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
Vvi18g110 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g111 . . . . . . . . . Cmo12g00615 . . . Car12g00657 . . Cpe07g00588 Bhi04g01582 . . . . . . Cla08g00947 Cam08g1400 Cec08g0981 Cco08g1103 Clacu08g1104 . Cre08g0888 . . . . . . . Cme03g01345 Blo17g00706 . Bda08g01171 . . Bpe05g00176 . . . . . Cma12g00677 . . . Cpe11g00792 . . . . . . . . . . . . . . . Lsi08g00793 . Chy03g00620 .
Vvi18g112 . . . . . . . . . . . . Car01g01579 . . Cpe06g00027 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo01g02067 Cmo09g00060 . . . Car09g00051 . . Bhi09g02898 Tan01g5098 . . Hepe01g2335 . . Cla11g01818 Cam11g1884 Cec11g1909 Cco11g1916 Clacu11g2048 Cmu11g1853 Cre11g2258 . . . .
Vvi18g113 . . . . . . . . . . . . . . . . . Bhi04g01580 . . . . . . . . . . . . . . . . . . . . Cme03g01346 . Blo18g00749 . Bda01g01559 Bpe02g01754 . Bma01g00704 . . . . . . . . . . . . . . . . . . . . . . . . . . Chy03g00621 .
Vvi18g114 Blo01g01626 . . . Bpe02g00316 . . Bma01g02401 . . . . . . . Cpe06g00028 . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00963 . . . . . . . Cmo09g00062 . . . Car09g00053 . . . . . . . . . . . . . . . . . . . .
Vvi18g115 Blo01g01625 . . . Bpe02g00317 . . Bma01g02400 Cmo05g01005 Cmo12g00612 . . . Car12g00654 Sed08g1831 . Cpe07g00585 Bhi04g01568 Tan02g1531 Cmetu03g1799 . Hepe08g1489 . Lcy13g2253 Cla08g00952 Cam08g1405 Cec08g0985 Cco08g1108 Clacu08g1109 . Cre08g0892 . . Cone17ag1445 Cone20ag0031 . . . Cme03g01352 . . Bda11g00962 . . . . . . . . Cma12g00674 Cma05g00987 Car05g00867 . Cpe11g00796 . . . . . . . . . . . . . . . Lsi08g00797 . Chy03g00627 .
Vvi18g116 Blo01g01624 Blo12g00860 . Bda03g00313 Bpe02g00318 Bpe04g00274 Bma04g00281 Bma01g02399 . . Cma01g02008 Cma09g00062 Car01g01577 . . Cpe06g00029 . . . . . . . . . . . . . . . Cone4ag2012 Cone7ag1927 . Cone20ag0032 Lsi04g01798 Csa04g02692 . . . . Bda11g00961 . . . . . . Cmo01g02066 Cmo09g00063 . . . Car09g00054 . Cpe02g00041 Bhi09g02913 . . . . . . Cla11g01817 Cam11g1883 Cec11g1906 Cco11g1915 Clacu11g2047 Cmu11g1852 Cre11g2257 . . Chy07g00383 Cme07g00064
Vvi18g117 Blo01g01623 Blo12g00861 . Bda03g00312 Bpe02g00319 Bpe04g00273 Bma04g00280 Bma01g02398 Cmo05g01006 Cmo12g00611 . . . Car12g00653 . . Cpe07g00584 Bhi04g01564 . . . Hepe08g1488 . Lcy13g2252 Cla08g00959 . . . . . . Cone4ag2011 . . . . . . Cme03g01353 . . Bda11g00960 . . . . . . . . Cma12g00673 Cma05g00988 Car05g00868 . Cpe11g00797 . . . . . . . . . . . . . . . Lsi08g00798 . Chy03g00628 .
