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
Vvi4g972 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0810 . . . . . Chy07g01247 . . . Bda11g01867 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g973 . . . . . . . . . . Cma03g00749 . Car03g00684 . . . Cpe10g00613 Bhi03g01297 . . . Hepe04g1513 . . Cla01g01907 . . Cco04g1711 . Cmu01g1888 . . . . . Lsi01g00675 . . Cme08g00847 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g03239 Chy02g00650 .
Vvi4g974 . . . . . . . . . . . Cma07g00488 . Car07g00429 Sed14g1119 Cpe19g00808 . Bhi03g01298 Tan03g1980 Cmetu08g1666 . Hepe04g1514 . . Cla01g01908 Cam01g1996 Cec04g1649 . . . Cre04g1565 . . Cone6ag1622 Cone9ag1547 Lsi01g00674 . . Cme08g00848 . . . . . . . . . . Cmo07g00486 . . . . . . . . . . . . . . . . . . . . . Csa06g03240 Chy02g00649 .
Vvi4g975 . . . . . . . . . . Cma03g00748 . Car03g00683 . . . Cpe10g00614 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo03g00776 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g976 Blo04g00918 Blo16g00045 . . Bpe15g00429 Bpe13g00444 . . . . . Cma07g00487 Car03g00682 Car07g00427 Sed14g1121 Cpe19g00810 Cpe10g00615 Bhi03g01300 Tan03g1982 Cmetu07g2099 . Hepe04g1516 . . Cla01g01911 Cam01g1998 Cec04g1653 Cco04g1715 Clacu01g2017 Cmu01g1891 Cre04g1567 . . . . Lsi01g00673 . Chy07g01246 . . . Bda11g01866 . . . Bma03g00990 . . Cmo03g00775 Cmo07g00485 . . . . . . . . . . . . . . . . . . . . . . Chy02g00647 .
Vvi4g977 Blo04g00917 . . . Bpe15g00428 . . . Cmo04g00877 Cmo16g00763 . . . . . . . . . . . . . . . . . . . . . Cone8ag0812 . . . . . Chy07g01245 . . . . . . . Bma03g00989 . Sed05g3619 . . Cma16g00706 . . . . Cpe14g00603 Bhi10g02010 Tan05g1308 Cmetu07g0234 . Hepe08g1015 . . . . . . . . . Lsi07g00150 Csa04g00453 . .
Vvi4g978 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone9ag1549 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g979 . . . Bda10g00135 . . . Bma15g00996 . . Cma03g00747 . Car03g00681 . Sed14g1122 . Cpe10g00616 Bhi03g01301 Tan03g1983 Cmetu08g0437 . Hepe04g1517 . . Cla01g01912 Cam01g1999 Cec04g1654 Cco04g1716 Clacu01g2018 Cmu01g1892 Cre04g1568 . . Cone6ag1624 . Lsi01g00672 . . Cme08g00849 . Blo06g00134 . . Bpe10g00120 . . . . Cmo03g00774 . . . . . . . . . . . . . . . . . . . . . . Csa06g03241 . .
Vvi4g980 Blo04g00916 Blo16g00046 . . Bpe15g00427 Bpe13g00443 . . Cmo04g00894 . Cma03g00745 Cma07g00485 Car03g00680 Car07g00426 Sed14g1123 Cpe19g00812 Cpe10g00617 Bhi03g01303 Tan03g1984 Cmetu03g1675 . Hepe04g1519 . . Cla01g01913 Cam01g2000 Cec04g1655 Cco04g1718 Clacu01g2019 Cmu01g1894 Cre04g1570 . . Cone6ag1625 Cone9ag1550 Lsi01g00671 . Chy07g01244 Cme08g00852 . . Bda11g01865 . . . Bma03g00988 Bma06g00120 . Cmo03g00772 Cmo07g00483 . . . . . . . . . . . . . Cla07g00812 Cam07g0875 Cec07g0928 Cco07g0916 Clacu07g0850 Cmu07g0854 Cre07g1212 . Csa06g03243 Chy02g00645 .
