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
Vvi17g826 Blo04g00719 . . . . . . . Cmo13g00893 Cmo18g00152 . . . . . Cpe20g00262 . . . . . . . . . . . . . . . . . Cone13ag0168 Cone19ag0165 . Csa01g00883 Chy12g01240 Cme12g01663 . . . Bda14g00797 . Bpe15g00653 Bma03g00769 . Sed01g1623 . . Cma13g00862 Cma18g00191 Car13g00705 Car18g00183 Cpe09g01004 . Bhi08g01660 Tan05g1970 Cmetu12g0808 . . . . Cla03g00287 Cam03g0304 Cec03g0298 Cco03g0313 Clacu03g0305 Cmu03g0915 Cre03g0607 . . . .
Vvi17g827 . Blo16g00238 . . . . . . . . Cma10g00092 Cma11g00066 Car10g00081 Car11g00060 Sed14g1459 . . Bhi02g00600 Tan09g2306 Cmetu12g0117 . . . . Cla06g01701 Cam06g1889 Cec06g1938 Cco06g1942 Clacu06g1845 Cmu06g1786 Cre06g2601 . . Cone13ag0169 Cone19ag0166 . . . . . . . . . . . . . Cmo10g00095 . . . . . . Cpe18g00870 . . . . . . . . . . . . . . . . . .
Vvi17g828 . . . . . . . . . . Cma10g00091 . Car10g00080 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo10g00094 . . . . . . Cpe18g00871 . . . . . . . . . . . . . . . . . .
Vvi17g829 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g830 . . . . . . . . Cmo13g00891 . . . . . . Cpe20g00264 . . . . . . . . . . . . . . . . . Cone13ag0175 . Lsi02g00414 Csa01g00885 Chy12g01238 Cme12g01661 . . . . . . . . . . . Cma13g00860 . Car13g00702 . . . Bhi08g01662 Tan05g1968 Cmetu12g1001 Lac10g0493 Hepe07g2197 . . Cla03g00289 Cam03g0307 Cec03g0301 Cco03g0315 Clacu03g0308 Cmu03g0918 Cre03g0609 . . . .
Vvi17g831 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g832 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g833 Blo04g00718 . . . . . . . Cmo13g00888 Cmo18g00154 . . . . . Cpe20g00265 . . . . . . . . . . . . . . . . . Cone13ag0177 Cone19ag0170 . Csa01g00886 Chy12g01236 Cme12g01659 . . . . . . Bma03g00767 . . . . Cma13g00859 Cma18g00192 Car13g00700 Car18g00186 Cpe09g01002 . Bhi08g01664 . . Lac10g0495 . . . . . . . . . . . . . .
Vvi17g834 Blo04g00717 . . . . . Bma06g00224 . . . Cma10g00090 Cma11g00064 Car10g00079 Car11g00058 Sed08g0074 . Cpe04g01586 Bhi02g00598 Tan09g2310 Cmetu02g0003 . . . . Cla06g01704 Cam06g1892 Cec06g1941 Cco06g1945 Clacu06g1848 Cmu06g1789 Cre06g2604 Cone2ag0932 Cone16ag0071 . . . . . . . . . . . Bpe15g00654 Bma03g00766 . . Cmo10g00093 Cmo11g00067 . . . . . Cpe18g00872 . . . . . . . . . . . . . . Lsi06g01592 . . Cme02g02012
Vvi17g835 Blo04g00716 . . . . . . . Cmo13g00886 Cmo18g00155 . . . . . Cpe20g00266 . . . . . . . . . . . . . . . Cone2ag0933 Cone16ag0070 . . Lsi02g00417 Csa01g00887 Chy12g01235 Cme12g01658 . . . Bda14g00794 . Bpe15g00655 Bma03g00765 . Sed01g1621 . . Cma13g00858 Cma18g00193 Car13g00699 Car18g00187 Cpe09g01001 . Bhi08g01665 Tan05g1965 Cmetu12g0910 Lac10g0496 Hepe07g2195 . . Cla03g00290 Cam03g0308 Cec03g0303 Cco03g0316 Clacu03g0309 Cmu03g0919 Cre03g0610 . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
