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
Vvi18g50 . . . . . . . . Cmo05g00983 Cmo12g00628 . . . . . . . Bhi04g01208 . . . . . . Cla08g00928 Cam08g1373 Cec08g0956 Cco08g1075 Clacu08g1081 . Cre08g0865 . . . . . . . Cme03g01328 . Blo18g00734 . Bda01g01572 Bpe02g01766 . Bma01g00693 . . . . Cma12g00693 Cma05g00964 Car05g00846 . Cpe11g00775 . . . . . . . . . . . . . . . . . Chy03g00597 .
Vvi18g51 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g52 . . . . . Bpe04g00290 Bma04g00297 . . . . Cma09g00027 . . . Cpe06g00005 . . . . . . . . . . . . . . . . . Cone17ag1477 . Lsi04g02418 Csa04g02735 . . . . . . . . . . Sed01g2401 . Cmo09g00029 . . . . . . Bhi09g02833 Tan01g5152 Cmetu07g0925 . Hepe01g2365 Mch11g0033 . Cla11g01848 Cam11g1914 Cec11g1939 Cco11g1953 Clacu11g2079 Cmu11g1883 Cre11g2291 . . Chy07g00422 Cme07g00027
Vvi18g53 . . . . . . . . . . . . Car01g01605 . . . . . . . . . . . . . . . . . . Cone4ag2036 . . . Lsi04g01835 Csa04g02733 . . . . . . . . . . . Cmo01g02094 . . . . . . Cpe02g00017 Bhi09g02835 Tan01g5151 Cmetu07g1435 . Hepe01g2364 Mch11g0035 . Cla11g01846 Cam11g1913 Cec11g1938 Cco11g1951 Clacu11g2077 Cmu11g1882 Cre11g2290 . . . Cme07g00030
Vvi18g54 Blo01g01646 Blo12g00846 . . Bpe02g00296 . . Bma01g02419 Cmo05g00984 Cmo12g00627 Cma01g02035 . Car01g01604 . . . . Bhi04g01211 . . . . . . Cla08g00929 . . . . . . . . . . Lsi04g01834 Csa04g02732 . Cme03g01329 . . Bda11g00986 . . . . . . Cmo01g02092 . Cma12g00692 Cma05g00965 Car05g00847 . Cpe11g00776 Cpe02g00018 Bhi09g02836 . . . . Mch11g0036 . Cla11g01845 . . . . . . Lsi08g00771 . Chy07g00419 .
Vvi18g55 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g56 . . . . . . . . . . Cma01g02033 Cma09g00032 Car01g01601 . . Cpe06g00007 . . . . . . . . . . . . . . . . . . . . Csa04g02729 . . . Blo18g00735 . Bda01g01571 Bpe02g01765 . . . Sed12g2182 Cmo01g02088 Cmo09g00033 . . . Car09g00027 . Cpe02g00020 Bhi09g02837 Tan01g5147 Cmetu07g1999 . . Mch11g0039 . Cla11g01842 Cam11g1910 Cec11g1935 Cco11g1947 Clacu11g2073 Cmu11g1879 Cre11g2287 . . Chy07g00415 Cme07g00034
Vvi18g57 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g58 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g59 . . . . . . . . Cmo05g00985 Cmo12g00626 . . . Car12g00666 . . Cpe07g00599 Bhi04g01215 . . . . . . Cla08g00932 Cam08g1378 Cec08g0959 Cco08g1079 Clacu08g1085 . Cre08g0868 . . Cone17ag1472 Cone20ag0006 . . . Cme03g01330 . Blo18g00736 . Bda01g01570 Bpe02g01764 . Bma01g00694 . . . . Cma12g00691 Cma05g00966 Car05g00848 . Cpe11g00777 . . . . . . . . . . . . . . . Lsi08g00773 . Chy03g00605 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 51555705 51558780 - Bda003839.2 Bda01g01570 1570
