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
Vvi4g1082 . Blo16g00073 . . . Bpe13g00424 . . Cmo04g00795 . . . . . . . . . . . . . . . . . . . . . . . . Cone6ag1667 Cone9ag1589 . . Chy07g01229 . . . Bda11g01844 . . . . Bma06g00104 . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00580 . .
Vvi4g1083 Blo04g00894 Blo16g00074 . Bda10g00172 . Bpe13g00423 . Bma15g00960 Cmo04g00794 . Cma03g00703 Cma07g00442 Car03g00645 Car07g00389 . Cpe19g00845 Cpe10g00649 Bhi03g00888 . . . . . . Cla01g01962 Cam01g2052 Cec04g1710 Cco04g1775 Clacu01g2073 Cmu01g1950 Cre04g1625 . . Cone6ag1668 Cone9ag1590 Lsi01g00620 . . Cme08g00909 . Blo06g00321 Bda11g01843 . . . . Bma06g00103 . Cmo03g00728 Cmo07g00440 . . . . . . . . . . . . . . . . . . . . . Csa06g03304 Chy02g00591 .
Vvi4g1084 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1085 . . . . . . . . Cmo04g00793 . . . . . . . . . . . . . . . . . . . . . . . Cone12ag0729 Cone6ag1670 Cone9ag1592 . . Chy07g01228 . Blo05g00823 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00582 . .
Vvi4g1086 Blo04g00893 . Bda04g00029 . . . . Bma15g00956 . . . Cma07g00441 . . . Cpe19g00846 Cpe10g00650 . . . . . . . . . . . . . . . . Cone6ag1671 . . . . . . . . . . . Bma03g00969 . . . Cmo07g00439 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1087 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1088 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1089 Blo04g00892 . . Bda10g00179 Bpe15g00466 . . Bma15g00953 . . Cma03g00700 Cma07g00439 Car03g00643 Car07g00387 . Cpe19g00847 Cpe10g00651 Bhi03g00885 . . . . . . Cla01g01964 . . . . . . . . Cone6ag1672 . Lsi01g00618 . . Cme08g00911 . Blo06g00317 . . Bpe10g00147 . Bma03g00968 . . Cmo03g00726 Cmo07g00437 . . . . . . . . . . . . . . . . . . . . . Csa06g03309 . .
Vvi4g1090 . . . . . . . . . Cmo16g00754 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma16g00695 . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1091 Blo04g00891 . . . . . . . . . Cma03g00698 . Car03g00642 . Sed08g1603 . Cpe10g00652 Bhi03g00883 Tan03g2056 Cmetu04g0515 . Hepe04g1578 . . Cla01g01965 Cam01g2057 Cec04g1715 Cco04g1780 Clacu01g2078 Cmu01g1955 Cre04g1629 Cone8ag0839 Cone12ag0726 . . Lsi01g00617 . . Cme08g00912 . . . . . . Bma03g00967 . . Cmo03g00725 . . . . . . . . . . . . . . . . . . . . . . Csa06g03310 Chy02g00587 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
4 447626 448867 - Bda018798.2 Bda04g00029 29
10 5344462 5346094 + Bda006659.1 Bda10g00172 172
10 5711796 5714979 - Bda006669.1 Bda10g00179 179
11 53635914 53637114 + Bda008780.1 Bda11g01843 1843
11 53638315 53641977 + Bda008781.1 Bda11g01844 1844
3 16489188 16490145 + XM_039027893.1 Bhi03g00883 883
3 16540561 16544206 - XM_039025469.1 Bhi03g00885 885
3 16612982 16614689 + XM_039026932.1 Bhi03g00888 888