Vvi18g118 . . . . . . . . Cmo05g01007 Cmo12g00610 . . . Car12g00652 Sed08g1827 . . Bhi04g01562 Tan02g1534 Cmetu03g1317 . Hepe08g1487 . Lcy13g2251 Cla08g00960 . . . . . . . . Cone17ag1444 Cone20ag0033 . . . Cme03g01354 . Blo18g00750 . Bda01g01558 Bpe02g01753 . Bma01g00705 . . . . Cma12g00672 Cma05g00989 Car05g00870 . Cpe11g00798 . . . . . . . . . . . . . . . Lsi08g00800 . Chy03g00629 .
Vvi18g119 Blo01g01622 . . . Bpe02g00320 . . Bma01g02397 . . Cma01g02007 . Car01g01576 . . . . . . . . . . . . . . . . . . Cone4ag2010 Cone7ag1926 . . Lsi04g01797 Csa04g02691 . . . . . . . . . . . Cmo01g02065 . . . . . . Cpe02g00042 . . . . . . . Cla11g01816 Cam11g1882 Cec11g1905 Cco11g1913 Clacu11g2046 Cmu11g1851 Cre11g2256 . . Chy07g00382 Cme07g00065
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 51481177 51488604 + Bda003827.1 Bda01g01558 1558
1 51489873 51493991 - Bda003828.1 Bda01g01559 1559
3 2695283 2699628 + Bda016272.1 Bda03g00312 312
3 2700301 2711620 - Bda016273.1 Bda03g00313 313
8 46731091 46731803 + Bda030116.1 Bda08g01171 1171
11 9374915 9378870 + Bda005721.1 Bda11g00960 960
11 9379605 9384041 - Bda005722.1 Bda11g00961 961
11 9389537 9393877 + Bda033069 Bda11g00962 962
11 9394554 9401417 - Bda005723.3 Bda11g00963 963
4 39524202 39536898 + XM_039030542.1 Bhi04g01562 1562
4 39548079 39560905 + XM_039030632.1 Bhi04g01564 1564
4 39571014 39585886 - XM_039029169.1 Bhi04g01568 1568
4 39826470 39840124 + XM_039028580.1 Bhi04g01580 1580
4 39841137 39842142 - XM_039030219.1 Bhi04g01582 1582
9 76124368 76127728 + XM_039040223.1 Bhi09g02898 2898
9 76166764 76174088 - XM_039041010.1 Bhi09g02913 2913
1 56113186 56117803 - BLOR01622 Blo01g01622 1622
1 56119551 56123598 + BLOR01623 Blo01g01623 1623
1 56124314 56133503 - BLOR01624 Blo01g01624 1624
1 56133605 56138663 + BLOR01625 Blo01g01625 1625
1 56139522 56146300 - BLOR01626 Blo01g01626 1626
12 26844826 26848950 + BLOR04879 Blo12g00860 860
12 26849693 26856512 - BLOR04880 Blo12g00861 861
17 19998493 19999193 - BLOR08252 Blo17g00706 706
18 20211534 20217052 + BLOR09237 Blo18g00749 749
18 20279676 20295541 - BLOR09238 Blo18g00750 750
1 6427475 6431719 + Bma000914.1 Bma01g00704 704
1 6433705 6439429 - Bma030200 Bma01g00705 705
1 81565051 81566751 - Bma003269.1 Bma01g02397 2397
1 81569398 81573293 + Bma003270.1 Bma01g02398 2398
1 81573947 81578395 - Bma003271.1 Bma01g02399 2399
1 81578124 81583047 + Bma030301 Bma01g02400 2400
1 81583625 81591694 - Bma003272.2 Bma01g02401 2401
4 2266597 2270840 + Bma018734.1 Bma04g00280 280
4 2271565 2276935 - Bma018735.1 Bma04g00281 281
2 2070789 2076841 + Bpe008157.1 Bpe02g00316 316
2 2077477 2079827 - Bpe008158.1 Bpe02g00317 317
