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
Vvi4g922 . . Bda04g00324 Bda10g00313 . . . . . . . Cma07g00755 . Car07g00742 . . . . . . . . . . . . . . . . . . . . . Lsi01g01055 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy02g00976 .
Vvi4g923 Blo04g00928 . . Bda10g00120 Bpe15g00439 . . Bma15g01008 . . . Cma07g00506 . . . Cpe19g00794 Cpe10g00590 Bhi03g01262 . . . . . . Cla01g01883 . . . . . . . Cone12ag0758 Cone6ag1605 Cone9ag1529 Lsi01g00703 . . Cme08g00822 . . . . Bpe10g00105 . . . . Cmo03g00805 Cmo07g00505 . . . . . . . . . . . . . . . . . . . . Lsi07g00267 Csa06g03213 Chy02g00672 .
Vvi4g924 . Blo16g00036 . . . Bpe13g00455 . . . . Cma03g00772 Cma07g00505 Car03g00702 Car07g00442 Sed14g1097 Cpe19g00796 Cpe10g00592 Bhi03g01267 Tan03g1954 Cmetu05g1256 . Hepe04g1486 . . Cla01g01884 Cam01g1975 Cec04g1627 Cco04g1691 Clacu01g1996 Cmu01g1866 Cre04g1547 . . . Cone9ag1530 Lsi01g00701 . . Cme08g00824 . . Bda11g01877 . . . . . . Cmo03g00802 Cmo07g00503 . . . . . . . . . . . . . . . . . . . . . Csa06g03215 Chy02g00671 .
Vvi4g925 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g926 . . Bda04g00065 . . . Bma09g00061 . . . Cma03g00770 . Car03g00700 . Sed10g0902 . Cpe10g00593 Bhi03g01268 Tan03g1957 Cmetu08g1080 . Hepe04g1488 . . Cla01g01885 Cam01g1977 Cec04g1628 Cco04g1693 Clacu01g1997 Cmu01g1867 Cre04g1549 . . . . Lsi01g00700 . . Cme08g00825 Blo05g00784 . . . . Bpe06g00055 . . . Cmo03g00799 . . . . . . . . . . . . . . . . . . . . . . Csa06g03217 Chy02g00669 .
Vvi4g927 Blo04g00927 Blo16g00037 Bda04g00064 . . Bpe13g00454 . . Cmo04g00828 . Cma03g00769 Cma07g00504 . Car07g00441 Sed07g1686 Cpe19g00797 . Bhi03g01269 Tan03g1958 Cmetu07g2129 . Hepe04g1489 . . Cla01g01886 Cam01g1978 Cec04g1629 Cco04g1694 Clacu01g1998 Cmu01g1868 Cre04g1550 Cone8ag0797 Cone12ag0756 . Cone9ag1531 Lsi01g00699 . Chy07g01276 Cme08g00826 . Blo06g00125 Bda11g01876 . Bpe10g00106 Bpe06g00054 . Bma06g00130 . Cmo03g00798 . . . . . . . . . . . . . . Cla07g00851 Cam07g0923 Cec07g0983 Cco07g0966 Clacu07g0899 Cmu07g0899 Cre07g1264 . Csa06g03219 Chy02g00668 .
Vvi4g928 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g929 . . . . . . . . . . Cma03g00768 Cma07g00503 Car03g00699 Car07g00440 Sed14g0331 Cpe19g00798 Cpe10g00595 Bhi03g01270 Tan03g1959 Cmetu11g1191 . Hepe04g1490 . . Cla01g01888 . Cec04g1630 Cco04g1696 . Cmu01g1869 . . . Cone6ag1606 . . . . Cme08g00827 . . . Bda14g01176 . . . . . . Cmo07g00502 . . . . . . . . . . . . . . . . . . . . . Csa06g03220 Chy02g00667 .