Vvi4g981 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0813 Cone12ag0764 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
10 3789088 3789978 - Bda006598.1 Bda10g00135 135
11 53736302 53737291 - Bda008803.1 Bda11g01865 1865
11 53740682 53741508 - Bda008804.1 Bda11g01866 1866
11 53744388 53745567 - Bda008805.1 Bda11g01867 1867
3 26911848 26920212 + XM_039026030.1 Bhi03g01297 1297
3 26920549 26922925 - XM_039026026.1 Bhi03g01298 1298
3 26960464 26961799 + XM_039027416.1 Bhi03g01300 1300
3 26978664 26979971 + XM_039025089.1 Bhi03g01301 1301
3 27021310 27024427 + XM_039026559.1 Bhi03g01303 1303
10 50301901 50311772 + XM_039046630.1 Bhi10g02010 2010
4 10741087 10742025 - BLOR13828 Blo04g00916 916
4 10752374 10753557 - BLOR13829 Blo04g00917 917
4 10785285 10786115 - BLOR13830 Blo04g00918 918
6 5417651 5418580 + BLOR16717 Blo06g00134 134
16 1863555 1864399 + BLOR07293 Blo16g00045 45
16 1874806 1875798 + BLOR07294 Blo16g00046 46
3 10644405 10645358 - Bma017330.1 Bma03g00988 988
3 10649011 10650191 - Bma031010 Bma03g00989 989
3 10655675 10656505 - Bma017331.1 Bma03g00990 990
6 1632572 1633561 - Bma022738.1 Bma06g00120 120
15 38618613 38619497 - Bma014279.1 Bma15g00996 996
10 2174071 2174973 + Bpe002423.1 Bpe10g00120 120
13 11967088 11968077 - Bpe006566.1 Bpe13g00443 443
13 11972502 11973219 - Bpe006567.1 Bpe13g00444 444
15 15790946 15791899 - Bpe001363.1 Bpe15g00427 427
15 15794409 15795605 - Bpe001364.1 Bpe15g00428 428
15 15800054 15800884 - Bpe001365.1 Bpe15g00429 429
1 33202561 33212161 - CaPI482276_01g019960.1 Cam01g1996 1996
1 33225662 33226414 + CaPI482276_01g019980.1 Cam01g1998 1998
1 33231219 33232182 + CaPI482276_01g019990.1 Cam01g1999 1999
1 33246538 33247545 + CaPI482276_01g020000.1 Cam01g2000 2000
7 21753348 21755650 - CaPI482276_07g008750.1 Cam07g0875 875
3 6018644 6020013 - Carg00640-RA Car03g00680 680
3 6022359 6023339 - Carg00641-RA Car03g00681 681
3 6024420 6025185 - Carg00642-RA Car03g00682 682
3 6030406 6040149 + Carg00643-RA Car03g00683 683
3 6040993 6041301 - Carg00644-RA Car03g00684 684
7 2171365 2172336 - Carg16049-RA Car07g00426 426
7 2177816 2178596 - Carg16048-RA Car07g00427 427
7 2182813 2185211 + Carg16046-RA Car07g00429 429
4 32256935 32257243 + CcPI632755_04g017110.1 Cco04g1711 1711
4 32279718 32280470 + CcPI632755_04g017150.1 Cco04g1715 1715
4 32285234 32286203 + CcPI632755_04g017160.1 Cco04g1716 1716
4 32300706 32301713 + CcPI632755_04g017180.1 Cco04g1718 1718
7 21139965 21142295 - CcPI632755_07g009160.1 Cco07g0916 916
4 35744489 35747117 - CePI673135_04g016490.1 Cec04g1649 1649
4 35771773 35772525 + CePI673135_04g016530.1 Cec04g1653 1653
4 35777208 35778041 + CePI673135_04g016540.1 Cec04g1654 1654
4 35792764 35793771 + CePI673135_04g016550.1 Cec04g1655 1655
7 23006035 23008388 - CePI673135_07g009280.1 Cec07g0928 928
2 3929084 3930097 - Chy2G029120.1 Chy02g00645 645
2 3945876 3946608 + Chy2G029140.1 Chy02g00647 647
2 3952454 3954625 + Chy2G029160.1 Chy02g00649 649
