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
Vvi19g144 . . . . . . . . . . . . Car01g01055 . Sed05g2533 . . Bhi09g03487 Tan01g4345 Cmetu07g2325 . Hepe01g1424 Mch11g1028 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g145 Blo03g00683 . . . . . . . . . Cma01g01234 Cma09g00831 . . . Cpe06g00662 Cpe02g00682 Bhi09g03484 . . . Hepe01g1422 Mch11g1029 . Cla11g01725 Cam11g1795 Cec11g1816 Cco11g1822 Clacu11g1954 Cmu11g1764 Cre11g2172 . . . . Lsi04g02033 Csa04g02305 Chy07g00041 Cme07g00553 . . . . . . . . . Cmo01g01287 Cmo09g00824 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g146 Blo03g00681 . . . . . . . . . . . . . . . . Bhi09g03482 Tan01g4350 . . Hepe01g1420 Mch11g1030 . Cla11g01726 Cam11g1796 Cec11g1817 Cco11g1823 Clacu11g1955 Cmu11g1765 Cre11g2173 . . . . Lsi04g02034 Csa04g02306 Chy07g00042 Cme07g00554 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g147 . . . . . . . . . . Cma01g01233 Cma09g00832 Car01g01054 Car09g00746 Sed05g2538 Cpe06g00663 Cpe02g00683 Bhi09g03480 Tan01g4352 Cmetu04g0980 . Hepe01g1419 Mch11g1032 . Cla11g01727 Cam11g1797 Cec11g1818 Cco11g1824 Clacu11g1956 Cmu11g1766 Cre11g2174 Cone6ag0180 Cone9ag0205 Cone14ag1040 Cone15ag1029 Lsi04g02035 Csa04g02307 Chy07g00043 Cme07g00555 . . . . . . . . . Cmo01g01286 Cmo09g00825 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g148 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g149 . . . . . . . . . Cmo04g00599 . . . . . . . . . . . . . . . . . . . . . . . Cone14ag1041 Cone15ag1030 . . . . . . . . . . . . . . . Cma04g00562 . Car04g00533 . . Cpe01g00507 . . . . . . . Cla07g00942 Cam07g1018 Cec07g1088 Cco07g1066 Clacu07g0987 Cmu07g0983 Cre07g1357 . . Chy07g00956 Cme07g01326
Vvi19g150 . . . . Bpe09g00247 . . Bma13g00939 . Cmo04g00598 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo10g00748 . Bda12g00825 . . . . . . . Cma04g00561 . Car04g00532 . . Cpe01g00506 . . . . . . . Cla07g00941 Cam07g1016 Cec07g1087 Cco07g1065 Clacu07g0986 Cmu07g0982 Cre07g1356 . . Chy07g00955 Cme07g01322
Vvi19g151 . . . . . . . . . . Cma01g01232 Cma09g00833 Car01g01053 Car09g00748 . Cpe06g00664 Cpe02g00684 Bhi09g03479 . . . Hepe01g1418 Mch11g1033 . Cla11g01728 Cam11g1798 Cec11g1819 Cco11g1825 Clacu11g1957 Cmu11g1767 Cre11g2175 . Cone10ag1362 . . Lsi04g02036 Csa04g02308 Chy07g00044 Cme07g00557 . . . . . . . . . Cmo01g01285 Cmo09g00827 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g152 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g153 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
12 37678082 37684980 - Bda033185 Bda12g00825 825
9 87843046 87845333 - XM_039041627.1 Bhi09g03479 3479
9 87934307 87937130 + XM_039041218.1 Bhi09g03480 3480
9 87937731 87942699 - XM_039041046.1 Bhi09g03482 3482
9 87950785 87955830 - XM_039042629.1 Bhi09g03484 3484
9 88057236 88062019 + XM_039041722.1 Bhi09g03487 3487
3 28581945 28585218 + BLOR11862 Blo03g00681 681
3 28657341 28660725 + BLOR11864 Blo03g00683 683
10 23506553 23526951 - BLOR02538 Blo10g00748 748
13 39894762 39914719 - Bma030608 Bma13g00939 939
9 1820188 1826881 + Bpe023917.1 Bpe09g00247 247
7 24453157 24477298 - CaPI482276_07g010160.1 Cam07g1016 1016
7 24498511 24502945 + CaPI482276_07g010180.1 Cam07g1018 1018
11 30486526 30489785 + CaPI482276_11g017950.1 Cam11g1795 1795
11 30493847 30497164 + CaPI482276_11g017960.1 Cam11g1796 1796
11 30498494 30500768 - CaPI482276_11g017970.1 Cam11g1797 1797
