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
Vvi4g962 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g963 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g964 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g965 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g966 . Blo16g00041 Bda04g00051 . . Bpe13g00448 . . . Cmo16g00717 Cma03g00753 . Car03g00688 . Sed14g1112 . Cpe10g00609 Bhi03g01289 Tan03g1975 Cmetu08g2019 . Hepe04g1507 . . Cla01g01903 Cam01g1992 Cec04g1644 Cco04g1707 Clacu01g2012 Cmu01g1883 Cre04g1561 Cone8ag0807 . . Cone9ag1544 Lsi01g00678 . Chy07g01296 Cme08g00844 Blo05g00795 . Bda11g01871 . . Bpe06g00046 . Bma06g00125 . Cmo03g00781 . Cma16g00660 . . . . Cpe14g00563 . . . . . . . Cla07g00874 Cam07g0946 Cec07g1013 Cco07g0991 Clacu07g0921 Cmu07g0921 Cre07g1290 Lsi07g00198 Csa06g03236 Chy02g00653 .
Vvi4g967 . Blo16g00042 . . . Bpe13g00447 . . Cmo04g00842 Cmo16g00718 . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy07g01297 . . . . . . . . . . . . Cma16g00661 . . . . Cpe14g00564 . . . . . . . Cla07g00875 Cam07g0947 Cec07g1014 Cco07g0992 Clacu07g0922 Cmu07g0922 Cre07g1291 Lsi07g00197 . . .
Vvi4g968 . Blo16g00043 . . . Bpe13g00446 . . Cmo04g00844 Cmo16g00721 . . . . . . . . . . . . . . . . . . . . . Cone8ag0808 . . . . . Chy07g01300 . . . Bda11g01869 . . . . Bma06g00123 . . . Cma16g00663 . . . . Cpe14g00567 . . . . . . . Cla07g00878 Cam07g0950 Cec07g1016 Cco07g0995 Clacu07g0925 Cmu07g0924 Cre07g1293 Lsi07g00195 Csa04g00500 . .
Vvi4g969 . . Bda04g00050 . . . . . . . Cma03g00751 Cma07g00490 Car03g00686 . . . Cpe10g00611 . . . . . . . . . . . . . . . . Cone6ag1620 Cone9ag1545 . . . . . . . . . . . . . Cmo03g00780 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g970 . . . . . . Bma09g00076 . . Cmo16g00663 Cma03g00750 . Car03g00685 . Sed14g1114 . . Bhi03g01291 Tan03g1978 Cmetu07g0294 . Hepe04g1510 . . . . . . . . . . . . . Lsi01g00676 . . . . . Bda11g01868 . . . . . . Cmo03g00779 . Cma16g00608 . . . . . . . . . . . . Cla07g00795 Cam07g0860 Cec07g0911 Cco07g0893 Clacu07g0834 Cmu07g0838 Cre07g1195 Lsi07g00266 . Chy02g00651 .