1 51562673 51565237 + Bda032958 Bda01g01571 1571
1 51567016 51567560 - Bda003840.1 Bda01g01572 1572
11 9605666 9607246 - Bda005749.1 Bda11g00986 986
4 29314019 29317525 + XM_039028320.1 Bhi04g01208 1208
4 29349587 29351546 + XM_039030158.1 Bhi04g01211 1211
4 29399699 29403944 + XM_039028999.1 Bhi04g01215 1215
9 75088591 75091741 + XM_039040909.1 Bhi09g02833 2833
9 75104786 75106388 - XM_039041162.1 Bhi09g02835 2835
9 75111736 75114467 + XM_039041161.1 Bhi09g02836 2836
9 75176016 75179085 + XM_039043850.1 Bhi09g02837 2837
1 56269632 56271720 - BLOR01646 Blo01g01646 1646
12 26735380 26737303 + BLOR04865 Blo12g00846 846
18 19741803 19742347 + BLOR09222 Blo18g00734 734
18 19743204 19745771 - BLOR09223 Blo18g00735 735
18 19760371 19763511 + BLOR09224 Blo18g00736 736
1 6363570 6364147 + Bma000902.1 Bma01g00693 693
1 6372976 6376080 + Bma000904.1 Bma01g00694 694
1 81842902 81844989 - Bma003291.1 Bma01g02419 2419
4 2371145 2372862 + Bma018751.1 Bma04g00297 297
2 1947261 1949355 + Bpe008139.1 Bpe02g00296 296
2 19946209 19949314 - Bpe009595.1 Bpe02g01764 1764
2 19958770 19961340 + Bpe025178 Bpe02g01765 1765
2 19964425 19964969 - Bpe009597.2 Bpe02g01766 1766
4 1858469 1860130 - Bpe014994.1 Bpe04g00290 290
8 20051414 20051997 + CaPI482276_08g013730.1 Cam08g1373 1373
8 20077747 20081321 + CaPI482276_08g013780.1 Cam08g1378 1378
11 31578047 31580836 - CaPI482276_11g019100.1 Cam11g1910 1910
11 31593504 31594844 + CaPI482276_11g019130.1 Cam11g1913 1913
11 31597549 31600115 - CaPI482276_11g019140.1 Cam11g1914 1914
1 13195087 13197921 - Carg21354-RA Car01g01601 1601
1 13202922 13205121 - Carg21351-RA Car01g01604 1604
1 13208394 13210037 + Carg21350-RA Car01g01605 1605
5 8345097 8345709 + Carg21893-RA Car05g00846 846
5 8353198 8355920 + Carg21892-RA Car05g00847 847
5 8362494 8366761 + Carg21891-RA Car05g00848 848
9 138307 140916 + Carg08610-RA Car09g00027 27
12 4507918 4510616 - Carg17636-RA Car12g00666 666
8 22551544 22552127 + CcPI632755_08g010750.1 Cco08g1075 1075
8 22587076 22593228 + CcPI632755_08g010790.1 Cco08g1079 1079
11 32051865 32054477 - CcPI632755_11g019470.1 Cco11g1947 1947
11 32067263 32068616 + CcPI632755_11g019510.1 Cco11g1951 1951
11 32071316 32073954 - CcPI632755_11g019530.1 Cco11g1953 1953
8 21404132 21404715 + CePI673135_08g009560.1 Cec08g0956 956
8 21430104 21433677 + CePI673135_08g009590.1 Cec08g0959 959
11 33496790 33499579 - CePI673135_11g019350.1 Cec11g1935 1935
11 33512315 33513668 + CePI673135_11g019380.1 Cec11g1938 1938
11 33517301 33519884 - CePI673135_11g019390.1 Cec11g1939 1939
