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
Vvi4g1002 . Blo16g00055 . Bda10g00140 . . . . . . Cma03g00736 . Car03g00671 Car07g00418 Sed14g1136 Cpe19g00818 Cpe10g00624 Bhi03g01326 Tan03g2002 Cmetu08g0549 . Hepe04g1528 . . Cla01g01922 Cam01g2008 Cec04g1667 Cco04g1728 Clacu01g2029 Cmu01g1904 Cre04g1579 Cone8ag0820 . Cone6ag1640 Cone9ag1560 Lsi01g00665 . . Cme08g00862 . Blo06g00138 Bda11g01856 . Bpe10g00122 . . . . . Cmo07g00475 . . . . . . . . . . . . . . . . . . . . . Csa06g03258 Chy02g00631 .
Vvi4g1003 . . . Bda10g00141 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0771 . . . . Chy07g01293 . . . . . Bpe10g00123 . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00550 . .
Vvi4g1004 . . Bda04g00040 . . . Bma09g00085 . . . . Cma07g00474 Car03g00670 Car07g00417 Sed14g1137 Cpe19g00819 . Bhi03g01327 Tan03g2003 Cmetu03g1081 . Hepe04g1529 . . Cla01g01923 Cam01g2009 Cec04g1668 Cco04g1729 Clacu01g2030 Cmu01g1905 Cre04g1580 . . Cone6ag1642 Cone9ag1561 Lsi01g00664 . . Cme08g00863 Blo05g00803 Blo06g00139 . . Bpe10g00125 Bpe06g00041 . . . Cmo03g00765 Cmo07g00473 . . . . . . . . . . . . . . . . . . . . . Csa06g03259 Chy02g00630 .
Vvi4g1005 . . . Bda10g00142 . . . . . . Cma03g00734 . Car03g00669 . . . . . . . . . . . . . . . . . . . . . . Lsi01g00663 . . . . . . . . . . . . Cmo03g00764 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1006 Blo04g00909 . . . Bpe15g00421 Bpe13g00435 . . . . Cma03g00733 . Car03g00668 . Sed14g1139 . Cpe10g00626 Bhi03g01328 Tan03g2005 Cmetu08g1811 . Hepe04g1531 . . Cla01g01926 Cam01g2012 Cec04g1670 Cco04g1733 Clacu01g2033 Cmu01g1908 Cre04g1583 . . . Cone9ag1562 Lsi01g00662 . . Cme08g00864 . . Bda11g01855 . . . . Bma06g00114 . Cmo03g00762 . . . . . . . . . . . . . . . . . . . . . . Csa06g03260 Chy02g00629 .
Vvi4g1007 . Blo16g00056 . . Bpe15g00420 Bpe13g00434 . . . . . . . . Sed10g0929 . . Bhi03g01329 Tan03g2006 Cmetu08g0691 . Hepe04g1532 . . . . . . . . . . Cone12ag0772 Cone6ag1643 Cone9ag1563 . . . . . . Bda11g01854 . . . Bma03g00983 Bma06g00113 Sed01g0292 . . . Cma20g00838 . . . . Bhi10g01986 Tan05g1285 Cmetu11g1831 . Hepe08g1002 . . . . . . . . . Lsi07g00247 . . .
Vvi4g1008 . . . . Bpe15g00419 . . . . Cmo16g00683 Cma03g00732 . . . . . . . . . . . . . . . . . . . . Cone8ag0823 . . . . . Chy07g01249 . . . . . . . . . . . . Cma16g00627 . . . . Cpe14g00535 . . . . . . . Cla07g00819 Cam07g0883 Cec07g0936 Cco07g0924 Clacu07g0858 Cmu07g0861 Cre07g1220 . . . .
Vvi4g1009 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1010 . . . . . . Bma09g00086 . . . . . . . . Cpe19g00820 . . . . . . . . Cla01g01928 . . Cco04g1735 . . Cre04g1586 . . . . . . . . Blo05g00804 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g03261 . .