2 2081143 2085585 + Bpe008159.1 Bpe02g00318 318
2 2086331 2090209 - Bpe008160.1 Bpe02g00319 319
2 2092085 2093807 + Bpe008161.1 Bpe02g00320 320
2 19880261 19887418 + Bpe009583.1 Bpe02g01753 1753
2 19889031 19893483 - Bpe009584.2 Bpe02g01754 1754
4 1767045 1771226 + Bpe025594 Bpe04g00273 273
4 1771964 1775939 - Bpe014981.3 Bpe04g00274 274
5 6695269 6696026 - Bpe017565.1 Bpe05g00176 176
8 20257834 20258580 - CaPI482276_08g014000.1 Cam08g1400 1400
8 20281863 20290177 + CaPI482276_08g014050.1 Cam08g1405 1405
11 31366705 31369612 - CaPI482276_11g018820.1 Cam11g1882 1882
11 31375059 31385560 - CaPI482276_11g018830.1 Cam11g1883 1883
11 31385591 31395080 - CaPI482276_11g018840.1 Cam11g1884 1884
1 13086658 13088915 - Carg21379-RA Car01g01576 1576
1 13090170 13094860 - Carg21378-RA Car01g01577 1577
1 13097975 13101048 - Carg21376-RA Car01g01579 1579
5 8487326 8491986 - Carg21872-RA Car05g00867 867
5 8492862 8500397 - Carg21871-RA Car05g00868 868
5 8505569 8509567 - Carg21869-RA Car05g00870 870
9 257153 260492 + Carg08634-RA Car09g00051 51
9 264786 270152 + Carg08636-RA Car09g00053 53
9 270881 275042 + Carg08637-RA Car09g00054 54
12 4407352 4412340 + Carg17650-RA Car12g00652 652
12 4413851 4419019 + Carg17649-RA Car12g00653 653
12 4419808 4425592 + Carg17648-RA Car12g00654 654
12 4436459 4437691 + Carg17645-RA Car12g00657 657
8 22775022 22775768 - CcPI632755_08g011030.1 Cco08g1103 1103
8 22799040 22805845 + CcPI632755_08g011080.1 Cco08g1108 1108
11 31823982 31826900 - CcPI632755_11g019130.1 Cco11g1913 1913
11 31839542 31851549 - CcPI632755_11g019150.1 Cco11g1915 1915
11 31851580 31861093 - CcPI632755_11g019160.1 Cco11g1916 1916
8 21615789 21616535 - CePI673135_08g009810.1 Cec08g0981 981
8 21647847 21655918 + CePI673135_08g009850.1 Cec08g0985 985
11 33271060 33273919 - CePI673135_11g019050.1 Cec11g1905 1905
11 33284058 33293934 - CePI673135_11g019060.1 Cec11g1906 1906
11 33306958 33314859 - CePI673135_11g019090.1 Cec11g1909 1909
3 8755409 8756148 + Chy3G056000.1 Chy03g00620 620
3 8757075 8763212 - Chy3G056010.1 Chy03g00621 621
3 8796141 8799888 + Chy3G056070.1 Chy03g00627 627
3 8803373 8809357 - Chy3G056080.1 Chy03g00628 628
3 8811211 8820231 - Chy3G056090.1 Chy03g00629 629
7 3064753 3066778 - Chy7G132120.1 Chy07g00382 382
7 3070677 3074415 - Chy7G132130.1 Chy07g00383 383
8 21031663 21032409 - ClG42_08g0110400.10 Clacu08g1104 1104
8 21055648 21062299 + ClG42_08g0110900.10 Clacu08g1109 1109
11 31405825 31408696 - ClG42_11g0204600.10 Clacu11g2046 2046
11 31414656 31419905 - ClG42_11g0204700.10 Clacu11g2047 2047
11 31426454 31434302 - ClG42_11g0204800.10 Clacu11g2048 2048
8 22043124 22044107 - ClCG08G009410.1 Cla08g00947 947