3 8543443 8544034 - Chy3G055770.1 Chy03g00597 597
3 8632948 8634963 + Chy3G055850.1 Chy03g00605 605
7 3261310 3263910 - Chy7G132450.1 Chy07g00415 415
7 3269000 3271328 - Chy7G132490.1 Chy07g00419 419
7 3280753 3282744 - Chy7G132520.1 Chy07g00422 422
8 20823433 20824016 + ClG42_08g0108100.10 Clacu08g1081 1081
8 20849632 20855865 + ClG42_08g0108500.10 Clacu08g1085 1085
11 31615775 31618564 - ClG42_11g0207300.10 Clacu11g2073 2073
11 31631168 31632508 + ClG42_11g0207700.10 Clacu11g2077 2077
11 31635177 31637767 - ClG42_11g0207900.10 Clacu11g2079 2079
8 21820413 21824047 + ClCG08G009210.1 Cla08g00928 928
8 21830396 21831732 + ClCG08G009220.1 Cla08g00929 929
8 21849254 21854286 + ClCG08G009230.1 Cla08g00932 932
11 32024422 32027211 - ClCG11G018950.1 Cla11g01842 1842
11 32032640 32041781 - ClCG11G018980.2 Cla11g01845 1845
11 32039763 32041304 + ClCG11G018990.1 Cla11g01846 1846
11 32043831 32046421 - ClCG11G019010.1 Cla11g01848 1848
1 12966779 12969625 - CmaCh01G020330.1 Cma01g02033 2033
1 12974230 12976967 - CmaCh01G020350.1 Cma01g02035 2035
5 7781704 7782514 + CmaCh05G009640.1 Cma05g00964 964
5 7790042 7792962 + CmaCh05G009650.1 Cma05g00965 965
5 7798380 7803312 + CmaCh05G009660.1 Cma05g00966 966
9 137993 145057 + CmaCh09G000270.1 Cma09g00027 27
9 148346 150955 + CmaCh09G000320.1 Cma09g00032 32
12 3735346 3738784 - CmaCh12G006910.1 Cma12g00691 691
12 3738810 3745095 - CmaCh12G006920.1 Cma12g00692 692
12 3749381 3752852 - CmaCh12G006930.1 Cma12g00693 693
3 22827386 22830890 + MELO3C026520.2.1 Cme03g01328 1328
3 22834792 22836837 + MELO3C026521.2.1 Cme03g01329 1329
3 22864568 22869179 + MELO3C026522.2.1 Cme03g01330 1330
7 205596 208518 + MELO3C017055.2.1 Cme07g00027 27
7 211090 212756 - MELO3C017053.2.1 Cme07g00030 30
7 225524 228428 + MELO3C017049.2.1 Cme07g00034 34
7 24602583 24605150 - PI0029114.1 Cmetu07g0925 925
7 24598477 24600117 + PI0019845.1 Cmetu07g1435 1435
7 24583657 24586229 - PI0019554.1 Cmetu07g1999 1999
1 14513362 14516181 - CmoCh01G020880.1 Cmo01g02088 2088
1 14521083 14523634 - CmoCh01G020920.1 Cmo01g02092 2092
1 14527783 14530137 + CmoCh01G020940.1 Cmo01g02094 2094
5 7919735 7920554 + CmoCh05G009830.1 Cmo05g00983 983
5 7928887 7931832 + CmoCh05G009840.1 Cmo05g00984 984
5 7938706 7943567 + CmoCh05G009850.1 Cmo05g00985 985
9 139751 142105 + CmoCh09G000290.1 Cmo09g00029 29
9 146708 149317 + CmoCh09G000330.1 Cmo09g00033 33
12 3915253 3918646 - CmoCh12G006260.1 Cmo12g00626 626
12 3922322 3924506 - CmoCh12G006270.1 Cmo12g00627 627
12 3928513 3929429 - CmoCh12G006280.1 Cmo12g00628 628
11 30865339 30868128 - CmPI595203_11g018790.1 Cmu11g1879 1879