Vvi4g930 . . Bda04g00063 Bda10g00121 . . . . . . . . Car03g00698 Car07g00439 Sed14g1098 Cpe19g00799 Cpe10g00596 Bhi03g01272 Tan03g1960 Cmetu08g0851 . Hepe04g1491 . . Cla01g01889 Cam01g1979 Cec04g1631 Cco04g1697 Clacu01g1999 Cmu01g1870 Cre04g1551 . . Cone6ag1607 Cone9ag1533 Lsi01g00696 . . Cme08g00828 Blo05g00785 Blo06g00126 . . Bpe10g00107 Bpe06g00053 . . . Cmo03g00796 . . . . . . . . . . . . . . . . . . . . . . Csa06g03222 Chy02g00666 .
Vvi4g931 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 1031813 1034645 - Bda018758.1 Bda04g00063 63
4 1067294 1068257 - Bda018756.1 Bda04g00064 64
4 1088592 1090306 - Bda018753.1 Bda04g00065 65
4 47372912 47373903 + Bda019206.1 Bda04g00324 324
10 2952239 2991722 + Bda006579.1 Bda10g00120 120
10 3166845 3169212 + Bda006580.2 Bda10g00121 121
10 32667082 32667990 + Bda007087.1 Bda10g00313 313
11 53819580 53820085 - Bda008814.1 Bda11g01876 1876
11 53823151 53828611 + Bda008815.2 Bda11g01877 1877
14 11240606 11243196 + Bda028028.1 Bda14g01176 1176
3 25942978 25944273 + XM_039027931.1 Bhi03g01262 1262
3 26219656 26227023 - XM_039027315.1 Bhi03g01267 1267
3 26228966 26232173 - XM_039026945.1 Bhi03g01268 1268
3 26265318 26267708 + XM_039027197.1 Bhi03g01269 1269
3 26270968 26274441 + XM_039027544.1 Bhi03g01270 1270
3 26323018 26327086 + XM_039026231.1 Bhi03g01272 1272
4 10974191 10975139 - BLOR13839 Blo04g00927 927
4 10987893 10989380 - BLOR13840 Blo04g00928 928
5 28753526 28755338 + BLOR15746 Blo05g00784 784
5 28923433 28926376 + BLOR15747 Blo05g00785 785
6 5047383 5050819 + BLOR16708 Blo06g00125 125
6 5096307 5098747 + BLOR16709 Blo06g00126 126
16 1750599 1755740 - BLOR07284 Blo16g00036 36
16 1764352 1765164 + BLOR07285 Blo16g00037 37
6 1738339 1739130 - Bma022748.1 Bma06g00130 130
9 1451693 1462303 + Bma028740.1 Bma09g00061 61
15 39426407 39428094 - Bma014292.1 Bma15g01008 1008
6 631164 633957 - Bpe019500.1 Bpe06g00053 53
6 648161 649014 - Bpe019501.1 Bpe06g00054 54
6 666608 668314 - Bpe019502.1 Bpe06g00055 55
10 1601333 1602993 + Bpe002405.1 Bpe10g00105 105
10 1801236 1802266 + Bpe002407.1 Bpe10g00106 106
10 1859362 1864057 + Bpe002409.1 Bpe10g00107 107
13 12050748 12051283 - Bpe006578.1 Bpe13g00454 454
13 12054391 12059330 + Bpe006579.1 Bpe13g00455 455
15 15870430 15871887 - Bpe001375.1 Bpe15g00439 439
1 33039869 33053779 - CaPI482276_01g019750.1 Cam01g1975 1975
1 33056675 33058403 - CaPI482276_01g019770.1 Cam01g1977 1977
1 33074518 33076511 + CaPI482276_01g019780.1 Cam01g1978 1978
1 33079108 33091946 + CaPI482276_01g019790.1 Cam01g1979 1979