2 3955343 3956436 - Chy2G029170.1 Chy02g00650 650
7 17179886 17181383 - Chy7G140740.1 Chy07g01244 1244
7 17184358 17186210 - Chy7G140750.1 Chy07g01245 1245
7 17188135 17189569 - Chy7G140760.1 Chy07g01246 1246
7 17200754 17207607 - Chy7G140770.1 Chy07g01247 1247
1 32074136 32074888 + ClG42_01g0201700.10 Clacu01g2017 2017
1 32079430 32080393 + ClG42_01g0201800.10 Clacu01g2018 2018
1 32094834 32095841 + ClG42_01g0201900.10 Clacu01g2019 2019
7 21459035 21461303 - ClG42_07g0085000.10 Clacu07g0850 850
1 33813698 33814006 + ClCG01G019570.1 Cla01g01907 1907
1 33814583 33816937 - ClCG01G019580.2 Cla01g01908 1908
1 33837867 33838619 + ClCG01G019610.2 Cla01g01911 1911
1 33843161 33844124 + ClCG01G019620.2 Cla01g01912 1912
1 33858466 33859572 + ClCG01G019630.2 Cla01g01913 1913
7 22610573 22612841 - ClCG07G008540.1 Cla07g00812 812
3 5899158 5899793 - CmaCh03G007450.1 Cma03g00745 745
3 5902812 5905501 - CmaCh03G007470.1 Cma03g00747 747
3 5911298 5921042 + CmaCh03G007480.1 Cma03g00748 748
3 5921791 5923947 - CmaCh03G007490.1 Cma03g00749 749
7 2110438 2111412 - CmaCh07G004850.1 Cma07g00485 485
7 2116069 2117166 - CmaCh07G004870.1 Cma07g00487 487
7 2120596 2123228 + CmaCh07G004880.1 Cma07g00488 488
16 3677599 3679790 + CmaCh16G007060.1 Cma16g00706 706
8 5585807 5588887 + MELO3C007828.2.1 Cme08g00847 847
8 5589145 5593068 - MELO3C007829.2.1 Cme08g00848 848
8 5593846 5595119 - MELO3C007830.2.1 Cme08g00849 849
8 5615815 5617560 + MELO3C007832.2.1 Cme08g00852 852
3 1875516 1878345 + PI0021326.1 Cmetu03g1675 1675
7 4566075 4568561 + PI0017885.1 Cmetu07g0234 234
7 4560879 4562412 + PI0024679.1 Cmetu07g2099 2099
8 21652562 21654700 - PI0028468.1 Cmetu08g0437 437
8 21641530 21644471 - PI0028957.1 Cmetu08g1666 1666
3 6406729 6407597 - CmoCh03G007720.1 Cmo03g00772 772
3 6410450 6411430 - CmoCh03G007740.1 Cmo03g00774 774
3 6413147 6414061 - CmoCh03G007750.1 Cmo03g00775 775
3 6419865 6429213 + CmoCh03G007760.1 Cmo03g00776 776
4 4412637 4415422 + CmoCh04G008770.1 Cmo04g00877 877
4 4510277 4515095 - CmoCh04G008940.1 Cmo04g00894 894
7 2202787 2203758 - CmoCh07G004830.1 Cmo07g00483 483
7 2209766 2210822 - CmoCh07G004850.1 Cmo07g00485 485
7 2215428 2218336 + CmoCh07G004860.1 Cmo07g00486 486
16 3834609 3842012 + CmoCh16G007630.1 Cmo16g00763 763
1 32399420 32399728 + CmPI595203_01g018880.1 Cmu01g1888 1888
1 32422599 32423351 + CmPI595203_01g018910.1 Cmu01g1891 1891
1 32427901 32428864 + CmPI595203_01g018920.1 Cmu01g1892 1892
1 32443308 32444312 + CmPI595203_01g018940.1 Cmu01g1894 1894
7 21680436 21682699 - CmPI595203_07g008540.1 Cmu07g0854 854
6 12510270 12512827 - Conep06aG0168600.1 Cone6ag1622 1622
6 12523202 12523525 + Conep06aG0168800.1 Cone6ag1624 1624
6 12526272 12528232 + Conep06aG0168900.1 Cone6ag1625 1625
8 8143915 8146561 + Conep08aG0083600.1 Cone8ag0810 810
8 8165685 8168534 + Conep08aG0083800.1 Cone8ag0812 812
8 8168696 8169603 - Conep08aG0083900.1 Cone8ag0813 813