Vvi4g1011 . . . . . . . . . . . . . . . . Cpe10g00628 . . . . . . . . . . . . . . Cone8ag0824 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 715762 717783 - Bda018783.1 Bda04g00040 40
10 4026424 4028109 + Bda006608.1 Bda10g00140 140
10 4064889 4068187 + Bda006609.2 Bda10g00141 141
10 4151015 4152532 + Bda006610.1 Bda10g00142 142
11 53694549 53695286 - Bda008792.1 Bda11g01854 1854
11 53697197 53697910 + Bda008793.1 Bda11g01855 1855
11 53698064 53701279 - Bda008794.1 Bda11g01856 1856
3 27168835 27173527 + XM_039026664.1 Bhi03g01326 1326
3 27176964 27179290 + XM_039027786.1 Bhi03g01327 1327
3 27235712 27238914 - XM_039025168.1 Bhi03g01328 1328
3 27297375 27298070 + XM_039026359.1 Bhi03g01329 1329
10 49567278 49568468 - XM_039044555.1 Bhi10g01986 1986
4 10656499 10660102 + BLOR13821 Blo04g00909 909
5 29386819 29406253 + BLOR15765 Blo05g00803 803
5 29434105 29435277 - BLOR15766 Blo05g00804 804
6 5512551 5519889 + BLOR16721 Blo06g00138 138
6 5539067 5540946 + BLOR16722 Blo06g00139 139
16 1921888 1923324 + BLOR07303 Blo16g00055 55
16 1927108 1928773 + BLOR07304 Blo16g00056 56
3 10490857 10491621 - Bma017326.1 Bma03g00983 983
6 1588101 1588757 - Bma022732.1 Bma06g00113 113
6 1594369 1595604 + Bma022733.1 Bma06g00114 114
9 2056666 2058922 + Bma028774.1 Bma09g00085 85
9 2143985 2145768 - Bma028776.3 Bma09g00086 86
6 487503 489746 - Bpe019485.1 Bpe06g00041 41
10 2280843 2282952 + Bpe002425.1 Bpe10g00122 122
10 2309032 2312296 + Bpe002426.1 Bpe10g00123 123
10 2326564 2328425 + Bpe002428.1 Bpe10g00125 125
13 11925068 11925805 - Bpe006558.1 Bpe13g00434 434
13 11926874 11928056 + Bpe006559.1 Bpe13g00435 435
15 15751514 15752911 + Bpe001355.1 Bpe15g00419 419
15 15754749 15755513 - Bpe001356.1 Bpe15g00420 420
15 15757296 15758569 + Bpe001357.2 Bpe15g00421 421
1 33312791 33317907 + CaPI482276_01g020080.1 Cam01g2008 2008
1 33320828 33322645 + CaPI482276_01g020090.1 Cam01g2009 2009
1 33326606 33329123 - CaPI482276_01g020120.1 Cam01g2012 2012
7 21896185 21898329 + CaPI482276_07g008830.1 Cam07g0883 883
3 5974619 5977139 + Carg00628-RA Car03g00668 668
3 5977082 5979401 - Carg00629-RA Car03g00669 669
3 5979668 5981909 - Carg00630-RA Car03g00670 670
3 5982722 5985658 - Carg00631-RA Car03g00671 671
7 2126995 2129481 - Carg16058-RA Car07g00417 417
7 2130302 2133694 - Carg16057-RA Car07g00418 418
4 32366775 32371786 + CcPI632755_04g017280.1 Cco04g1728 1728
4 32374780 32376594 + CcPI632755_04g017290.1 Cco04g1729 1729
4 32380407 32382942 - CcPI632755_04g017330.1 Cco04g1733 1733
4 32391140 32391751 - CcPI632755_04g017350.1 Cco04g1735 1735
7 21330320 21332553 + CcPI632755_07g009240.1 Cco07g0924 924
4 35863373 35868590 + CePI673135_04g016670.1 Cec04g1667 1667
4 35871479 35873293 + CePI673135_04g016680.1 Cec04g1668 1668