14 6140531 6144917 + Bda027563.1 Bda14g00794 794
14 6151476 6154373 - Bda027566.1 Bda14g00797 797
2 11349596 11351549 + XM_039023288.1 Bhi02g00598 598
2 11400634 11404456 - XM_039024365.1 Bhi02g00600 600
8 46789688 46794399 + XM_039038338.1 Bhi08g01660 1660
8 46820476 46826082 + XM_039038167.1 Bhi08g01662 1662
8 46833115 46835768 + XM_039038660.1 Bhi08g01664 1664
8 46836319 46840444 - XM_039038659.1 Bhi08g01665 1665
4 6599069 6601765 + BLOR13628 Blo04g00716 716
4 6604747 6605877 + BLOR13629 Blo04g00717 717
4 6606444 6607534 - BLOR13630 Blo04g00718 718
4 6612328 6615282 - BLOR13631 Blo04g00719 719
16 5450718 5452807 + BLOR07486 Blo16g00238 238
3 7005179 7008703 + Bma017067.1 Bma03g00765 765
3 7009485 7010948 + Bma017068.1 Bma03g00766 766
3 7011536 7013202 - Bma017069.1 Bma03g00767 767
3 7015098 7017977 - Bma017071.1 Bma03g00769 769
6 2652013 2653467 + Bma022841.1 Bma06g00224 224
15 17276916 17280572 + Bpe001586.1 Bpe15g00653 653
15 17288699 17290162 - Bpe001587.1 Bpe15g00654 654
15 17291114 17293813 - Bpe001588.1 Bpe15g00655 655
3 4291666 4295610 + CaPI482276_03g003040.1 Cam03g0304 304
3 4312720 4314545 + CaPI482276_03g003070.1 Cam03g0307 307
3 4315165 4319590 - CaPI482276_03g003080.1 Cam03g0308 308
6 29923654 29926491 + CaPI482276_06g018890.1 Cam06g1889 1889
6 29941218 29942636 - CaPI482276_06g018920.1 Cam06g1892 1892
10 359965 361404 + Carg10311-RA Car10g00079 79
10 362851 364950 + Carg10312-RA Car10g00080 80
10 365566 368611 - Carg10313-RA Car10g00081 81
11 326497 327921 + Carg20196-RA Car11g00058 58
11 334803 335611 - Carg20198-RA Car11g00060 60
13 8297851 8305806 + Carg07649-RA Car13g00699 699
13 8300150 8306484 - Carg07650-RA Car13g00700 700
13 8309604 8314196 - Carg07652-RA Car13g00702 702
13 8316695 8321185 - Carg07655-RA Car13g00705 705
18 1009558 1013609 + Carg06750-RA Car18g00183 183
18 1022199 1024085 + Carg06753-RA Car18g00186 186
18 1022231 1028778 - Carg06754-RA Car18g00187 187
3 3499922 3503861 + CcPI632755_03g003130.1 Cco03g0313 313
3 3510489 3522782 + CcPI632755_03g003150.1 Cco03g0315 315
3 3523355 3527774 - CcPI632755_03g003160.1 Cco03g0316 316
6 29656891 29659728 + CcPI632755_06g019420.1 Cco06g1942 1942
6 29673745 29675961 - CcPI632755_06g019450.1 Cco06g1945 1945
3 3426146 3430105 + CePI673135_03g002980.1 Cec03g0298 298
3 3447418 3449041 + CePI673135_03g003010.1 Cec03g0301 301
3 3450613 3454238 - CePI673135_03g003030.1 Cec03g0303 303
6 32730833 32733063 + CePI673135_06g019380.1 Cec06g1938 1938
6 32748230 32749648 - CePI673135_06g019410.1 Cec06g1941 1941
12 17046544 17049516 + Chy12G218350.1 Chy12g01235 1235
12 17050984 17052820 - Chy12G218360.1 Chy12g01236 1236
12 17058690 17062782 - Chy12G218380.1 Chy12g01238 1238
12 17065474 17069299 - Chy12G218400.1 Chy12g01240 1240
3 3587633 3591576 + ClG42_03g0030500.10 Clacu03g0305 305