11 30880737 30882077 + CmPI595203_11g018820.1 Cmu11g1882 1882
11 30884757 30887347 - CmPI595203_11g018830.1 Cmu11g1883 1883
4 14124480 14125997 + Conep04aG0210100.1 Cone4ag2036 2036
17 9950615 9955033 - Conep17aG0151300.1 Cone17ag1472 1472
17 9970144 9974040 - Conep17aG0151800.1 Cone17ag1477 1477
20 62669 66866 + Conep20aG0000600.1 Cone20ag0006 6
2 102283 104323 - Cp4.1LG02g08570.1 Cpe02g00017 17
2 107368 110047 + Cp4.1LG02g08680.1 Cpe02g00018 18
2 114404 117193 + Cp4.1LG02g08660.1 Cpe02g00020 20
6 15335 17284 + Cp4.1LG06g00030.1 Cpe06g00005 5
6 20833 23442 + Cp4.1LG06g00010.1 Cpe06g00007 7
7 4026030 4029773 - Cp4.1LG07g05680.1 Cpe07g00599 599
11 6270957 6277886 + Cp4.1LG11g07720.1 Cpe11g00775 775
11 6287183 6290375 + Cp4.1LG11g07710.1 Cpe11g00776 776
11 6297615 6302280 + Cp4.1LG11g07730.1 Cpe11g00777 777
8 21792123 21792706 + CrPI670011_08g008650.1 Cre08g0865 865
8 21817766 21821350 + CrPI670011_08g008680.1 Cre08g0868 868
11 34549742 34552531 - CrPI670011_11g022870.1 Cre11g2287 2287
11 34565168 34566520 + CrPI670011_11g022900.1 Cre11g2290 2290
11 34569255 34572008 - CrPI670011_11g022910.1 Cre11g2291 2291
4 26269706 26272306 - CsaV3_4G037550.1 Csa04g02729 2729
4 26277046 26280078 - CsaV3_4G037580.1 Csa04g02732 2732
4 26284886 26286213 + CsaV3_4G037590.1 Csa04g02733 2733
4 26288388 26291513 - CsaV3_4G037610.1 Csa04g02735 2735
1 88091331 88092975 + Hsped.01g23640.1 Hepe01g2364 2364
1 88093289 88098167 - Hsped.01g23650.1 Hepe01g2365 2365
4 25461530 25463471 - Lsi04G018340.1 Lsi04g01834 1834
4 25467485 25469446 + Lsi04G018350.1 Lsi04g01835 1835
4 31310179 31313197 - Lsi04G024180.1 Lsi04g02418 2418
8 16099082 16109859 + Lsi08G007710.1 Lsi08g00771 771
8 16122612 16128336 + Lsi08G007730.1 Lsi08g00773 773
11 232670 235837 + MC11g0029 Mch11g0033 33
11 237820 239868 - MC11g0030 Mch11g0035 35
11 243426 245805 + MC11g0031 Mch11g0036 36
11 251682 254309 + MC11g0034 Mch11g0039 39
1 18018905 18021634 + Sed0020070.1 Sed01g2401 2401
12 32349292 32351769 + Sed0011906.1 Sed12g2182 2182
1 116670480 116673068 - Tan0010443.1 Tan01g5147 5147
1 116687251 116688602 + Tan0013625.1 Tan01g5151 5151
1 116696426 116698626 - Tan0003864.1 Tan01g5152 5152
18 565467 568841 + Vvi18g50 Vvi18g50 50
18 572033 577186 + Vvi18g51 Vvi18g51 51
18 579116 582064 + Vvi18g52 Vvi18g52 52
18 582108 583745 - Vvi18g53 Vvi18g53 53
18 589626 592148 + Vvi18g54 Vvi18g54 54
18 593667 597777 - Vvi18g55 Vvi18g55 55
18 599935 601322 + Vvi18g56 Vvi18g56 56
18 601321 605100 - Vvi18g57 Vvi18g57 57
18 613489 614195 + Vvi18g58 Vvi18g58 58
18 614194 619058 + Vvi18g59 Vvi18g59 59
       

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