7 22790873 22793565 + CaPI482276_07g009230.1 Cam07g0923 923
3 6103484 6107604 - Carg00658-RA Car03g00698 698
3 6108304 6111148 - Carg00659-RA Car03g00699 699
3 6122307 6123831 + Carg00660-RA Car03g00700 700
3 6126014 6133409 + Carg00662-RA Car03g00702 702
7 2224683 2230435 - Carg16036-RA Car07g00439 439
7 2231481 2235674 - Carg16035-RA Car07g00440 440
7 2236257 2237343 - Carg16034-RA Car07g00441 441
7 2241852 2249123 + Carg16033-RA Car07g00442 442
7 3824383 3827700 + Carg05264-RA Car07g00742 742
4 32085929 32099569 - CcPI632755_04g016910.1 Cco04g1691 1691
4 32102525 32104249 - CcPI632755_04g016930.1 Cco04g1693 1693
4 32120647 32122601 + CcPI632755_04g016940.1 Cco04g1694 1694
4 32132921 32135207 + CcPI632755_04g016960.1 Cco04g1696 1696
4 32135231 32138214 + CcPI632755_04g016970.1 Cco04g1697 1697
7 22358800 22361553 + CcPI632755_07g009660.1 Cco07g0966 966
4 35580477 35594315 - CePI673135_04g016270.1 Cec04g1627 1627
4 35597608 35599307 - CePI673135_04g016280.1 Cec04g1628 1628
4 35616947 35618981 + CePI673135_04g016290.1 Cec04g1629 1629
4 35622314 35631465 + CePI673135_04g016300.1 Cec04g1630 1630
4 35631489 35634476 + CePI673135_04g016310.1 Cec04g1631 1631
7 24158517 24161267 + CePI673135_07g009830.1 Cec07g0983 983
2 4041247 4043951 - Chy2G029330.1 Chy02g00666 666
2 4044918 4050080 - Chy2G029340.1 Chy02g00667 667
2 4050615 4053587 - Chy2G029350.1 Chy02g00668 668
2 4065971 4067733 + Chy2G029360.1 Chy02g00669 669
2 4070189 4081531 + Chy2G029380.1 Chy02g00671 671
2 4083527 4085604 - Chy2G029390.1 Chy02g00672 672
2 6502600 6505013 + Chy2G032430.1 Chy02g00976 976
7 17481412 17483594 + Chy7G141060.1 Chy07g01276 1276
1 31886627 31900550 - ClG42_01g0199600.10 Clacu01g1996 1996
1 31903366 31905093 - ClG42_01g0199700.10 Clacu01g1997 1997
1 31921185 31923171 + ClG42_01g0199800.10 Clacu01g1998 1998
1 31926481 31938651 + ClG42_01g0199900.10 Clacu01g1999 1999
7 22560695 22563390 + ClG42_07g0089900.10 Clacu07g0899 899
1 33635380 33642761 + ClCG01G019300.2 Cla01g01883 1883
1 33642313 33659027 - ClCG01G019310.2 Cla01g01884 1884
1 33659957 33663566 - ClCG01G019330.1 Cla01g01885 1885
1 33680655 33685700 + ClCG01G019340.1 Cla01g01886 1886
1 33686062 33694532 + ClCG01G019350.2 Cla01g01888 1888
1 33695246 33698232 + ClCG01G019360.1 Cla01g01889 1889
7 23751856 23754548 + ClCG07G008960.1 Cla07g00851 851
3 5987278 5994631 - CmaCh03G007680.1 Cma03g00768 768
3 5995766 5997148 - CmaCh03G007690.1 Cma03g00769 769
3 6000921 6002585 + CmaCh03G007700.1 Cma03g00770 770
3 6004628 6013065 + CmaCh03G007720.1 Cma03g00772 772