3 3603090 3610485 + ClG42_03g0030800.10 Clacu03g0308 308
3 3611049 3615492 - ClG42_03g0030900.10 Clacu03g0309 309
6 28974531 28977368 + ClG42_06g0184500.10 Clacu06g1845 1845
6 28992074 28993492 - ClG42_06g0184800.10 Clacu06g1848 1848
3 3528175 3534027 + ClCG03G002990.1 Cla03g00287 287
3 3540049 3552343 + ClCG03G003010.2 Cla03g00289 289
3 3553417 3557742 - ClCG03G003030.1 Cla03g00290 290
6 30598998 30602464 + ClCG06G017420.2 Cla06g01701 1701
6 30617493 30618911 - ClCG06G017450.1 Cla06g01704 1704
10 367857 370776 + CmaCh10G000900.1 Cma10g00090 90
10 370862 373115 + CmaCh10G000910.1 Cma10g00091 91
10 373193 376936 - CmaCh10G000920.1 Cma10g00092 92
11 325512 327027 + CmaCh11G000640.1 Cma11g00064 64
11 334910 336386 - CmaCh11G000660.1 Cma11g00066 66
13 7061331 7065489 + CmaCh13G008580.1 Cma13g00858 858
13 7065796 7068365 - CmaCh13G008590.1 Cma13g00859 859
13 7071001 7077197 - CmaCh13G008600.1 Cma13g00860 860
13 7077823 7083014 - CmaCh13G008620.1 Cma13g00862 862
18 990409 994566 + CmaCh18G001910.1 Cma18g00191 191
18 1003202 1005894 + CmaCh18G001920.1 Cma18g00192 192
18 1004778 1010220 - CmaCh18G001930.1 Cma18g00193 193
2 26325934 26327814 + MELO3C026259.2.1 Cme02g02012 2012
12 23634019 23638894 + MELO3C002302.2.1 Cme12g01658 1658
12 23637435 23640091 - MELO3C002301.2.1 Cme12g01659 1659
12 23645819 23650373 - MELO3C002299.2.1 Cme12g01661 1661
12 23652724 23657322 - MELO3C002297.2.1 Cme12g01663 1663
2 24624561 24625994 + PI0009499.1 Cmetu02g0003 3
12 5158957 5161883 - PI0028016.1 Cmetu12g0117 117
12 2643499 2648027 + PI0003885.1 Cmetu12g0808 808
12 2662557 2668060 - PI0006384.7 Cmetu12g0910 910
12 2650846 2654937 + PI0025338.1 Cmetu12g1001 1001
10 404853 406295 + CmoCh10G000930.1 Cmo10g00093 93
10 407738 409837 + CmoCh10G000940.1 Cmo10g00094 94
10 410087 412941 - CmoCh10G000950.1 Cmo10g00095 95
11 316878 318302 + CmoCh11G000670.1 Cmo11g00067 67
13 7991434 7994910 + CmoCh13G008860.1 Cmo13g00886 886
13 7996850 7997556 - CmoCh13G008880.1 Cmo13g00888 888
13 8001849 8007668 - CmoCh13G008910.1 Cmo13g00891 891
13 8009145 8013199 - CmoCh13G008930.1 Cmo13g00893 893
18 1062554 1066477 + CmoCh18G001520.1 Cmo18g00152 152
18 1075375 1077643 + CmoCh18G001540.1 Cmo18g00154 154
18 1078095 1082019 - CmoCh18G001550.1 Cmo18g00155 155
3 3829731 3833676 + CmPI595203_03g009150.1 Cmu03g0915 915
3 3850715 3852550 + CmPI595203_03g009180.1 Cmu03g0918 918
3 3853925 3857559 - CmPI595203_03g009190.1 Cmu03g0919 919
6 28879435 28881964 + CmPI595203_06g017860.1 Cmu06g1786 1786
6 28896276 28897694 - CmPI595203_06g017890.1 Cmu06g1789 1789
2 35075010 35076864 - Conep02aG0196600.1 Cone2ag0932 932
2 35077677 35081306 - Conep02aG0196700.1 Cone2ag0933 933
13 1048392 1052644 + Conep13aG0017300.1 Cone13ag0168 168
13 1053186 1056317 + Conep13aG0017400.1 Cone13ag0169 169
13 1067005 1071315 + Conep13aG0018000.1 Cone13ag0175 175