4 10208407 10209109 + BLOR13803 Blo04g00891 891
4 10232082 10235768 - BLOR13804 Blo04g00892 892
4 10285800 10289132 - BLOR13805 Blo04g00893 893
4 10317171 10318333 + BLOR13806 Blo04g00894 894
5 29975002 29985729 + BLOR15785 Blo05g00823 823
6 18196826 18205783 + BLOR16900 Blo06g00317 317
6 18407264 18411608 + BLOR16904 Blo06g00321 321
16 2077899 2081500 - BLOR07321 Blo16g00073 73
16 2107024 2108998 - BLOR07322 Blo16g00074 74
3 10259784 10260458 + Bma017306.1 Bma03g00967 967
3 10273893 10275271 - Bma017307.1 Bma03g00968 968
3 10281854 10284904 - Bma017308.1 Bma03g00969 969
6 1487047 1488242 + Bma022722.1 Bma06g00103 103
6 1497659 1501272 + Bma022724.1 Bma06g00104 104
15 36006463 36018410 - Bma014213.1 Bma15g00953 953
15 36137684 36139966 - Bma014216.1 Bma15g00956 956
15 36260262 36262332 + Bma014220.1 Bma15g00960 960
10 3315057 3319329 + Bpe002455.1 Bpe10g00147 147
13 11855165 11856343 + Bpe006548.1 Bpe13g00423 423
13 11864990 11868692 + Bpe006549.1 Bpe13g00424 424
15 16043450 16046281 + Bpe001400.2 Bpe15g00466 466
1 33624074 33625068 - CaPI482276_01g020520.1 Cam01g2052 2052
1 33667528 33668228 - CaPI482276_01g020570.1 Cam01g2057 2057
3 5812283 5813762 + Carg00602-RA Car03g00642 642
3 5816124 5817732 - Carg00603-RA Car03g00643 643
3 5830640 5831512 + Carg00605-RA Car03g00645 645
7 1952590 1954406 - Carg07967-RA Car07g00387 387
7 1970360 1971260 + Carg07969-RA Car07g00389 389
4 32691770 32692814 - CcPI632755_04g017750.1 Cco04g1775 1775
4 32735905 32736614 - CcPI632755_04g017800.1 Cco04g1780 1780
4 36182194 36183203 - CePI673135_04g017100.1 Cec04g1710 1710
4 36224741 36225450 - CePI673135_04g017150.1 Cec04g1715 1715
2 3560160 3560866 + Chy2G028540.1 Chy02g00587 587
2 3597169 3598189 + Chy2G028580.1 Chy02g00591 591
7 17059251 17073579 - Chy7G140580.1 Chy07g01228 1228
7 17084276 17095300 + Chy7G140590.1 Chy07g01229 1229
1 32478251 32479266 - ClG42_01g0207300.10 Clacu01g2073 2073
1 32523988 32524688 - ClG42_01g0207800.10 Clacu01g2078 2078
1 34257220 34258628 - ClCG01G020130.1 Cla01g01962 1962
1 34295529 34297665 + ClCG01G020150.2 Cla01g01964 1964
1 34304511 34305910 - ClCG01G020160.1 Cla01g01965 1965
3 5722107 5723675 + CmaCh03G006980.1 Cma03g00698 698
3 5726463 5727004 - CmaCh03G007000.1 Cma03g00700 700
3 5739510 5740812 + CmaCh03G007030.1 Cma03g00703 703
7 1917403 1922542 - CmaCh07G004390.1 Cma07g00439 439
7 1934435 1937827 - CmaCh07G004410.1 Cma07g00441 441
7 1941184 1942658 + CmaCh07G004420.1 Cma07g00442 442
16 3626141 3634785 + CmaCh16G006950.1 Cma16g00695 695
8 5976207 5977952 - MELO3C007886.2.1 Cme08g00909 909
8 6007319 6009679 + MELO3C007888.2.1 Cme08g00911 911
8 6015477 6017122 - MELO3C007889.2.1 Cme08g00912 912
4 3828771 3829962 + PI0027779.1 Cmetu04g0515 515
3 6219312 6220628 + CmoCh03G007250.1 Cmo03g00725 725
3 6220271 6225621 - CmoCh03G007260.1 Cmo03g00726 726
