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
Vvi3g366 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g367 . . . . . . . . . . Cma02g00392 Cma20g00844 Car02g00255 Car20g00731 . . . Bhi05g01245 Tan02g0784 Cmetu01g1772 . . . . . . . . . . . . . . . Lsi10g00378 . . . . . . . . . . . Sed01g0298 Cmo02g00399 Cmo20g00855 . . . . . . Bhi10g01996 Tan05g1294 Cmetu11g1946 . . . . . . . . . . . . Csa02g01267 . Cme11g00123
Vvi3g368 . . . Bda08g00941 Bpe07g00424 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy11g00373 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g369 . . . . . . . . . . . Cma20g00845 . . Sed04g3918 . . Bhi05g01243 Tan02g0785 Cmetu01g0437 . Hepe02g0491 . . . . . . . . . . . . . Lsi10g00377 . . . . . . . . . . . Sed05g3616 . . . . . . . . Bhi10g01997 Tan05g1295 Cmetu11g0943 . Hepe08g1010 . . . . . . . . . . Csa02g01266 . Cme11g00122
Vvi3g370 . . . Bda08g00939 . . Bma05g00446 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe16g00246 . . . . . . . . . . . . . . . . . . .
Vvi3g371 . . . . . . Bma05g00447 . . . . . . . Sed11g1039 . . Bhi05g01241 Tan02g1978 Cmetu01g0347 . . . . . . . . . . . . . . . Lsi10g00376 . . . . . . . . . . . . . . . . . . . Cpe05g01264 Bhi10g01998 Tan05g1296 . . . . . . . . . . . . . Csa02g01265 . Cme11g00121
Vvi3g372 Blo02g00805 . . Bda08g00938 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1156 Cone8ag1205 . . . . . . . . . . . . . . Sed01g0300 . . . . . . Cpe16g00245 . Bhi10g01999 Tan05g1297 Cmetu11g2121 . Hepe08g1011 . . . . . . . . . . . . .
Vvi3g373 . Blo15g00703 . . Bpe07g00425 . . Bma12g00507 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g374 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g375 . . . . . . . . . . Cma02g00394 . Car02g00256 . . . . . . . . . . . . . . . . . . . . . . Lsi10g00375 . Chy11g00374 . . . . . . . . . Sed05g3617 . . . . . . . Cpe05g01263 Bhi10g02000 Tan05g1298 Cmetu11g1012 . Hepe08g1012 . . . . . . . . . . Csa02g01264 . Cme11g00120
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 17491180 17497714 + Bda029582.1 Bda08g00938 938
8 17519720 17520557 - Bda029583.1 Bda08g00939 939
8 17607634 17609191 + Bda029587.1 Bda08g00941 941
5 44857234 44865978 + XM_039032518.1 Bhi05g01241 1241
5 45039964 45048784 + XM_039032652.1 Bhi05g01243 1243
5 45189667 45195218 + XM_039032656.1 Bhi05g01245 1245
10 49889829 49892305 - XM_039044822.1 Bhi10g01996 1996
10 49920499 49923166 - XM_039044923.1 Bhi10g01997 1997
10 49941421 49943934 - XM_039044644.1 Bhi10g01998 1998
10 49947280 49950576 - XM_039044902.1 Bhi10g01999 1999
10 50011460 50016780 - XM_039046694.1 Bhi10g02000 2000
2 27837245 27844967 + BLOR10535 Blo02g00805 805
15 22339372 22342430 - BLOR07097 Blo15g00703 703
5 14958287 14959820 - Bma021302.1 Bma05g00446 446
5 14960218 14962322 - Bma031187 Bma05g00447 447
12 16198148 16199041 + Bma007571.1 Bma12g00507 507
7 4746965 4761493 - Bpe021248.1 Bpe07g00424 424
7 4783671 4784564 + Bpe021249.1 Bpe07g00425 425
2 1740703 1742839 - Carg22940-RA Car02g00255 255
2 1743719 1745370 - Carg22941-RA Car02g00256 256
20 4265086 4271440 - Carg26478-RA Car20g00731 731
11 3451040 3454835 - Chy11G189530.1 Chy11g00373 373