9 11231780 11233413 - Conep09aG0159500.1 Cone9ag1547 1547
9 11247581 11251579 - Conep09aG0159700.1 Cone9ag1549 1549
9 11257951 11258910 + Conep09aG0159800.1 Cone9ag1550 1550
12 7037293 7039770 - Conep12aG0078700.1 Cone12ag0764 764
10 3559196 3562768 + Cp4.1LG10g00910.1 Cpe10g00613 613
10 3561766 3571500 - Cp4.1LG10g00770.1 Cpe10g00614 614
10 3576895 3578308 + Cp4.1LG10g00610.1 Cpe10g00615 615
10 3578926 3579906 + Cp4.1LG10g00640.1 Cpe10g00616 616
10 3583021 3583671 + Cp4.1LG10g00650.1 Cpe10g00617 617
14 3839037 3841320 + Cp4.1LG14g01230.1 Cpe14g00603 603
19 6066328 6080914 - Cp4.1LG19g09200.1 Cpe19g00808 808
19 6078708 6079486 + Cp4.1LG19g09270.1 Cpe19g00810 810
19 6085016 6085987 + Cp4.1LG19g09350.1 Cpe19g00812 812
4 34246607 34249241 - CrPI670011_04g015650.1 Cre04g1565 1565
4 34269260 34270012 + CrPI670011_04g015670.1 Cre04g1567 1567
4 34274570 34275533 + CrPI670011_04g015680.1 Cre04g1568 1568
4 34289540 34290547 + CrPI670011_04g015700.1 Cre04g1570 1570
7 25402115 25404404 - CrPI670011_07g012120.1 Cre07g1212 1212
4 2829074 2832700 - CsaV3_4G004530.1 Csa04g00453 453
6 27349398 27352324 + CsaV3_6G046250.1 Csa06g03239 3239
6 27352318 27355888 - CsaV3_6G046260.1 Csa06g03240 3240
6 27356356 27358000 - CsaV3_6G046270.1 Csa06g03241 3241
6 27375407 27379138 + CsaV3_6G046290.1 Csa06g03243 3243
4 70676832 70677873 + Hsped.04g15130.1 Hepe04g1513 1513
4 70678659 70681199 - Hsped.04g15140.1 Hepe04g1514 1514
4 70712151 70712916 + Hsped.04g15160.1 Hepe04g1516 1516
4 70715864 70717159 + Hsped.04g15170.1 Hepe04g1517 1517
4 70729031 70730869 + Hsped.04g15190.1 Hepe04g1519 1519
8 9696336 9699017 + Hsped.08g10150.1 Hepe08g1015 1015
1 5411171 5412178 - Lsi01G006710.1 Lsi01g00671 671
1 5424533 5425366 - Lsi01G006720.1 Lsi01g00672 672
1 5428572 5429462 - Lsi01G006730.1 Lsi01g00673 673
1 5445460 5448367 + Lsi01G006740.1 Lsi01g00674 674
1 5448801 5452124 - Lsi01G006750.1 Lsi01g00675 675
7 1600852 1605837 - Lsi07G001500.1 Lsi07g00150 150
5 44523120 44527504 + Sed0027094.1 Sed05g3619 3619
14 20655268 20659383 - Sed0013382.2 Sed14g1119 1119
14 20685050 20686141 + Sed0015276.1 Sed14g1121 1121
14 20687629 20688789 + Sed0008156.1 Sed14g1122 1122
14 20699515 20701323 + Sed0000818.1 Sed14g1123 1123
3 74854645 74856914 - Tan0016499.1 Tan03g1980 1980
3 74890821 74891585 + Tan0022446.1 Tan03g1982 1982
3 74893708 74895312 + Tan0004752.1 Tan03g1983 1983
3 74903103 74909933 + Tan0013253.1 Tan03g1984 1984
5 15832692 15833358 + Tan0021888.1 Tan05g1308 1308
4 18389366 18393847 + Vvi4g972 Vvi4g972 972
4 18395061 18396178 + Vvi4g973 Vvi4g973 973
4 18396751 18400758 - Vvi4g974 Vvi4g974 974
4 18401346 18413421 - Vvi4g975 Vvi4g975 975
4 18421692 18423027 + Vvi4g976 Vvi4g976 976
4 18428527 18430772 + Vvi4g977 Vvi4g977 977
4 18430781 18437824 - Vvi4g978 Vvi4g978 978
4 18439820 18444620 + Vvi4g979 Vvi4g979 979
4 18450984 18454288 + Vvi4g980 Vvi4g980 980
4 18456921 18459114 - Vvi4g981 Vvi4g981 981
       

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