8 22069917 22078186 + ClCG08G009470.2 Cla08g00952 952
8 22165815 22173108 - ClCG08G009540.1 Cla08g00959 959
8 22176612 22185503 - ClCG08G009550.2 Cla08g00960 960
11 31813329 31816127 - ClCG11G018640.1 Cla11g01816 1816
11 31821117 31832484 - ClCG11G018650.2 Cla11g01817 1817
11 31834166 31842158 - ClCG11G018670.2 Cla11g01818 1818
1 12860467 12862757 - CmaCh01G020070.1 Cma01g02007 2007
1 12863903 12869050 - CmaCh01G020080.1 Cma01g02008 2008
5 7924148 7929292 - CmaCh05G009870.1 Cma05g00987 987
5 7930429 7937113 - CmaCh05G009880.1 Cma05g00988 988
5 7940377 7946298 - CmaCh05G009890.1 Cma05g00989 989
9 277158 281959 + CmaCh09G000620.1 Cma09g00062 62
12 3629310 3634594 + CmaCh12G006720.1 Cma12g00672 672
12 3635385 3640716 + CmaCh12G006730.1 Cma12g00673 673
12 3641188 3646613 + CmaCh12G006740.1 Cma12g00674 674
12 3657613 3659073 + CmaCh12G006770.1 Cma12g00677 677
3 23001883 23003261 + MELO3C026535.2.1 Cme03g01345 1345
3 23003652 23010283 - MELO3C026536.2.1 Cme03g01346 1346
3 23046067 23050130 + MELO3C026542.2.1 Cme03g01352 1352
3 23053055 23059423 - MELO3C026543.2.1 Cme03g01353 1353
3 23061535 23070873 - MELO3C026544.2.1 Cme03g01354 1354
7 408642 413366 + MELO3C017016.2.1 Cme07g00064 64
7 417733 420220 + MELO3C017015.2.1 Cme07g00065 65
3 6321753 6332124 + PI0000746.1 Cmetu03g1317 1317
3 6341320 6346105 - PI0014547.1 Cmetu03g1799 1799
1 14404314 14406603 - CmoCh01G020650.1 Cmo01g02065 2065
1 14407783 14414603 - CmoCh01G020660.1 Cmo01g02066 2066
1 14416493 14420377 - CmoCh01G020670.1 Cmo01g02067 2067
5 8078684 8083442 - CmoCh05G010050.1 Cmo05g01005 1005
5 8084381 8092056 - CmoCh05G010060.1 Cmo05g01006 1006
5 8096091 8101602 - CmoCh05G010070.1 Cmo05g01007 1007
9 270185 271063 + CmoCh09G000600.1 Cmo09g00060 60
9 274892 284237 + CmoCh09G000620.1 Cmo09g00062 62
9 284756 289589 + CmoCh09G000630.1 Cmo09g00063 63
12 3815204 3819768 + CmoCh12G006100.1 Cmo12g00610 610
12 3820714 3825889 + CmoCh12G006110.1 Cmo12g00611 611
12 3826713 3832807 + CmoCh12G006120.1 Cmo12g00612 612
12 3843401 3844968 + CmoCh12G006150.1 Cmo12g00615 615
11 30655769 30658645 - CmPI595203_11g018510.1 Cmu11g1851 1851
11 30664076 30674429 - CmPI595203_11g018520.1 Cmu11g1852 1852
11 30674460 30683967 - CmPI595203_11g018530.1 Cmu11g1853 1853
4 14006586 14008567 - Conep04aG0207500.1 Cone4ag2010 2010
4 14010682 14015484 + Conep04aG0207600.1 Cone4ag2011 2011
4 14016330 14019794 - Conep04aG0207700.1 Cone4ag2012 2012
7 12303742 12306272 - Conep07aG0198400.1 Cone7ag1926 1926
7 12310282 12314655 - Conep07aG0198500.1 Cone7ag1927 1927
17 9828561 9832340 + Conep17aG0148500.1 Cone17ag1444 1444
17 9834079 9836478 + Conep17aG0148600.1 Cone17ag1445 1445
20 172969 175405 - Conep20aG0003100.1 Cone20ag0031 31
