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
Vvi19g164 . . . . . . Bma10g00490 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g00583 . . . . . . . . . . . . . Cla05g00997 Cam05g1088 Cec05g1096 Cco05g1090 Clacu05g1082 Cmu05g1032 Cre05g1106 . . . .
Vvi19g165 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g166 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g00636 . . . . . . . . . . Sed07g1851 . . . . . . . . Bhi11g00780 Tan01g1553 Cmetu06g2423 . . Mch10g0653 . . . . . . . . . . . .
Vvi19g167 . . . . . . Bma10g00491 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g168 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma04g00555 . . . . . . . . . . . . . . . . . . . Lsi05g00790 . Chy06g01167 .
Vvi19g169 . . . . . . . . . Cmo04g00589 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car04g00525 . . Cpe01g00498 . . . . . . . . . . . . . . . . . .
Vvi19g170 . . . . Bpe09g00245 . . Bma13g00940 Cmo16g00439 . . . . . . . . . . . . . . . Cla10g00660 Cam10g0656 Cec10g0680 Cco10g0652 Clacu10g0679 Cmu10g1503 Cre10g0883 . . Cone14ag1047 Cone15ag1035 . . . . . Blo10g00749 . Bda12g00871 . . . . . . . . Cma16g00407 . Car16g00371 Cpe14g00341 . . . . . . . . Cla05g00998 Cam05g1089 Cec05g1097 Cco05g1091 Clacu05g1083 Cmu05g1033 Cre05g1108 . . Chy06g01166 .
Vvi19g171 . . . . . . . . . . . Cma09g00836 . Car09g00751 Sed05g2541 Cpe06g00667 . Bhi09g03472 Tan01g4356 Cmetu07g0939 . Hepe01g1415 Mch11g1036 . Cla11g01731 Cam11g1800 Cec11g1821 Cco11g1827 Clacu11g1959 Cmu11g1769 Cre11g2177 . . Cone14ag1048 . Lsi04g02040 Csa04g02310 Chy07g00046 Cme07g00564 . . . . . . . . . . Cmo09g00831 . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g172 . . . . Bpe09g00244 . . . . . Cma01g01231 . Car01g01052 . Sed04g2426 . Cpe02g00685 Bhi09g03470 Tan01g4359 Cmetu07g1823 . Hepe01g1414 . . Cla11g01732 Cam11g1801 Cec11g1822 Cco11g1828 Clacu11g1960 Cmu11g1770 . . . . . Lsi04g02041 Csa04g02311 Chy07g00047 Cme07g00565 . . . Bda12g00828 . . Bma07g01160 . . Cmo01g01284 . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g173 . . . . Bpe09g00243 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda12g00829 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
12 37839919 37840455 - Bda009344.1 Bda12g00828 828
12 37842975 37843472 - Bda009345.1 Bda12g00829 829
12 39412470 39416683 - Bda009401.7 Bda12g00871 871
9 87806317 87809347 + XM_039041132.1 Bhi09g03470 3470
9 87828070 87831094 + XM_039040900.1 Bhi09g03472 3472
11 21157120 21161964 + XM_039049570.1 Bhi11g00780 780
10 23539829 23551426 - BLOR02539 Blo10g00749 749
7 45884172 45886605 + Bma026393.1 Bma07g01160 1160
10 5786908 5788281 + Bma004179.1 Bma10g00490 490
10 5796240 5797613 + Bma004180.1 Bma10g00491 491
13 39949208 39957784 - Bma010023.1 Bma13g00940 940
9 1768538 1769028 + Bpe023913.1 Bpe09g00243 243
9 1772510 1773046 + Bpe023914.1 Bpe09g00244 244
9 1783051 1791590 + Bpe023915.1 Bpe09g00245 245
5 9932799 9936236 - CaPI482276_05g010880.1 Cam05g1088 1088
5 9945005 9954229 - CaPI482276_05g010890.1 Cam05g1089 1089
10 10217891 10220482 - CaPI482276_10g006560.1 Cam10g0656 656
11 30520113 30529786 - CaPI482276_11g018000.1 Cam11g1800 1800
11 30529875 30532259 - CaPI482276_11g018010.1 Cam11g1801 1801
1 9916362 9920785 + Carg14716-RA Car01g01052 1052
4 2943107 2947349 + Carg13182-RA Car04g00525 525
9 4458097 4461382 - Carg17073-RA Car09g00751 751
16 2291582 2301982 + Carg11338-RA Car16g00371 371
5 9699719 9703105 - CcPI632755_05g010900.1 Cco05g1090 1090
5 9712076 9721298 - CcPI632755_05g010910.1 Cco05g1091 1091
10 9002978 9005568 - CcPI632755_10g006520.1 Cco10g0652 652
11 30931233 30943358 - CcPI632755_11g018270.1 Cco11g1827 1827
11 30943450 30945838 - CcPI632755_11g018280.1 Cco11g1828 1828
5 9678540 9681898 - CePI673135_05g010960.1 Cec05g1096 1096
5 9693612 9702847 - CePI673135_05g010970.1 Cec05g1097 1097
10 9448632 9451205 - CePI673135_10g006800.1 Cec10g0680 680