13 1079716 1080953 + Conep13aG0018200.1 Cone13ag0177 177
16 356792 360640 + Conep16aG0007100.1 Cone16ag0070 70
16 360952 362951 + Conep16aG0007200.1 Cone16ag0071 71
19 949314 953201 + Conep19aG0017100.1 Cone19ag0165 165
19 953893 959116 + Conep19aG0017200.1 Cone19ag0166 166
19 971452 972519 + Conep19aG0017600.1 Cone19ag0170 170
4 12368260 12370346 - Cp4.1LG04g15820.1 Cpe04g01586 1586
9 8877785 8881461 + Cp4.1LG09g10060.1 Cpe09g01001 1001
9 8880959 8884817 - Cp4.1LG09g10090.1 Cpe09g01002 1002
9 8892408 8895766 - Cp4.1LG09g10110.1 Cpe09g01004 1004
18 7964351 7970242 + Cp4.1LG18g08640.1 Cpe18g00870 870
18 7964884 7969844 - Cp4.1LG18g08780.1 Cpe18g00871 871
18 7971397 7972842 - Cp4.1LG18g08690.1 Cpe18g00872 872
20 1473569 1479869 + Cp4.1LG20g02680.1 Cpe20g00262 262
20 1480360 1484803 + Cp4.1LG20g02710.1 Cpe20g00264 264
20 1487676 1490167 + Cp4.1LG20g02650.1 Cpe20g00265 265
20 1491133 1494741 - Cp4.1LG20g02810.1 Cpe20g00266 266
3 4998563 5002478 + CrPI670011_03g006070.1 Cre03g0607 607
3 5009185 5021317 + CrPI670011_03g006090.1 Cre03g0609 609
3 5021396 5026515 - CrPI670011_03g006100.1 Cre03g0610 610
6 33704064 33706600 + CrPI670011_06g026010.1 Cre06g2601 2601
6 33721523 33722941 - CrPI670011_06g026040.1 Cre06g2604 2604
1 5507175 5511714 + CsaV3_1G008830.1 Csa01g00883 883
1 5513946 5519350 + CsaV3_1G008850.1 Csa01g00885 885
1 5523550 5526665 + CsaV3_1G008860.1 Csa01g00886 886
1 5525442 5530552 - CsaV3_1G008870.1 Csa01g00887 887
7 66352175 66356503 + Hsped.07g21950.1 Hepe07g2195 2195
7 66367093 66371582 - Hsped.07g21970.1 Hepe07g2197 2197
10 3786250 3790732 + Lag0024538.1 Lac10g0493 493
10 3795729 3797654 + Lag0024540.1 Lac10g0495 495
10 3798994 3802406 - Lag0024541.1 Lac10g0496 496
2 3460434 3465254 + Lsi02G004140.1 Lsi02g00414 414
2 3474516 3479096 - Lsi02G004170.1 Lsi02g00417 417
6 26309646 26311079 + Lsi06G015920.1 Lsi06g01592 1592
1 11779009 11783214 + Sed0026130.1 Sed01g1621 1621
1 11796140 11799780 - Sed0026079.1 Sed01g1623 1623
8 387998 389924 + Sed0002628.1 Sed08g0074 74
14 23070659 23073448 - Sed0022771.1 Sed14g1459 1459
5 69268198 69272108 + Tan0013002.1 Tan05g1965 1965
5 69282571 69287133 - Tan0005887.1 Tan05g1968 1968
5 69291880 69296857 - Tan0013233.1 Tan05g1970 1970
9 72970771 72974439 + Tan0010967.1 Tan09g2306 2306
9 72988908 72990862 - Tan0018864.1 Tan09g2310 2310
17 10869021 10874179 + Vvi17g826 Vvi17g826 826
17 10874998 10877438 + Vvi17g827 Vvi17g827 827
17 10878777 10880874 - Vvi17g828 Vvi17g828 828
17 10881835 10883746 + Vvi17g829 Vvi17g829 829
17 10885566 10892759 + Vvi17g830 Vvi17g830 830
17 10893490 10895941 - Vvi17g831 Vvi17g831 831
17 10911780 10912037 + Vvi17g832 Vvi17g832 832
17 10948914 10954865 + Vvi17g833 Vvi17g833 833
17 10957676 10965768 - Vvi17g834 Vvi17g834 834
17 10966271 10980533 - Vvi17g835 Vvi17g835 835
       

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