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
Vvi3g226 . . . . . . . . Cmo19g00776 Cmo11g01762 . . . . . Cpe04g00615 . Bhi05g01656 Tan02g0632 . . . . . . . . . . . . Cone12ag1254 Cone8ag1309 . . . Csa07g00140 . Cme01g01207 . . . . . . . Bma08g00585 . . . . Cma19g00763 . . . . . . . . . . . . . . . . . . Lsi11g01240 . Chy01g00646 Cme11g01172
Vvi3g227 . . . . . . . . . . . Cma20g00731 . Car20g00631 . . . . . . . . . . . . . . . . . Cone12ag1255 Cone8ag1310 . . . . . . . . . . . . . . . . Cmo20g00728 . . . . Cpe16g00336 . . . . . . . . Cla02g01083 Cam02g1161 Cec02g1159 Cco02g1207 Clacu02g1152 Cmu02g1114 Cre02g1418 . . . .
Vvi3g228 . . . . . . . . . . . Cma20g00720 . Car20g00621 . . . . . . . . . . . . . . . . . . . . . . . . . Blo04g00602 . . . . . . . Sed05g3003 . Cmo20g00718 . . Car11g01407 . Cpe16g00345 Cpe05g01342 Bhi10g01246 Tan05g1061 Cmetu10g1643 . . . . . . . . . . . . . . .
Vvi3g229 . . . . . . . . . . . Cma20g00719 . Car20g00620 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo20g00717 . . . . Cpe16g00346 Cpe05g01341 . . . . . . . . . . . . . . . . . .
Vvi3g230 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi10g01244 . . . . . . . . . . . . . . . . Cme11g01078
Vvi3g231 . . . . . . . . . . Cma02g00289 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi10g01243 . . . . . . . . . . . . . . . . .
Vvi3g232 . . . . . . . . . . Cma02g00290 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo02g00284 . . . . . . . Bhi10g01242 . . . Hepe08g0335 . . . . . . . . . . . . Cme11g01060
Vvi3g233 . . . . . . . . . . Cma02g00291 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed01g0637 Cmo02g00285 . . . . . . . Bhi10g01241 Tan05g1063 Cmetu02g1944 . . . . . . . . . . . . . . .
Vvi3g234 . . . . . . . . . . Cma02g00292 . Car02g00171 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo02g00286 . . . . . . . Bhi10g01240 Tan05g1064 . . Hepe08g0334 . . . . . . . . . . . . .
Vvi3g235 . Blo15g00431 Bda06g00437 . . . . . . . Cma02g00293 . Car02g00172 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sed05g3471 Cmo02g00287 . . . . . . . Bhi10g01237 Tan05g1065 Cmetu11g0158 . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 6437032 6439417 + Bda023682.1 Bda06g00437 437
5 54551723 54554490 + XM_039031533.1 Bhi05g01656 1656
10 27921359 27929361 - XM_039045528.1 Bhi10g01237 1237
10 28472387 28481761 + XM_039044516.1 Bhi10g01240 1240
10 28472387 28481569 + XM_039044517.1 Bhi10g01241 1241
10 28472388 28481761 + XM_039044515.1 Bhi10g01242 1242
10 28743218 28747962 + XM_039046234.1 Bhi10g01243 1243
10 28743219 28748062 + XM_039046233.1 Bhi10g01244 1244
10 28975028 28977591 - XM_039045622.1 Bhi10g01246 1246
4 5198894 5202821 - BLOR13514 Blo04g00602 602
15 6194219 6202068 - BLOR06825 Blo15g00431 431
8 36411673 36412573 + Bma027866.1 Bma08g00585 585
2 22686724 22695162 + CaPI482276_02g011610.1 Cam02g1161 1161
2 1015437 1036801 - Carg19760-RA Car02g00171 171
2 1036812 1039082 - Carg19761-RA Car02g00172 172
11 11533407 11537687 - Carg18123-RA Car11g01407 1407
20 3471161 3474262 - Carg16140-RA Car20g00620 620