11 30512776 30514495 + CaPI482276_11g017980.1 Cam11g1798 1798
1 9919656 9920968 - Carg14717-RA Car01g01053 1053
1 9925086 9926509 + Carg14718-RA Car01g01054 1054
1 9934783 9937098 + Carg14719-RA Car01g01055 1055
4 2986311 2993887 - Carg13175-RA Car04g00532 532
4 2996088 2999870 + Carg13174-RA Car04g00533 533
9 4438312 4439871 - Carg17068-RA Car09g00746 746
9 4445775 4447517 + Carg17070-RA Car09g00748 748
7 24150609 24176349 - CcPI632755_07g010650.1 Cco07g1065 1065
7 24198067 24202283 + CcPI632755_07g010660.1 Cco07g1066 1066
11 30900490 30901361 + CcPI632755_11g018220.1 Cco11g1822 1822
11 30901462 30911124 + CcPI632755_11g018230.1 Cco11g1823 1823
11 30912410 30914653 - CcPI632755_11g018240.1 Cco11g1824 1824
11 30926190 30927908 + CcPI632755_11g018250.1 Cco11g1825 1825
7 26015953 26039443 - CePI673135_07g010870.1 Cec07g1087 1087
7 26065182 26070125 + CePI673135_07g010880.1 Cec07g1088 1088
11 32353432 32356691 + CePI673135_11g018160.1 Cec11g1816 1816
11 32359830 32364135 + CePI673135_11g018170.1 Cec11g1817 1817
11 32365332 32367624 - CePI673135_11g018180.1 Cec11g1818 1818
11 32379324 32381042 + CePI673135_11g018190.1 Cec11g1819 1819
7 387960 391302 + Chy7G128710.1 Chy07g00041 41
7 400560 403737 + Chy7G128720.1 Chy07g00042 42
7 404691 406417 - Chy7G128730.1 Chy07g00043 43
7 415502 417127 + Chy7G128740.1 Chy07g00044 44
7 14144447 14188356 - Chy7G137850.1 Chy07g00955 955
7 14190986 14194380 + Chy7G137860.1 Chy07g00956 956
7 24269162 24292364 - ClG42_07g0098600.10 Clacu07g0986 986
7 24312029 24317511 + ClG42_07g0098700.10 Clacu07g0987 987
11 30522757 30525997 + ClG42_11g0195400.10 Clacu11g1954 1954
11 30530072 30533388 + ClG42_11g0195500.10 Clacu11g1955 1955
11 30534716 30537012 - ClG42_11g0195600.10 Clacu11g1956 1956
11 30549033 30550752 + ClG42_11g0195700.10 Clacu11g1957 1957
7 25571547 25594990 - ClCG07G009890.2 Cla07g00941 941
7 25616272 25620284 + ClCG07G009900.1 Cla07g00942 942
11 30871158 30874400 + ClCG11G017680.2 Cla11g01725 1725
11 30874607 30891239 + ClCG11G017690.1 Cla11g01726 1726
11 30892573 30894869 - ClCG11G017700.1 Cla11g01727 1727
11 30908301 30910020 + ClCG11G017710.2 Cla11g01728 1728
1 8880307 8882305 - CmaCh01G012320.1 Cma01g01232 1232
1 8885230 8887022 + CmaCh01G012330.1 Cma01g01233 1233
1 8887488 8891809 - CmaCh01G012340.1 Cma01g01234 1234
4 2852721 2860490 - CmaCh04G005610.1 Cma04g00561 561
4 2862063 2865925 + CmaCh04G005620.1 Cma04g00562 562
9 4081071 4090563 + CmaCh09G008310.1 Cma09g00831 831
9 4091241 4092903 - CmaCh09G008320.1 Cma09g00832 832
9 4097760 4099709 + CmaCh09G008330.1 Cma09g00833 833
7 4655462 4658855 + MELO3C032359.2.1 Cme07g00553 553
7 4664112 4667529 + MELO3C025624.2.1 Cme07g00554 554
7 4668034 4670058 - MELO3C025623.2.1 Cme07g00555 555
7 4685146 4687725 + MELO3C025622.2.1 Cme07g00557 557
7 18666605 18683112 - MELO3C016086.2.1 Cme07g01322 1322
7 18701558 18705281 + MELO3C016089.2.1 Cme07g01326 1326
4 30213577 30216472 - PI0016656.1 Cmetu04g0980 980
7 21711619 21716503 - PI0013713.1 Cmetu07g2325 2325
1 10235231 10237131 - CmoCh01G012850.1 Cmo01g01285 1285
1 10240838 10243449 + CmoCh01G012860.1 Cmo01g01286 1286
1 10243120 10247638 - CmoCh01G012870.1 Cmo01g01287 1287
4 2980970 2988404 - CmoCh04G005980.1 Cmo04g00598 598
4 2991061 2993430 + CmoCh04G005990.1 Cmo04g00599 599
9 4240801 4250316 + CmoCh09G008240.1 Cmo09g00824 824
9 4250825 4252597 - CmoCh09G008250.1 Cmo09g00825 825