3 6238667 6239909 + CmoCh03G007280.1 Cmo03g00728 728
4 3962338 3974572 - CmoCh04G007930.1 Cmo04g00793 793
4 3978002 3981615 + CmoCh04G007940.1 Cmo04g00794 794
4 3982886 3988410 + CmoCh04G007950.1 Cmo04g00795 795
7 2008627 2010408 - CmoCh07G004370.1 Cmo07g00437 437
7 2019370 2022762 - CmoCh07G004390.1 Cmo07g00439 439
7 2026405 2027869 + CmoCh07G004400.1 Cmo07g00440 440
16 3782567 3784423 + CmoCh16G007540.1 Cmo16g00754 754
1 32815443 32816455 - CmPI595203_01g019500.1 Cmu01g1950 1950
1 32859998 32860698 - CmPI595203_01g019550.1 Cmu01g1955 1955
6 12686146 12688894 - Conep06aG0173200.1 Cone6ag1667 1667
6 12689471 12691452 - Conep06aG0173300.1 Cone6ag1668 1668
6 12695803 12700516 + Conep06aG0173500.1 Cone6ag1670 1670
6 12702590 12705997 + Conep06aG0173600.1 Cone6ag1671 1671
6 12709471 12711123 + Conep06aG0173700.1 Cone6ag1672 1672
8 8414127 8415112 - Conep08aG0086500.1 Cone8ag0839 839
9 11404564 11407317 - Conep09aG0163900.1 Cone9ag1589 1589
9 11408047 11409462 - Conep09aG0164000.1 Cone9ag1590 1590
9 11412526 11418788 + Conep09aG0164200.1 Cone9ag1592 1592
12 6669601 6670047 + Conep12aG0074900.1 Cone12ag0726 726
12 6687971 6693657 - Conep12aG0075200.1 Cone12ag0729 729
10 3738125 3738859 - Cp4.1LG10g00390.1 Cpe10g00649 649
10 3742794 3746200 + Cp4.1LG10g00460.1 Cpe10g00650 650
10 3751973 3753727 + Cp4.1LG10g00400.1 Cpe10g00651 651
10 3756668 3758229 - Cp4.1LG10g00350.1 Cpe10g00652 652
19 6255132 6256838 - Cp4.1LG19g09030.1 Cpe19g00845 845
19 6260586 6263980 + Cp4.1LG19g08970.1 Cpe19g00846 846
19 6272117 6274356 + Cp4.1LG19g08980.1 Cpe19g00847 847
4 34663164 34664168 - CrPI670011_04g016250.1 Cre04g1625 1625
4 34707348 34708048 - CrPI670011_04g016290.1 Cre04g1629 1629
4 3810629 3816151 - CsaV3_4G005800.1 Csa04g00580 580
4 3831401 3839382 + CsaV3_4G005820.1 Csa04g00582 582
6 27677901 27679613 - CsaV3_6G046900.1 Csa06g03304 3304
6 27708185 27710344 + CsaV3_6G046950.1 Csa06g03309 3309
6 27715754 27717181 - CsaV3_6G046960.1 Csa06g03310 3310
4 71286270 71287336 - Hsped.04g15780.1 Hepe04g1578 1578
1 4940151 4941473 + Lsi01G006170.1 Lsi01g00617 617
1 4951592 4952169 - Lsi01G006180.1 Lsi01g00618 618
1 4986878 4988713 + Lsi01G006200.1 Lsi01g00620 620
8 31162492 31164080 - Sed0021901.1 Sed08g1603 1603
3 75558649 75560115 - Tan0004566.1 Tan03g2056 2056
4 19607424 19615893 - Vvi4g1082 Vvi4g1082 1082
4 19619114 19622397 - Vvi4g1083 Vvi4g1083 1083
4 19631410 19632575 - Vvi4g1084 Vvi4g1084 1084
4 19637856 19646091 + Vvi4g1085 Vvi4g1085 1085
4 19652827 19656380 + Vvi4g1086 Vvi4g1086 1086
4 19662095 19665583 - Vvi4g1087 Vvi4g1087 1087
4 19667489 19672853 - Vvi4g1088 Vvi4g1088 1088
4 19681002 19683689 + Vvi4g1089 Vvi4g1089 1089
4 19688492 19690839 - Vvi4g1090 Vvi4g1090 1090
4 19696476 19697718 - Vvi4g1091 Vvi4g1091 1091
       

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