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
Vvi5g99 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g100 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag0111 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g101 . . . . . . . . Cmo08g01233 . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa06g01756 Chy11g01554 . . Blo07g00157 . . . . . Bma06g01479 Sed04g4010 . . Cma08g01263 . Car08g01133 . . Cpe17g00054 Bhi12g01908 Tan06g2736 Cmetu11g1056 . . . . . . . . . . . Lsi09g01473 . . .
Vvi5g102 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe05g00749 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g103 Blo01g00056 . . Bda08g00309 . . . Bma05g01019 Cmo08g01232 Cmo17g00347 . . . . . . . . . . . . . . Cla06g00441 Cam06g0468 Cec06g0474 . Clacu06g0455 Cmu06g0456 Cre06g1231 . . Cone7ag0112 Cone4ag0116 . Csa06g01758 Chy11g01553 . . . . . Bpe05g00819 . . . Sed04g1761 . . Cma08g01262 Cma17g00357 Car08g01132 Car17g00328 Cpe12g00309 Cpe17g00053 Bhi12g01907 Tan06g2735 Cmetu11g2266 Lac11g0914 Hepe03g0061 . Lcy12g0785 . . . . . . . Lsi09g01472 . . Cme11g02064
Vvi5g104 . . . . . . . . . . Cma06g01553 . Car06g01318 . . . . Bhi01g01067 . . . . . Lcy11g1357 Cla06g00442 . . . . . . . . . . . Csa06g01759 . Cme06g00771 Blo02g00484 . . . . . Bma02g00922 . . Cmo06g01552 Cmo14g01631 Cma08g01261 Cma17g00356 Car08g01131 . Cpe12g00308 . Bhi12g01906 . . . . . Lcy12g0784 Cla05g00689 . . . . . . . Csa03g01504 Chy06g00741 .
Vvi5g105 Blo01g00057 . Bda03g01163 Bda08g00308 Bpe04g01107 . Bma04g01138 Bma05g01020 Cmo08g01229 Cmo17g00345 . . . . . . . . . . . . . . Cla06g00443 Cam06g0471 Cec06g0476 Cco06g0474 Clacu06g0457 Cmu06g0458 Cre06g1233 . . Cone7ag0113 Cone4ag0117 . Csa06g01760 Chy11g01551 . . . . . Bpe05g00820 . . . . . . Cma08g01259 Cma17g00355 Car08g01130 Car17g00327 Cpe12g00305 Cpe17g00051 Bhi12g01905 . . . . . . . . . . . . . Lsi09g01471 . . Cme11g02061
Vvi5g106 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g107 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0733 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g108 . . . . . Bpe14g01106 . . . . Cma06g01552 . Car06g01317 Car14g01414 Sed02g1145 Cpe08g00162 Cpe03g01340 Bhi01g01066 Tan10g1057 Cmetu06g1456 . Hepe05g1398 . Lcy11g1360 . . . . . . . . . Cone7ag0114 Cone4ag0118 . . . Cme06g00769 Blo02g00485 . . Bda13g00209 . . Bma02g00921 . . Cmo06g01551 Cmo14g01632 . . . . . . . . . . . . . Cla05g00688 Cam05g0752 Cec05g0760 . Clacu05g0744 Cmu05g0709 . . Csa03g01502 Chy06g00739 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 12965762 12969329 + Bda017225.1 Bda03g01163 1163
8 3201164 3204619 + Bda024744.1 Bda08g00308 308
8 3206161 3211420 - Bda024745.1 Bda08g00309 309
13 2647826 2648782 - Bda001082.1 Bda13g00209 209
1 19887137 19889499 - XM_039047156.1 Bhi01g01066 1066
1 19936143 19943785 - XM_039024246.1 Bhi01g01067 1067
12 60834616 60839693 + XM_039018587.1 Bhi12g01905 1905
12 60840378 60846039 - XM_039018589.1 Bhi12g01906 1906
12 60870190 60876495 - XM_039019819.1 Bhi12g01907 1907
12 60937299 60941920 - XM_039050708.1 Bhi12g01908 1908
1 721785 729014 + BLOR00056 Blo01g00056 56
1 730387 733843 - BLOR00057 Blo01g00057 57
2 7204274 7205912 + BLOR10214 Blo02g00484 484