7 2163688 2173256 - CmaCh07G005030.1 Cma07g00503 503
7 2173580 2174910 - CmaCh07G005040.1 Cma07g00504 504
7 2179002 2190893 + CmaCh07G005050.1 Cma07g00505 505
7 2191531 2192973 - CmaCh07G005060.1 Cma07g00506 506
7 3350210 3354373 + CmaCh07G007550.1 Cma07g00755 755
8 5447276 5448971 + MELO3C007805.2.1 Cme08g00822 822
8 5456156 5462889 - MELO3C007807.2.1 Cme08g00824 824
8 5463907 5467245 - MELO3C007808.2.1 Cme08g00825 825
8 5480551 5482026 + MELO3C007809.2.1 Cme08g00826 826
8 5484208 5487792 + MELO3C007810.2.1 Cme08g00827 827
8 5489091 5493681 + MELO3C007811.2.1 Cme08g00828 828
5 3377637 3383309 - PI0019223.1 Cmetu05g1256 1256
7 4262273 4265047 - PI0026927.1 Cmetu07g2129 2129
8 21550994 21553670 + PI0002832.1 Cmetu08g0851 851
8 21524581 21526320 - PI0008138.1 Cmetu08g1080 1080
11 3719012 3724833 - PI0016677.1 Cmetu11g1191 1191
3 6493621 6497790 - CmoCh03G007960.1 Cmo03g00796 796
3 6497862 6505046 - CmoCh03G007980.1 Cmo03g00798 798
3 6509606 6511224 + CmoCh03G007990.1 Cmo03g00799 799
3 6513270 6521206 + CmoCh03G008020.1 Cmo03g00802 802
3 6526951 6528378 - CmoCh03G008050.1 Cmo03g00805 805
4 4132503 4134035 + CmoCh04G008280.1 Cmo04g00828 828
7 2267677 2278713 - CmoCh07G005020.1 Cmo07g00502 502
7 2283129 2290140 + CmoCh07G005030.1 Cmo07g00503 503
7 2295378 2296817 - CmoCh07G005050.1 Cmo07g00505 505
1 32235186 32249121 - CmPI595203_01g018660.1 Cmu01g1866 1866
1 32251453 32253631 - CmPI595203_01g018670.1 Cmu01g1867 1867
1 32269744 32271731 + CmPI595203_01g018680.1 Cmu01g1868 1868
1 32275019 32284188 + CmPI595203_01g018690.1 Cmu01g1869 1869
1 32284212 32287199 + CmPI595203_01g018700.1 Cmu01g1870 1870
7 22791708 22794406 + CmPI595203_07g008990.1 Cmu07g0899 899
6 12423254 12424702 + Conep06aG0166800.1 Cone6ag1605 1605
6 12440854 12443491 + Conep06aG0166900.1 Cone6ag1606 1606
6 12444611 12448204 + Conep06aG0167000.1 Cone6ag1607 1607
8 8001313 8001818 - Conep08aG0082300.1 Cone8ag0797 797
9 11142637 11144076 + Conep09aG0157500.1 Cone9ag1529 1529
9 11145504 11150706 - Conep09aG0157600.1 Cone9ag1530 1530
9 11160124 11161379 + Conep09aG0157700.1 Cone9ag1531 1531
9 11169867 11173301 + Conep09aG0157900.1 Cone9ag1533 1533
12 6991505 6992771 + Conep12aG0077900.1 Cone12ag0756 756
12 7001836 7003269 - Conep12aG0078100.1 Cone12ag0758 758
10 3462622 3464825 + Cp4.1LG10g01090.1 Cpe10g00590 590
10 3469372 3477541 - Cp4.1LG10g01030.1 Cpe10g00592 592
10 3479482 3481435 - Cp4.1LG10g00750.1 Cpe10g00593 593
10 3488252 3491308 + Cp4.1LG10g00840.1 Cpe10g00595 595
10 3491811 3497548 + Cp4.1LG10g00830.1 Cpe10g00596 596
