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
Vvi3g566 . . . . . . . . Cmo19g00665 . Cma02g00412 . Car02g00270 . Sed04g3529 . Cpe15g00529 Bhi05g01212 Tan02g0822 Cmetu01g1993 . Hepe02g0524 . . Cla02g00536 Cam02g0555 Cec02g0557 Cco02g0568 Clacu02g0556 Cmu02g0553 Cre02g0884 . . . . Lsi10g00351 . Chy11g00398 Cme01g01443 Blo04g00504 . . Bda14g00543 Bpe15g00873 . Bma03g00544 . . Cmo02g00416 . . Cma19g00655 . Car19g00498 . Cpe05g01247 Bhi10g02033 Tan05g1328 Cmetu11g1857 . . . . . . . . . . . Lsi11g01085 Csa02g01239 Chy01g00803 .
Vvi3g567 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g568 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone10ag1162 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g569 . . . Bda08g00901 . . Bma05g00475 . . . Cma02g00409 . Car02g00268 . . . . . . . . . . . . . . . . . . . . . . Lsi10g00353 . Chy11g00395 . . . . . . . . . . Cmo02g00413 . . . . . . Cpe05g01249 Bhi10g02028 Tan05g1325 Cmetu11g1874 . Hepe08g1028 . . . . . . . . . . Csa02g01243 . .
Vvi3g570 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g571 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g572 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g573 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone3ag1155 Cone10ag1163 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g574 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g575 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 16407422 16410632 + Bda029519.1 Bda08g00901 901
14 3963963 3981658 - Bda027289.2 Bda14g00543 543
5 43200966 43220607 - XM_039031775.1 Bhi05g01212 1212
10 50766609 50770352 - XM_039046909.1 Bhi10g02028 2028
10 50806995 50830638 + XM_039046994.1 Bhi10g02033 2033
4 4240846 4257264 - BLOR13416 Blo04g00504 504
3 4440739 4458402 - Bma016830.1 Bma03g00544 544
5 17762557 17765870 - Bma021371.1 Bma05g00475 475
15 18689386 18711711 + Bpe001795.2 Bpe15g00873 873
2 6356520 6377243 + CaPI482276_02g005550.1 Cam02g0555 555
2 1816775 1820827 - Carg22953-RA Car02g00268 268
2 1825222 1840407 + Carg22955-RA Car02g00270 270
19 6560580 6580407 - Carg22025-RA Car19g00498 498
2 5466325 5486993 + CcPI632755_02g005680.1 Cco02g0568 568
2 5389981 5409295 + CePI673135_02g005570.1 Cec02g0557 557
1 6538355 6569668 + Chy1G008030.1 Chy01g00803 803
11 3740254 3744672 - Chy11G189750.1 Chy11g00395 395
11 3759639 3782846 + Chy11G189780.1 Chy11g00398 398
2 5324576 5345269 + ClG42_02g0055600.10 Clacu02g0556 556
2 5581725 5605253 + ClCG02G005170.2 Cla02g00536 536
2 2063992 2067875 - CmaCh02G004090.1 Cma02g00409 409
2 2072534 2089254 + CmaCh02G004120.1 Cma02g00412 412
19 6895461 6915342 - CmaCh19G006550.1 Cma19g00655 655
1 18547235 18564982 + MELO3C012545.2.1 Cme01g01443 1443
1 6570923 6595292 + PI0013678.1 Cmetu01g1993 1993
11 27268514 27275434 - PI0012771.1 Cmetu11g1857 1857
11 27289866 27294264 + PI0002890.1 Cmetu11g1874 1874
2 2134974 2138994 - CmoCh02G004130.1 Cmo02g00413 413
2 2144326 2161977 + CmoCh02G004160.1 Cmo02g00416 416
19 7123884 7144220 - CmoCh19G006650.1 Cmo19g00665 665
2 5242798 5263487 + CmPI595203_02g005530.1 Cmu02g0553 553
3 30170016 30171205 - Conep03aG0166000.1 Cone3ag1155 1155
10 8427730 8430883 + Conep10aG0119600.1 Cone10ag1162 1162
10 8436040 8437254 - Conep10aG0119700.1 Cone10ag1163 1163
5 8727150 8743377 - Cp4.1LG05g12450.1 Cpe05g01247 1247
5 8747306 8754292 + Cp4.1LG05g12410.1 Cpe05g01249 1249
15 6173046 6192856 - Cp4.1LG15g05360.1 Cpe15g00529 529
2 5850508 5865500 + CrPI670011_02g008840.1 Cre02g0884 884
2 12147983 12166274 - CsaV3_2G014550.1 Csa02g01239 1239
2 12178556 12183454 + CsaV3_2G014590.1 Csa02g01243 1243
2 5261641 5278293 + Hsped.02g05240.1 Hepe02g0524 524
8 9872173 9876392 - Hsped.08g10280.1 Hepe08g1028 1028
10 5485012 5504602 - Lsi10G003510.1 Lsi10g00351 351
10 5525270 5529276 + Lsi10G003530.1 Lsi10g00353 353
11 18928167 18950144 - Lsi11G010850.1 Lsi11g01085 1085
4 44705642 44731879 - Sed0019364.1 Sed04g3529 3529
2 8613155 8641960 + Tan0004730.1 Tan02g0822 822
5 16729575 16734782 - Tan0011672.1 Tan05g1325 1325
5 16919520 16995038 + Tan0016623.1 Tan05g1328 1328
3 5494121 5528939 - Vvi3g566 Vvi3g566 566
3 5536346 5538415 + Vvi3g567 Vvi3g567 567
3 5548049 5553974 + Vvi3g568 Vvi3g568 568
3 5554222 5560456 - Vvi3g569 Vvi3g569 569
3 5563522 5567438 + Vvi3g570 Vvi3g570 570
3 5578027 5578995 + Vvi3g571 Vvi3g571 571
3 5579523 5580226 + Vvi3g572 Vvi3g572 572
3 5580251 5581364 - Vvi3g573 Vvi3g573 573
3 5581838 5591761 + Vvi3g574 Vvi3g574 574
3 5599271 5602934 + Vvi3g575 Vvi3g575 575
       

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