 + Vvi1g466 Vvi1g466 466
1 5030549 5057195 + Vvi1g467 Vvi1g467 467
1 5061080 5062107 + Vvi1g468 Vvi1g468 468
1 5078517 5079633 + Vvi1g469 Vvi1g469 469
1 5080173 5087724 + Vvi1g470 Vvi1g470 470
       

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