9 4259257 4261405 + CmoCh09G008270.1 Cmo09g00827 827
7 24513001 24537263 - CmPI595203_07g009820.1 Cmu07g0982 982
7 24556933 24562414 + CmPI595203_07g009830.1 Cmu07g0983 983
11 29778207 29781447 + CmPI595203_11g017640.1 Cmu11g1764 1764
11 29785517 29788832 + CmPI595203_11g017650.1 Cmu11g1765 1765
11 29790159 29792449 - CmPI595203_11g017660.1 Cmu11g1766 1766
11 29804425 29806144 + CmPI595203_11g017670.1 Cmu11g1767 1767
6 856491 856885 + Conep06aG0018100.1 Cone6ag0180 180
9 871968 873236 + Conep09aG0020700.1 Cone9ag0205 205
10 10609845 10613733 - Conep10aG0140400.1 Cone10ag1362 1362
14 8779291 8781511 - Conep14aG0106100.1 Cone14ag1040 1040
14 8790528 8793429 - Conep14aG0106200.1 Cone14ag1041 1041
15 8550755 8552745 - Conep15aG0105100.1 Cone15ag1029 1029
15 8556351 8559399 - Conep15aG0105200.1 Cone15ag1030 1030
1 2912147 2919992 - Cp4.1LG01g01470.1 Cpe01g00506 506
1 2921516 2925554 + Cp4.1LG01g01600.1 Cpe01g00507 507
2 4302909 4307145 + Cp4.1LG02g01940.1 Cpe02g00682 682
2 4307671 4309337 - Cp4.1LG02g01850.1 Cpe02g00683 683
2 4312688 4314570 + Cp4.1LG02g01930.1 Cpe02g00684 684
6 4119484 4129354 + Cp4.1LG06g06620.1 Cpe06g00662 662
6 4128591 4131679 - Cp4.1LG06g06700.1 Cpe06g00663 663
6 4137002 4139389 + Cp4.1LG06g06590.1 Cpe06g00664 664
7 28440251 28461441 - CrPI670011_07g013560.1 Cre07g1356 1356
7 28485017 28490044 + CrPI670011_07g013570.1 Cre07g1357 1357
11 33427879 33431077 + CrPI670011_11g021720.1 Cre11g2172 2172
11 33436864 33453103 + CrPI670011_11g021730.1 Cre11g2173 2173
11 33454382 33456678 - CrPI670011_11g021740.1 Cre11g2174 2174
11 33468511 33470230 + CrPI670011_11g021750.1 Cre11g2175 2175
4 23594567 23598381 + CsaV3_4G033310.1 Csa04g02305 2305
4 23605583 23608754 + CsaV3_4G033320.1 Csa04g02306 2306
4 23609265 23612205 - CsaV3_4G033330.1 Csa04g02307 2307
4 23620295 23626963 + CsaV3_4G033340.1 Csa04g02308 2308
1 79390171 79392496 - Hsped.01g14180.1 Hepe01g1418 1418
1 79407367 79409279 + Hsped.01g14190.1 Hepe01g1419 1419
1 79410480 79414914 - Hsped.01g14200.1 Hepe01g1420 1420
1 79424977 79426300 - Hsped.01g14220.1 Hepe01g1422 1422
1 79451319 79456035 + Hsped.01g14240.1 Hepe01g1424 1424
4 27446735 27451538 + Lsi04G020330.1 Lsi04g02033 2033
4 27460551 27464837 + Lsi04G020340.1 Lsi04g02034 2034
4 27466069 27469164 - Lsi04G020350.1 Lsi04g02035 2035
4 27480875 27483761 + Lsi04G020360.1 Lsi04g02036 2036
11 7155040 7160022 - MC11g0840 Mch11g1028 1028
11 7171436 7176133 + MC11g0841 Mch11g1029 1029
11 7178746 7183142 + MC11g_new0189 Mch11g1030 1030
11 7189870 7192255 - MC11g0843 Mch11g1032 1032
11 7203271 7206319 + MC11g0844 Mch11g1033 1033
5 37349981 37354619 - Sed0018014.1 Sed05g2533 2533
5 37388305 37390767 - Sed0000931.3 Sed05g2538 2538
1 108387308 108392922 - Tan0009374.1 Tan01g4345 4345
1 108448021 108451118 + Tan0007983.1 Tan01g4350 4350
1 108462215 108464247 - Tan0021528.1 Tan01g4352 4352
19 1882744 1897497 - Vvi19g144 Vvi19g144 144
19 1908115 1925741 + Vvi19g145 Vvi19g145 145
19 1928970 1945302 + Vvi19g146 Vvi19g146 146
19 1945317 1947525 - Vvi19g147 Vvi19g147 147
19 1953374 1979475 - Vvi19g148 Vvi19g148 148
19 1981263 1985197 - Vvi19g149 Vvi19g149 149
19 1996596 2012013 + Vvi19g150 Vvi19g150 150
19 2014868 2018538 + Vvi19g151 Vvi19g151 151
19 2019133 2022522 - Vvi19g152 Vvi19g152 152
19 2024588 2027866 + Vvi19g153 Vvi19g153 153
       

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