2 7253407 7254335 + BLOR10215 Blo02g00485 485
7 2046997 2051594 + BLOR18089 Blo07g00157 157
2 48561267 48562202 - Bma015704.1 Bma02g00921 921
2 48664531 48666136 - Bma015705.1 Bma02g00922 922
4 28524319 28527885 - Bma019855.1 Bma04g01138 1138
5 48705450 48710964 + Bma031223 Bma05g01019 1019
5 48712346 48715865 - Bma022175.1 Bma05g01020 1020
6 51394495 51395085 + Bma024591.1 Bma06g01479 1479
4 8902377 8905939 + Bpe015782.1 Bpe04g01107 1107
5 20907746 20913548 + Bpe018163.1 Bpe05g00749 749
5 21478564 21484074 + Bpe018231.1 Bpe05g00819 819
5 21485326 21488752 - Bpe018232.1 Bpe05g00820 820
14 8273879 8274832 + Bpe014481.1 Bpe14g01106 1106
5 6534493 6542961 - CaPI482276_05g007520.1 Cam05g0752 752
6 6816509 6823429 + CaPI482276_06g004680.1 Cam06g0468 468
6 6837682 6841075 - CaPI482276_06g004710.1 Cam06g0471 471
6 9417269 9419382 - Carg23745-RA Car06g01317 1317
6 9421279 9422992 - Carg23744-RA Car06g01318 1318
8 7638838 7644110 + Carg18872-RA Car08g01130 1130
8 7644084 7648952 - Carg18873-RA Car08g01131 1131
8 7650107 7654342 - Carg18874-RA Car08g01132 1132
8 7654769 7655979 - Carg18875-RA Car08g01133 1133
14 11900914 11903233 + Carg19636-RA Car14g01414 1414
17 2038697 2042114 + Carg05533-RA Car17g00327 327
17 2041951 2055484 - Carg05534-RA Car17g00328 328
6 5235482 5238772 - CcPI632755_06g004740.1 Cco06g0474 474
5 6262629 6265360 - CePI673135_05g007600.1 Cec05g0760 760
6 5345885 5352808 + CePI673135_06g004740.1 Cec06g0474 474
6 5366809 5370201 - CePI673135_06g004760.1 Cec06g0476 476
6 5049752 5055427 - Chy6G112670.1 Chy06g00739 739
6 5058214 5060948 - Chy6G112690.1 Chy06g00741 741
11 22049164 22052431 + Chy11G201310.1 Chy11g01551 1551
11 22065922 22070775 - Chy11G201330.1 Chy11g01553 1553
11 22072058 22081406 - Chy11G201340.1 Chy11g01554 1554
5 6255593 6264152 - ClG42_05g0074400.10 Clacu05g0744 744
6 5351252 5358846 + ClG42_06g0045500.10 Clacu06g0455 455
6 5372133 5375510 - ClG42_06g0045700.10 Clacu06g0457 457
5 6383462 6386798 - ClCG05G006400.1 Cla05g00688 688
5 6390581 6393712 - ClCG05G006405.1 Cla05g00689 689
6 5372511 5396469 + ClCG06G004720.2 Cla06g00441 441
6 5402521 5409303 + ClCG06G004750.1 Cla06g00442 442
6 5410502 5415147 - ClCG06G004760.1 Cla06g00443 443
6 9715361 9717638 - CmaCh06G015520.1 Cma06g01552 1552
6 9718726 9720686 - CmaCh06G015530.1 Cma06g01553 1553
8 7673711 7678149 + CmaCh08G012590.1 Cma08g01259 1259
8 7677253 7682130 - CmaCh08G012610.1 Cma08g01261 1261
8 7683178 7687867 - CmaCh08G012620.1 Cma08g01262 1262
8 7688155 7689678 - CmaCh08G012630.1 Cma08g01263 1263
17 1951074 1958907 + CmaCh17G003550.1 Cma17g00355 355
17 1957995 1962909 - CmaCh17G003560.1 Cma17g00356 356
17 1965201 1980584 - CmaCh17G003570.1 Cma17g00357 357
6 5080480 5081823 - MELO3C006698.2.1 Cme06g00769 769
6 5085848 5088743 - MELO3C006700.2.1 Cme06g00771 771
11 28332846 28339314 + MELO3C021285.2.1 Cme11g02061 2061
11 28350604 28355741 - MELO3C021283.2.1 Cme11g02064 2064
6 5300869 5302335 - PI0009456.1 Cmetu06g1456 1456
11 3874797 3878375 + PI0024164.1 Cmetu11g1056 1056
11 3880162 3884997 + PI0029077.1 Cmetu11g2266 2266
6 10913181 10915521 - CmoCh06G015510.1 Cmo06g01551 1551
6 10917887 10919845 - CmoCh06G015520.1 Cmo06g01552 1552