Vvi4g971 . Blo16g00044 Bda04g00049 . . Bpe13g00445 . . . . . . . . . . Cpe10g00612 . . . . . . . Cla01g01906 Cam01g1995 Cec04g1647 Cco04g1710 Clacu01g2015 Cmu01g1887 Cre04g1564 . . Cone6ag1621 Cone9ag1546 . . Chy07g01231 Cme08g00846 Blo05g00796 . . . . Bpe06g00045 . Bma06g00121 . Cmo03g00778 . . . . . . . . . . . . . . Cla07g00797 Cam07g0861 Cec07g0912 Cco07g0897 Clacu07g0835 Cmu07g0839 Cre07g1196 Lsi07g00265 Csa06g03238 . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 823616 828718 + Bda018774.1 Bda04g00049 49
4 829159 830872 - Bda018773.1 Bda04g00050 50
4 836679 838025 - Bda018771.1 Bda04g00051 51
11 53746279 53754964 + Bda008806.1 Bda11g01868 1868
11 53755770 53761871 - Bda008807.1 Bda11g01869 1869
11 53763472 53764843 - Bda008808.4 Bda11g01871 1871
3 26778590 26784704 + XM_039025556.1 Bhi03g01289 1289
3 26786616 26792757 - XM_039025555.1 Bhi03g01291 1291
5 29218156 29219253 + BLOR15757 Blo05g00795 795
5 29240317 29244692 - BLOR15758 Blo05g00796 796
16 1815772 1825431 + BLOR07289 Blo16g00041 41
16 1825714 1826809 - BLOR07290 Blo16g00042 42
16 1827286 1834841 + BLOR07291 Blo16g00043 43
16 1838098 1844575 - BLOR07292 Blo16g00044 44
6 1656439 1662293 + Bma022740.2 Bma06g00121 121
6 1684947 1690921 - Bma022742.1 Bma06g00123 123
6 1692481 1693828 - Bma022743.1 Bma06g00125 125
9 1898735 1902989 - Bma028761.1 Bma09g00076 76
6 524049 528919 + Bpe019490.2 Bpe06g00045 45
6 533960 534993 - Bpe019491.1 Bpe06g00046 46
13 11987631 11997931 + Bpe006568.3 Bpe13g00445 445
13 11998766 12004834 - Bpe024944 Bpe13g00446 446
13 12005332 12006190 + Bpe006571.1 Bpe13g00447 447
13 12006463 12007498 - Bpe006572.1 Bpe13g00448 448
1 33178356 33186850 + CaPI482276_01g019920.1 Cam01g1992 1992
1 33192103 33200182 - CaPI482276_01g019950.1 Cam01g1995 1995
7 21465067 21478418 - CaPI482276_07g008600.1 Cam07g0860 860
7 21488060 21499281 - CaPI482276_07g008610.1 Cam07g0861 861
7 23289155 23292471 + CaPI482276_07g009460.1 Cam07g0946 946
7 23298388 23301419 - CaPI482276_07g009470.1 Cam07g0947 947
7 23323527 23335231 + CaPI482276_07g009500.1 Cam07g0950 950
3 6042925 6048412 + Carg00645-RA Car03g00685 685
3 6048035 6050703 - Carg00646-RA Car03g00686 686
3 6052188 6054552 - Carg00648-RA Car03g00688 688
4 32226868 32241103 + CcPI632755_04g017070.1 Cco04g1707 1707
4 32246560 32255579 - CcPI632755_04g017100.1 Cco04g1710 1710
7 20837420 20843061 - CcPI632755_07g008930.1 Cco07g0893 893
7 20879887 20881841 - CcPI632755_07g008970.1 Cco07g0897 897
7 22828407 22831729 + CcPI632755_07g009910.1 Cco07g0991 991
7 22837618 22840585 - CcPI632755_07g009920.1 Cco07g0992 992
7 22871518 22883362 + CcPI632755_07g009950.1 Cco07g0995 995
4 35712807 35727875 + CePI673135_04g016440.1 Cec04g1644 1644
4 35734022 35741347 - CePI673135_04g016470.1 Cec04g1647 1647