11 32386543 32396242 - CePI673135_11g018210.1 Cec11g1821 1821
11 32396334 32398716 - CePI673135_11g018220.1 Cec11g1822 1822
6 10345355 10355359 + Chy6G116940.1 Chy06g01166 1166
6 10359210 10361220 + Chy6G116950.1 Chy06g01167 1167
7 422745 430823 - Chy7G128760.1 Chy07g00046 46
7 432440 434938 - Chy7G128770.1 Chy07g00047 47
5 9668254 9671670 - ClG42_05g0108200.10 Clacu05g1082 1082
5 9680533 9689763 - ClG42_05g0108300.10 Clacu05g1083 1083
10 9508551 9511132 - ClG42_10g0067900.10 Clacu10g0679 679
11 30556332 30564966 - ClG42_11g0195900.10 Clacu11g1959 1959
11 30566136 30568514 - ClG42_11g0196000.10 Clacu11g1960 1960
5 10033305 10036973 - ClCG05G009230.2 Cla05g00997 997
5 10050366 10059804 - ClCG05G009240.1 Cla05g00998 998
10 10042918 10045792 - ClCG10G007030.2 Cla10g00660 660
11 30921289 30924534 - ClCG11G017740.2 Cla11g01731 1731
11 30925375 30927934 - ClCG11G017750.2 Cla11g01732 1732
1 8877366 8880310 + CmaCh01G012310.1 Cma01g01231 1231
4 2814143 2816042 + CmaCh04G005550.1 Cma04g00555 555
9 4119935 4123637 - CmaCh09G008360.1 Cma09g00836 836
16 2019010 2029219 + CmaCh16G004070.1 Cma16g00407 407
7 4842809 4846140 - MELO3C025618.2.1 Cme07g00564 564
7 4847560 4850620 - MELO3C025617.2.1 Cme07g00565 565
6 24006519 24013437 + PI0021883.3 Cmetu06g2423 2423
7 21769048 21772214 - PI0001936.1 Cmetu07g0939 939
7 21773176 21776099 - PI0014484.1 Cmetu07g1823 1823
1 10232322 10235239 + CmoCh01G012840.1 Cmo01g01284 1284
4 2938658 2941634 + CmoCh04G005890.1 Cmo04g00589 589
9 2868439 2869947 - CmoCh09G005830.1 Cmo09g00583 583
9 4271988 4275948 - CmoCh09G008310.1 Cmo09g00831 831
16 2089973 2100383 + CmoCh16G004390.1 Cmo16g00439 439
5 9508364 9511789 - CmPI595203_05g010320.1 Cmu05g1032 1032
5 9520637 9529867 - CmPI595203_05g010330.1 Cmu05g1033 1033
10 10125468 10128049 - CmPI595203_10g015030.1 Cmu10g1503 1503
11 29811731 29820360 - CmPI595203_11g017690.1 Cmu11g1769 1769
11 29821493 29823871 - CmPI595203_11g017700.1 Cmu11g1770 1770
14 8819772 8827166 - Conep14aG0106800.1 Cone14ag1047 1047
14 8827900 8830425 - Conep14aG0106900.1 Cone14ag1048 1048
15 8588510 8596213 - Conep15aG0105700.1 Cone15ag1035 1035
1 2871667 2873821 + Cp4.1LG01g01790.1 Cpe01g00498 498
2 4314686 4317511 - Cp4.1LG02g01900.1 Cpe02g00685 685
6 4149833 4153829 - Cp4.1LG06g06670.1 Cpe06g00667 667
14 2076510 2087211 + Cp4.1LG14g03760.1 Cpe14g00341 341
5 10382903 10386368 - CrPI670011_05g011060.1 Cre05g1106 1106
5 10403956 10404762 - CrPI670011_05g011080.1 Cre05g1108 1108
10 10107550 10110131 - CrPI670011_10g008830.1 Cre10g0883 883
11 33475870 33488054 - CrPI670011_11g021770.1 Cre11g2177 2177
3 5491495 5495848 - CsaV3_3G006360.1 Csa03g00636 636
4 23632727 23636644 - CsaV3_4G033360.1 Csa04g02310 2310
4 23637717 23640215 - CsaV3_4G033370.1 Csa04g02311 2311
1 79370204 79374064 + Hsped.01g14140.1 Hepe01g1414 1414
1 79375636 79378881 + Hsped.01g14150.1 Hepe01g1415 1415
4 27496726 27500235 - Lsi04G020400.1 Lsi04g02040 2040
4 27502028 27505177 - Lsi04G020410.1 Lsi04g02041 2041
5 11452183 11457551 + Lsi05G007900.1 Lsi05g00790 790
10 4488390 4490881 - MC10g0540 Mch10g0653 653
11 7215684 7219067 - MC11g0847 Mch11g1036 1036
4 37528452 37531031 + Sed0026268.1 Sed04g2426 2426
5 37401896 37404566 - Sed0012116.2 Sed05g2541 2541
7 24229740 24232917 - Sed0011001.1 Sed07g1851 1851
1 15845983 15849779 + Tan0014206.1 Tan01g1553 1553
1 108505636 108509148 - Tan0011756.1 Tan01g4356 4356
1 108517143 108520245 - Tan0011285.3 Tan01g4359 4359
19 2155949 2157323 - Vvi19g164 Vvi19g164 164
19 2170948 2179821 + Vvi19g165 Vvi19g165 165
19 2189218 2190591 - Vvi19g166 Vvi19g166 166
19 2195914 2203758 + Vvi19g167 Vvi19g167 167
19 2206256 2219341 + Vvi19g168 Vvi19g168 168
19 2219865 2232444 + Vvi19g169 Vvi19g169 169
19 2237269 2251390 - Vvi19g170 Vvi19g170 170
19 2252693 2257913 - Vvi19g171 Vvi19g171 171
19 2259484 2272052 - Vvi19g172 Vvi19g172 172
19 2279863 2280893 - Vvi19g173 Vvi19g173 173
       

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