11 3460066 3463817 - Chy11G189540.1 Chy11g00374 374
2 1991994 1994008 - CmaCh02G003920.1 Cma02g00392 392
2 1995000 2003022 - CmaCh02G003940.1 Cma02g00394 394
20 4043610 4045636 - CmaCh20G008440.1 Cma20g00844 844
20 4047710 4050582 - CmaCh20G008450.1 Cma20g00845 845
11 1132774 1136327 + MELO3C023302.2.1 Cme11g00120 120
11 1152522 1157068 + MELO3C023303.2.1 Cme11g00121 121
11 1158139 1160696 + MELO3C023304.2.1 Cme11g00122 122
11 1163731 1166304 + MELO3C023305.2.1 Cme11g00123 123
1 1172755 1174904 - PI0026075.1 Cmetu01g0347 347
1 6003752 6011882 - PI0022027.1 Cmetu01g0437 437
1 5985505 5995807 - PI0021289.2 Cmetu01g1772 1772
11 27507016 27509407 + PI0022006.1 Cmetu11g0943 943
11 27483773 27487069 + PI0020636.1 Cmetu11g1012 1012
11 27512694 27513431 + PI0016455.1 Cmetu11g1946 1946
11 27501943 27505375 + PI0021060.1 Cmetu11g2121 2121
2 2060707 2065303 - CmoCh02G003990.1 Cmo02g00399 399
20 4302016 4308964 - CmoCh20G008550.1 Cmo20g00855 855
8 10247344 10253193 + Conep08aG0124200.1 Cone8ag1205 1205
12 9218731 9220534 + Conep12aG0119500.1 Cone12ag1156 1156
5 8824096 8826852 + Cp4.1LG05g12550.1 Cpe05g01263 1263
5 8827948 8831120 + Cp4.1LG05g12510.1 Cpe05g01264 1264
16 4500867 4504015 + Cp4.1LG16g02380.1 Cpe16g00245 245
16 4505107 4507530 + Cp4.1LG16g02390.1 Cpe16g00246 246
2 12354798 12357629 + CsaV3_2G014800.1 Csa02g01264 1264
2 12359415 12362815 + CsaV3_2G014810.1 Csa02g01265 1265
2 12363449 12366223 + CsaV3_2G014820.1 Csa02g01266 1266
2 12368145 12370567 + CsaV3_2G014830.1 Csa02g01267 1267
2 4802751 4826438 - Hsped.02g04910.1 Hepe02g0491 491
8 9623174 9632909 - Hsped.08g10100.1 Hepe08g1010 1010
8 9634131 9637324 - Hsped.08g10110.1 Hepe08g1011 1011
8 9642761 9644750 - Hsped.08g10120.1 Hepe08g1012 1012
10 5763626 5768494 + Lsi10G003750.1 Lsi10g00375 375
10 5772225 5775716 + Lsi10G003760.1 Lsi10g00376 376
10 5779206 5781810 + Lsi10G003770.1 Lsi10g00377 377
10 5784438 5790229 + Lsi10G003780.1 Lsi10g00378 378
1 2280525 2283721 - Sed0023874.1 Sed01g0298 298
1 2285390 2289072 - Sed0000248.1 Sed01g0300 300
4 47306278 47309758 - Sed0002300.1 Sed04g3918 3918
5 44478132 44480614 - Sed0026601.1 Sed05g3616 3616
5 44487751 44490973 - Sed0023124.1 Sed05g3617 3617
11 25677169 25681960 - Sed0023848.1 Sed11g1039 1039
2 7489517 7510368 - Tan0008899.1 Tan02g0784 784
2 7543791 7559197 - Tan0021616.1 Tan02g0785 785
2 88583807 88589795 - Tan0022426.1 Tan02g1978 1978
5 15105395 15107384 - Tan0009200.1 Tan05g1294 1294
5 15163066 15165284 - Tan0017400.1 Tan05g1295 1295
5 15163066 15165284 - Tan0017400.2 Tan05g1296 1296
5 15211732 15215004 - Tan0015183.1 Tan05g1297 1297
5 15292637 15307829 - Tan0000514.1 Tan05g1298 1298
3 3408621 3411094 + Vvi3g366 Vvi3g366 366
3 3412164 3417863 - Vvi3g367 Vvi3g367 367
3 3421313 3425591 - Vvi3g368 Vvi3g368 368
3 3430129 3433815 - Vvi3g369 Vvi3g369 369
3 3436868 3442629 - Vvi3g370 Vvi3g370 370
3 3451339 3455891 - Vvi3g371 Vvi3g371 371
3 3457457 3461294 - Vvi3g372 Vvi3g372 372
3 3461862 3463814 + Vvi3g373 Vvi3g373 373
3 3468311 3475880 + Vvi3g374 Vvi3g374 374
3 3477197 3481070 - Vvi3g375 Vvi3g375 375
       

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