7 22659591 22672950 - CePI673135_07g009110.1 Cec07g0911 911
7 22682608 22694932 - CePI673135_07g009120.1 Cec07g0912 912
7 24738604 24743847 + CePI673135_07g010130.1 Cec07g1013 1013
7 24749803 24752817 - CePI673135_07g010140.1 Cec07g1014 1014
7 24794142 24805867 + CePI673135_07g010160.1 Cec07g1016 1016
2 3958912 3964200 + Chy2G029180.1 Chy02g00651 651
2 3966218 3970098 - Chy2G029200.1 Chy02g00653 653
7 17101909 17114559 - Chy7G140610.1 Chy07g01231 1231
7 17635788 17645040 + Chy7G141260.1 Chy07g01296 1296
7 17646483 17648979 - Chy7G141270.1 Chy07g01297 1297
7 17656421 17667099 + Chy7G141300.1 Chy07g01300 1300
1 32020670 32035059 + ClG42_01g0201200.10 Clacu01g2012 2012
1 32041427 32047545 - ClG42_01g0201500.10 Clacu01g2015 2015
7 21161808 21164738 - ClG42_07g0083400.10 Clacu07g0834 834
7 21167434 21203221 - ClG42_07g0083500.10 Clacu07g0835 835
7 23093196 23098257 + ClG42_07g0092100.10 Clacu07g0921 921
7 23104009 23107013 - ClG42_07g0092200.10 Clacu07g0922 922
7 23130872 23142611 + ClG42_07g0092500.10 Clacu07g0925 925
1 33782392 33797349 + ClCG01G019520.2 Cla01g01903 1903
1 33804429 33811433 - ClCG01G019560.1 Cla01g01906 1906
7 22298648 22317430 - ClCG07G008340.2 Cla07g00795 795
7 22332134 22340625 - ClCG07G008370.2 Cla07g00797 797
7 24326046 24334142 + ClCG07G009200.2 Cla07g00874 874
7 24338986 24343347 - ClCG07G009210.2 Cla07g00875 875
7 24367752 24380209 + ClCG07G009230.2 Cla07g00878 878
3 5923899 5930303 + CmaCh03G007500.1 Cma03g00750 750
3 5929846 5931616 - CmaCh03G007510.1 Cma03g00751 751
3 5932825 5936192 - CmaCh03G007530.1 Cma03g00753 753
7 2124545 2125315 - CmaCh07G004900.1 Cma07g00490 490
16 3143932 3162527 - CmaCh16G006080.1 Cma16g00608 608
16 3439388 3443507 + CmaCh16G006600.1 Cma16g00660 660
16 3444279 3447879 - CmaCh16G006610.1 Cma16g00661 661
16 3453707 3462214 + CmaCh16G006630.1 Cma16g00663 663
8 5564448 5584823 + MELO3C007825.2.1 Cme08g00844 844
8 5579690 5584847 - MELO3C007827.2.1 Cme08g00846 846
7 4642027 4654868 + PI0020954.1 Cmetu07g0294 294
8 21627230 21630648 + PI0015777.1 Cmetu08g2019 2019
3 6432371 6436865 + CmoCh03G007780.1 Cmo03g00778 778
3 6436890 6437821 + CmoCh03G007790.1 Cmo03g00779 779
3 6437453 6440980 - CmoCh03G007800.1 Cmo03g00780 780
3 6442031 6452899 - CmoCh03G007810.1 Cmo03g00781 781
4 4202254 4204333 - CmoCh04G008420.1 Cmo04g00842 842
4 4209253 4219618 + CmoCh04G008440.1 Cmo04g00844 844
16 3287498 3302219 - CmoCh16G006630.1 Cmo16g00663 663
16 3585446 3588871 + CmoCh16G007170.1 Cmo16g00717 717
16 3589498 3592985 - CmoCh16G007180.1 Cmo16g00718 718
16 3599294 3607276 + CmoCh16G007210.1 Cmo16g00721 721
1 32369041 32372396 + CmPI595203_01g018830.1 Cmu01g1883 1883
1 32389071 32397155 - CmPI595203_01g018870.1 Cmu01g1887 1887
7 21380297 21393629 - CmPI595203_07g008380.1 Cmu07g0838 838