4 35877177 35879808 - CePI673135_04g016700.1 Cec04g1670 1670
7 23160324 23162506 + CePI673135_07g009360.1 Cec07g0936 936
2 3856862 3859467 + Chy2G028960.1 Chy02g00629 629
2 3860297 3862049 - Chy2G028970.1 Chy02g00630 630
2 3864192 3867557 - Chy2G028980.1 Chy02g00631 631
7 17221459 17224240 + Chy7G140790.1 Chy07g01249 1249
7 17610862 17618049 + Chy7G141230.1 Chy07g01293 1293
1 32163379 32168486 + ClG42_01g0202900.10 Clacu01g2029 2029
1 32168854 32173297 + ClG42_01g0203000.10 Clacu01g2030 2030
1 32177146 32179777 - ClG42_01g0203300.10 Clacu01g2033 2033
7 21618788 21620900 + ClG42_07g0085800.10 Clacu07g0858 858
1 33931179 33936821 + ClCG01G019720.1 Cla01g01922 1922
1 33936615 33941732 + ClCG01G019730.2 Cla01g01923 1923
1 33945013 33947981 - ClCG01G019760.1 Cla01g01926 1926
1 33953245 33965393 - ClCG01G019780.1 Cla01g01928 1928
7 22781897 22784180 + ClCG07G008610.1 Cla07g00819 819
3 5851716 5853330 + CmaCh03G007320.1 Cma03g00732 732
3 5856219 5858878 + CmaCh03G007330.1 Cma03g00733 733
3 5858869 5861004 - CmaCh03G007340.1 Cma03g00734 734
3 5861482 5876017 - CmaCh03G007360.1 Cma03g00736 736
7 2070701 2075085 - CmaCh07G004740.1 Cma07g00474 474
16 3233193 3235104 + CmaCh16G006270.1 Cma16g00627 627
20 4015522 4016223 - CmaCh20G008380.1 Cma20g00838 838
8 5676981 5681749 + MELO3C007841.2.1 Cme08g00862 862
8 5683392 5685978 + MELO3C007842.2.1 Cme08g00863 863
8 5686375 5689466 - MELO3C007843.2.1 Cme08g00864 864
3 6919824 6922801 + PI0028986.1 Cmetu03g1081 1081
8 21737600 21742776 + PI0015638.1 Cmetu08g0549 549
8 21752604 21753415 + PI0006622.1 Cmetu08g0691 691
8 21746707 21749932 - PI0010249.1 Cmetu08g1811 1811
11 27586521 27587647 + PI0028238.1 Cmetu11g1831 1831
3 6361868 6364535 + CmoCh03G007620.1 Cmo03g00762 762
3 6364525 6367262 - CmoCh03G007640.1 Cmo03g00764 764
3 6367471 6370458 - CmoCh03G007650.1 Cmo03g00765 765
7 2161870 2166145 - CmoCh07G004730.1 Cmo07g00473 473
7 2166193 2169231 - CmoCh07G004750.1 Cmo07g00475 475
16 3376495 3378469 + CmoCh16G006830.1 Cmo16g00683 683
1 32511925 32517034 + CmPI595203_01g019040.1 Cmu01g1904 1904
1 32519972 32521789 + CmPI595203_01g019050.1 Cmu01g1905 1905
1 32525664 32528296 - CmPI595203_01g019080.1 Cmu01g1908 1908
7 21840038 21842151 + CmPI595203_07g008610.1 Cmu07g0861 861
6 12574124 12577438 + Conep06aG0170400.1 Cone6ag1640 1640
6 12581179 12584189 + Conep06aG0170600.1 Cone6ag1642 1642
6 12585338 12586323 + Conep06aG0170700.1 Cone6ag1643 1643
8 8196845 8201696 + Conep08aG0084600.1 Cone8ag0820 820
8 8211752 8213700 + Conep08aG0084900.1 Cone8ag0823 823
8 8223024 8226543 - Conep08aG0085000.1 Cone8ag0824 824
9 11296246 11299464 + Conep09aG0160800.1 Cone9ag1560 1560
9 11300249 11301253 + Conep09aG0160900.1 Cone9ag1561 1561
9 11301380 11303087 - Conep09aG0161000.1 Cone9ag1562 1562