19 6002027 6003544 + Cp4.1LG19g09500.1 Cpe19g00794 794
19 6008596 6015982 - Cp4.1LG19g09380.1 Cpe19g00796 796
19 6020182 6021111 + Cp4.1LG19g09540.1 Cpe19g00797 797
19 6021387 6025598 + Cp4.1LG19g09520.1 Cpe19g00798 798
19 6026592 6031168 + Cp4.1LG19g09470.1 Cpe19g00799 799
4 34081366 34095109 - CrPI670011_04g015470.1 Cre04g1547 1547
4 34098045 34099773 - CrPI670011_04g015490.1 Cre04g1549 1549
4 34116401 34118445 + CrPI670011_04g015500.1 Cre04g1550 1550
4 34121729 34133857 + CrPI670011_04g015510.1 Cre04g1551 1551
7 26560183 26562965 + CrPI670011_07g012640.1 Cre07g1264 1264
6 27222812 27224349 + CsaV3_6G045990.1 Csa06g03213 3213
6 27231979 27239010 - CsaV3_6G046010.1 Csa06g03215 3215
6 27241170 27242940 - CsaV3_6G046030.1 Csa06g03217 3217
6 27254198 27256020 + CsaV3_6G046050.1 Csa06g03219 3219
6 27257598 27261281 + CsaV3_6G046060.1 Csa06g03220 3220
6 27264439 27267123 + CsaV3_6G046080.1 Csa06g03222 3222
4 70496479 70506007 - Hsped.04g14860.1 Hepe04g1486 1486
4 70508749 70510530 - Hsped.04g14880.1 Hepe04g1488 1488
4 70530975 70532866 + Hsped.04g14890.1 Hepe04g1489 1489
4 70535241 70538441 + Hsped.04g14900.1 Hepe04g1490 1490
4 70542033 70546063 + Hsped.04g14910.1 Hepe04g1491 1491
1 5555083 5565627 - Lsi01G006960.1 Lsi01g00696 696
1 5567910 5570219 - Lsi01G006990.1 Lsi01g00699 699
1 5588466 5592284 + Lsi01G007000.1 Lsi01g00700 700
1 5594235 5602035 + Lsi01G007010.1 Lsi01g00701 701
1 5614144 5615577 - Lsi01G007030.1 Lsi01g00703 703
1 8757168 8763319 + Lsi01G010550.1 Lsi01g01055 1055
7 2909441 2923151 - Lsi07G002670.1 Lsi07g00267 267
7 15100056 15102957 + Sed0020162.1 Sed07g1686 1686
10 6951234 6953528 + Sed0007579.1 Sed10g0902 902
14 3397525 3405887 - Sed0017165.2 Sed14g0331 331
14 20463767 20471894 - Sed0009119.2 Sed14g1097 1097
14 20482606 20486292 + Sed0024040.1 Sed14g1098 1098
3 74668757 74677243 - Tan0011908.2 Tan03g1954 1954
3 74681292 74683111 - Tan0017859.1 Tan03g1957 1957
3 74705302 74707112 + Tan0006560.1 Tan03g1958 1958
3 74710200 74713544 + Tan0003511.1 Tan03g1959 1959
3 74719775 74722352 + Tan0004413.1 Tan03g1960 1960
4 17682214 17686563 - Vvi4g922 Vvi4g922 922
4 17705303 17707037 + Vvi4g923 Vvi4g923 923
4 17711958 17747277 - Vvi4g924 Vvi4g924 924
4 17749564 17753874 + Vvi4g925 Vvi4g925 925
4 17782216 17785665 - Vvi4g926 Vvi4g926 926
4 17798123 17799885 + Vvi4g927 Vvi4g927 927
4 17802190 17803264 - Vvi4g928 Vvi4g928 928
4 17821354 17829046 + Vvi4g929 Vvi4g929 929
4 17832553 17863982 + Vvi4g930 Vvi4g930 930
4 17864180 17864801 - Vvi4g931 Vvi4g931 931
       

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