7 21403790 21416073 - CmPI595203_07g008390.1 Cmu07g0839 839
7 23330235 23335327 + CmPI595203_07g009210.1 Cmu07g0921 921
7 23341081 23344058 - CmPI595203_07g009220.1 Cmu07g0922 922
7 23367916 23379670 + CmPI595203_07g009240.1 Cmu07g0924 924
6 12501690 12503311 + Conep06aG0168400.1 Cone6ag1620 1620
6 12503250 12506886 - Conep06aG0168500.1 Cone6ag1621 1621
8 8126927 8129837 + Conep08aG0083300.1 Cone8ag0807 807
8 8134350 8142827 + Conep08aG0083400.1 Cone8ag0808 808
9 11220343 11221717 + Conep09aG0159100.1 Cone9ag1544 1544
9 11222536 11223366 + Conep09aG0159200.1 Cone9ag1545 1545
9 11223772 11227353 - Conep09aG0159300.1 Cone9ag1546 1546
10 3545984 3550465 + Cp4.1LG10g00890.1 Cpe10g00609 609
10 3550743 3552923 + Cp4.1LG10g00960.1 Cpe10g00611 611
10 3552269 3559012 - Cp4.1LG10g00760.1 Cpe10g00612 612
14 3577427 3581756 + Cp4.1LG14g01510.1 Cpe14g00563 563
14 3582301 3585815 - Cp4.1LG14g01470.1 Cpe14g00564 564
14 3592133 3603559 + Cp4.1LG14g01530.1 Cpe14g00567 567
4 34219556 34229724 + CrPI670011_04g015610.1 Cre04g1561 1561
4 34235296 34243433 - CrPI670011_04g015640.1 Cre04g1564 1564
7 24964550 24980093 - CrPI670011_07g011950.1 Cre07g1195 1195
7 24996358 24998544 - CrPI670011_07g011960.1 Cre07g1196 1196
7 27077399 27083159 + CrPI670011_07g012900.1 Cre07g1290 1290
7 27089413 27092391 - CrPI670011_07g012910.1 Cre07g1291 1291
7 27123305 27135086 + CrPI670011_07g012930.1 Cre07g1293 1293
4 3278676 3281081 - CsaV3_4G005000.1 Csa04g00500 500
6 27338012 27341438 + CsaV3_6G046220.1 Csa06g03236 3236
6 27343467 27348800 - CsaV3_6G046240.1 Csa06g03238 3238
4 70648016 70649983 + Hsped.04g15070.1 Hepe04g1507 1507
4 70658049 70663369 - Hsped.04g15100.1 Hepe04g1510 1510
1 5452050 5458429 + Lsi01G006760.1 Lsi01g00676 676
1 5460332 5470533 - Lsi01G006780.1 Lsi01g00678 678
7 2117719 2130549 - Lsi07G001950.1 Lsi07g00195 195
7 2139601 2142230 + Lsi07G001970.1 Lsi07g00197 197
7 2144750 2150352 - Lsi07G001980.1 Lsi07g00198 198
7 2880052 2890282 + Lsi07G002650.1 Lsi07g00265 265
7 2891358 2906569 + Lsi07G002660.1 Lsi07g00266 266
14 20619497 20631505 + Sed0009390.1 Sed14g1112 1112
14 20636716 20642978 - Sed0017564.1 Sed14g1114 1114
3 74834054 74839610 + Tan0004560.1 Tan03g1975 1975
3 74843772 74849369 - Tan0004611.1 Tan03g1978 1978
4 18219166 18219838 + Vvi4g962 Vvi4g962 962
4 18230192 18230728 - Vvi4g963 Vvi4g963 963
4 18230752 18231994 + Vvi4g964 Vvi4g964 964
4 18275833 18276875 + Vvi4g965 Vvi4g965 965
4 18296442 18301052 + Vvi4g966 Vvi4g966 966
4 18301282 18304437 - Vvi4g967 Vvi4g967 967
4 18329571 18348704 + Vvi4g968 Vvi4g968 968
4 18349889 18353020 + Vvi4g969 Vvi4g969 969
4 18354304 18370077 - Vvi4g970 Vvi4g970 970
4 18370562 18382064 - Vvi4g971 Vvi4g971 971
       

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