9 11304026 11304832 + Conep09aG0161100.1 Cone9ag1563 1563
12 7079747 7083064 + Conep12aG0079400.1 Cone12ag0771 771
12 7090411 7091001 + Conep12aG0079500.1 Cone12ag0772 772
10 3615528 3619757 + Cp4.1LG10g00620.1 Cpe10g00624 624
10 3623210 3627835 - Cp4.1LG10g00530.1 Cpe10g00626 626
10 3629748 3631957 - Cp4.1LG10g00580.1 Cpe10g00628 628
14 3370330 3372673 + Cp4.1LG14g01790.1 Cpe14g00535 535
19 6119425 6122924 + Cp4.1LG19g09240.1 Cpe19g00818 818
19 6123938 6126620 + Cp4.1LG19g09330.1 Cpe19g00819 819
19 6130001 6131570 + Cp4.1LG19g09310.1 Cpe19g00820 820
4 34355027 34360145 + CrPI670011_04g015790.1 Cre04g1579 1579
4 34363117 34364933 + CrPI670011_04g015800.1 Cre04g1580 1580
4 34368939 34371462 - CrPI670011_04g015830.1 Cre04g1583 1583
4 34378716 34382560 - CrPI670011_04g015860.1 Cre04g1586 1586
7 25584952 25587270 + CrPI670011_07g012200.1 Cre07g1220 1220
4 3666523 3670142 + CsaV3_4G005500.1 Csa04g00550 550
6 27434481 27439712 + CsaV3_6G046440.1 Csa06g03258 3258
6 27439853 27443429 + CsaV3_6G046450.1 Csa06g03259 3259
6 27440564 27446916 - CsaV3_6G046460.1 Csa06g03260 3260
6 27448277 27453505 - CsaV3_6G046470.1 Csa06g03261 3261
4 70819529 70824146 + Hsped.04g15280.1 Hepe04g1528 1528
4 70826144 70827998 + Hsped.04g15290.1 Hepe04g1529 1529
4 70832777 70835466 - Hsped.04g15310.1 Hepe04g1531 1531
4 70842187 70842873 + Hsped.04g15320.1 Hepe04g1532 1532
8 9548965 9549645 - Hsped.08g10020.1 Hepe08g1002 1002
1 5324101 5327157 + Lsi01G006620.1 Lsi01g00662 662
1 5328955 5331090 - Lsi01G006630.1 Lsi01g00663 663
1 5331986 5334387 - Lsi01G006640.1 Lsi01g00664 664
1 5334436 5341220 - Lsi01G006650.1 Lsi01g00665 665
7 2707923 2708645 + Lsi07G002470.1 Lsi07g00247 247
1 2249407 2250833 - Sed0016213.1 Sed01g0292 292
10 7292550 7293511 + Sed0010817.1 Sed10g0929 929
14 20779982 20784254 + Sed0024753.1 Sed14g1136 1136
14 20789427 20791690 + Sed0015781.1 Sed14g1137 1137
14 20798883 20801950 - Sed0014839.1 Sed14g1139 1139
3 74993553 74997822 + Tan0017002.2 Tan03g2002 2002
3 75000250 75002078 + Tan0004237.1 Tan03g2003 2003
3 75008743 75011778 - Tan0020480.1 Tan03g2005 2005
3 75020285 75021050 + Tan0015120.1 Tan03g2006 2006
5 14467179 14468495 - Tan0000285.1 Tan05g1285 1285
4 18598156 18604366 + Vvi4g1002 Vvi4g1002 1002
4 18606816 18616260 + Vvi4g1003 Vvi4g1003 1003
4 18617294 18620099 + Vvi4g1004 Vvi4g1004 1004
4 18620124 18623814 + Vvi4g1005 Vvi4g1005 1005
4 18625063 18629091 - Vvi4g1006 Vvi4g1006 1006
4 18633897 18634656 + Vvi4g1007 Vvi4g1007 1007
4 18646488 18655154 - Vvi4g1008 Vvi4g1008 1008
4 18658130 18658817 - Vvi4g1009 Vvi4g1009 1009
4 18658839 18666934 - Vvi4g1010 Vvi4g1010 1010
4 18678516 18680377 - Vvi4g1011 Vvi4g1011 1011
       

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