20 175928 178834 + Conep20aG0003200.1 Cone20ag0032 32
20 180023 182895 - Conep20aG0003300.1 Cone20ag0033 33
2 213831 219074 + Cp4.1LG02g08440.1 Cpe02g00041 41
2 220120 222684 + Cp4.1LG02g08350.1 Cpe02g00042 42
6 140191 146292 + Cp4.1LG06g00240.1 Cpe06g00027 27
6 146734 153004 + Cp4.1LG06g00270.1 Cpe06g00028 28
6 153533 158461 + Cp4.1LG06g00250.1 Cpe06g00029 29
7 3921885 3927147 + Cp4.1LG07g05960.1 Cpe07g00584 584
7 3927951 3934212 + Cp4.1LG07g05970.1 Cpe07g00585 585
7 3944486 3945860 + Cp4.1LG07g05840.1 Cpe07g00588 588
11 6412235 6413505 - Cp4.1LG11g07930.1 Cpe11g00792 792
11 6433955 6439316 - Cp4.1LG11g07960.1 Cpe11g00796 796
11 6439728 6447042 - Cp4.1LG11g07950.1 Cpe11g00797 797
11 6450785 6456343 - Cp4.1LG11g08030.1 Cpe11g00798 798
8 21998493 21999239 - CrPI670011_08g008880.1 Cre08g0888 888
8 22023120 22030107 + CrPI670011_08g008920.1 Cre08g0892 892
11 34331455 34334287 - CrPI670011_11g022560.1 Cre11g2256 2256
11 34340472 34350213 - CrPI670011_11g022570.1 Cre11g2257 2257
11 34350244 34359677 - CrPI670011_11g022580.1 Cre11g2258 2258
4 26082192 26084651 - CsaV3_4G037170.1 Csa04g02691 2691
4 26087473 26092316 - CsaV3_4G037180.1 Csa04g02692 2692
1 87898715 87901298 - Hsped.01g23350.1 Hepe01g2335 2335
8 18465425 18476900 + Hsped.08g14870.1 Hepe08g1487 1487
8 18486883 18492992 + Hsped.08g14880.1 Hepe08g1488 1488
8 18499356 18503461 + Hsped.08g14890.1 Hepe08g1489 1489
13 41460816 41467927 + Maker00025242 Lcy13g2251 2251
13 41470560 41476828 + Maker00025303 Lcy13g2252 2252
13 41478374 41482527 + Maker00025451 Lcy13g2253 2253
4 25194598 25198120 - Lsi04G017970.1 Lsi04g01797 1797
4 25205185 25210385 - Lsi04G017980.1 Lsi04g01798 1798
8 16328430 16329677 - Lsi08G007930.1 Lsi08g00793 793
8 16354724 16359522 + Lsi08G007970.1 Lsi08g00797 797
8 16360566 16367619 - Lsi08G007980.1 Lsi08g00798 798
8 16374594 16381581 - Lsi08G008000.1 Lsi08g00800 800
8 33034883 33045340 + Sed0022458.1 Sed08g1827 1827
8 33057320 33063754 + Sed0006319.1 Sed08g1831 1831
1 116392938 116396793 - Tan0012516.2 Tan01g5098 5098
2 65309318 65313812 + Tan0019096.1 Tan02g1531 1531
2 65533770 65546396 - Tan0008897.1 Tan02g1534 1534
18 1084790 1087907 - Vvi18g110 Vvi18g110 110
18 1093020 1094144 + Vvi18g111 Vvi18g111 111
18 1095418 1099360 - Vvi18g112 Vvi18g112 112
18 1101731 1110711 - Vvi18g113 Vvi18g113 113
18 1111707 1129725 + Vvi18g114 Vvi18g114 114
18 1129775 1134072 - Vvi18g115 Vvi18g115 115
18 1136684 1144425 + Vvi18g116 Vvi18g116 116
18 1145340 1156720 - Vvi18g117 Vvi18g117 117
18 1159046 1167591 - Vvi18g118 Vvi18g118 118
18 1170163 1172152 + Vvi18g119 Vvi18g119 119
       

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