8 7790083 7794568 + CmoCh08G012290.1 Cmo08g01229 1229
8 7799805 7804722 - CmoCh08G012320.1 Cmo08g01232 1232
8 7805074 7806494 - CmoCh08G012330.1 Cmo08g01233 1233
14 12959927 12962161 + CmoCh14G016310.1 Cmo14g01631 1631
14 12963221 12965516 + CmoCh14G016320.1 Cmo14g01632 1632
17 2080768 2087516 + CmoCh17G003450.1 Cmo17g00345 345
17 2094151 2099416 - CmoCh17G003470.1 Cmo17g00347 347
5 6097581 6107677 - CmPI595203_05g007090.1 Cmu05g0709 709
6 5153938 5160938 + CmPI595203_06g004560.1 Cmu06g0456 456
6 5174839 5178238 - CmPI595203_06g004580.1 Cmu06g0458 458
4 549411 553268 + Conep04aG0012000.1 Cone4ag0116 116
4 555445 559804 - Conep04aG0012100.1 Cone4ag0117 117
4 562036 563011 + Conep04aG0012200.1 Cone4ag0118 118
7 478247 480441 + Conep07aG0011200.1 Cone7ag0111 111
7 480710 484342 + Conep07aG0011300.1 Cone7ag0112 112
7 485941 490144 - Conep07aG0011400.1 Cone7ag0113 113
7 491471 492554 + Conep07aG0011500.1 Cone7ag0114 114
14 4077055 4081383 + Conep14aG0074900.1 Cone14ag0733 733
3 10884567 10887184 + Cp4.1LG03g11770.1 Cpe03g01340 1340
8 1053286 1055737 + Cp4.1LG08g05170.1 Cpe08g00162 162
12 2020284 2027364 + Cp4.1LG12g03010.1 Cpe12g00305 305
12 2030099 2031025 - Cp4.1LG12g03120.1 Cpe12g00308 308
12 2034254 2039753 - Cp4.1LG12g03110.1 Cpe12g00309 309
17 325022 334267 + Cp4.1LG17g00460.1 Cpe17g00051 51
17 337594 342409 - Cp4.1LG17g00400.1 Cpe17g00053 53
17 342812 343557 - Cp4.1LG17g00390.1 Cpe17g00054 54
6 6209648 6217205 + CrPI670011_06g012310.1 Cre06g1231 1231
6 6237123 6240516 - CrPI670011_06g012330.1 Cre06g1233 1233
3 11142640 11144259 - CsaV3_3G015020.1 Csa03g01502 1502
3 11146686 11149681 - CsaV3_3G015040.1 Csa03g01504 1504
6 15463395 15466525 + CsaV3_6G022510.1 Csa06g01756 1756
6 15467606 15472347 + CsaV3_6G022530.1 Csa06g01758 1758
6 15480017 15487835 + CsaV3_6G022540.1 Csa06g01759 1759
6 15488058 15493330 - CsaV3_6G022550.1 Csa06g01760 1760
3 734829 743257 + Hsped.03g00610.1 Hepe03g0061 61
5 62815586 62818661 + Hsped.05g13980.1 Hepe05g1398 1398
11 9892162 9897584 - Lag0031552.1 Lac11g0914 914
11 37283027 37286159 + Maker00031284 Lcy11g1357 1357
11 37302254 37304791 + Maker00031509 Lcy11g1360 1360
12 10149117 10153874 - Maker00025121 Lcy12g0784 784
12 10180187 10185863 - Maker00024966 Lcy12g0785 785
9 22703529 22706915 + Lsi09G014710.1 Lsi09g01471 1471
9 22707498 22727529 - Lsi09G014720.1 Lsi09g01472 1472
9 22729597 22734993 - Lsi09G014730.1 Lsi09g01473 1473
2 48633605 48636436 + Sed0010751.1 Sed02g1145 1145
4 32241170 32246960 + Sed0012111.1 Sed04g1761 1761
4 47790779 47792889 - Sed0020654.1 Sed04g4010 4010
6 79661340 79666891 - Tan0003397.2 Tan06g2735 2735
6 79669105 79672045 - Tan0002091.1 Tan06g2736 2736
10 9598680 9601808 - Tan0001500.1 Tan10g1057 1057
5 1068310 1072981 + Vvi5g99 Vvi5g99 99
5 1075444 1078705 + Vvi5g100 Vvi5g100 100
5 1083852 1085029 + Vvi5g101 Vvi5g101 101
5 1085705 1087504 + Vvi5g102 Vvi5g102 102
5 1088146 1099307 + Vvi5g103 Vvi5g103 103
5 1104508 1106640 + Vvi5g104 Vvi5g104 104
5 1115774 1121049 - Vvi5g105 Vvi5g105 105
5 1124495 1124822 - Vvi5g106 Vvi5g106 106
5 1135153 1141477 + Vvi5g107 Vvi5g107 107
5 1144679 1145755 + Vvi5g108 Vvi5g108 108
       

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