20 3475534 3478400 - Carg16141-RA Car20g00621 621
20 3540370 3548483 + Carg16151-RA Car20g00631 631
2 22416795 22425341 + CcPI632755_02g012070.1 Cco02g1207 1207
2 27034371 27042911 + CePI673135_02g011590.1 Cec02g1159 1159
1 4546798 4549380 - Chy1G006460.1 Chy01g00646 646
2 22808183 22816715 + ClG42_02g0115200.10 Clacu02g1152 1152
2 22942418 22951254 + ClCG02G011090.2 Cla02g01083 1083
2 1348373 1352720 - CmaCh02G002890.1 Cma02g00289 289
2 1354075 1357415 - CmaCh02G002900.1 Cma02g00290 290
2 1358732 1362414 - CmaCh02G002910.1 Cma02g00291 291
2 1366250 1367922 - CmaCh02G002920.1 Cma02g00292 292
2 1367977 1373835 - CmaCh02G002930.1 Cma02g00293 293
19 7554904 7557366 - CmaCh19G007630.1 Cma19g00763 763
20 3326383 3329388 - CmaCh20G007190.1 Cma20g00719 719
20 3330493 3333575 - CmaCh20G007200.1 Cma20g00720 720
20 3399023 3407499 + CmaCh20G007310.1 Cma20g00731 731
1 15280987 15283334 + MELO3C013313.2.1 Cme01g01207 1207
11 15640213 15646141 + MELO3C013512.2.1 Cme11g01060 1060
11 15908163 15915018 + MELO3C034758.2.1 Cme11g01078 1078
11 17829136 17830624 + MELO3C013600.2.1 Cme11g01172 1172
2 20322613 20327036 - PI0017806.1 Cmetu02g1944 1944
10 11008520 11011105 - PI0027881.1 Cmetu10g1643 1643
11 11178483 11186783 + PI0028207.1 Cmetu11g0158 158
2 1403337 1407910 - CmoCh02G002840.1 Cmo02g00284 284
2 1410004 1413419 - CmoCh02G002850.1 Cmo02g00285 285
2 1414493 1418825 - CmoCh02G002860.1 Cmo02g00286 286
2 1424176 1427905 - CmoCh02G002870.1 Cmo02g00287 287
11 12425640 12427018 - CmoCh11G017620.1 Cmo11g01762 1762
19 7821992 7824428 - CmoCh19G007760.1 Cmo19g00776 776
20 3528783 3532315 - CmoCh20G007170.1 Cmo20g00717 717
20 3533427 3536584 - CmoCh20G007180.1 Cmo20g00718 718
20 3600462 3609113 + CmoCh20G007280.1 Cmo20g00728 728
2 22672110 22680645 + CmPI595203_02g011140.1 Cmu02g1114 1114
8 10655434 10656616 - Conep08aG0134800.1 Cone8ag1309 1309
8 10658646 10662701 - Conep08aG0134900.1 Cone8ag1310 1310
12 9658169 9658889 - Conep12aG0129500.1 Cone12ag1254 1254
12 9660071 9665891 - Conep12aG0129600.1 Cone12ag1255 1255
4 6394727 6395953 - Cp4.1LG04g04650.1 Cpe04g00615 615
5 9439065 9442834 - Cp4.1LG05g13400.1 Cpe05g01341 1341
5 9444374 9446567 - Cp4.1LG05g13410.1 Cpe05g01342 1342
16 5162832 5170873 - Cp4.1LG16g03380.1 Cpe16g00336 336
16 5233611 5236612 + Cp4.1LG16g03480.1 Cpe16g00345 345
16 5237850 5241121 + Cp4.1LG16g03490.1 Cpe16g00346 346
2 24699569 24708110 + CrPI670011_02g014180.1 Cre02g1418 1418
7 1240827 1242787 + CsaV3_7G001400.1 Csa07g00140 140
8 3015949 3022492 - Hsped.08g03340.1 Hepe08g0334 334
8 3023101 3028249 - Hsped.08g03350.1 Hepe08g0335 335
11 21038133 21040644 - Lsi11G012400.1 Lsi11g01240 1240
1 4596017 4608517 + Sed0008674.1 Sed01g0637 637
5 40614735 40617172 + Sed0014704.1 Sed05g3003 3003
5 43509662 43515813 + Sed0006573.1 Sed05g3471 3471
2 5823879 5826054 + Tan0008242.1 Tan02g0632 632
5 8961932 8964424 - Tan0011728.1 Tan05g1061 1061
5 9028964 9038308 + Tan0003351.1 Tan05g1063 1063
5 9092467 9107786 + Tan0019880.1 Tan05g1064 1064
5 9170559 9188921 + Tan0007843.1 Tan05g1065 1065
3 2208256 2209744 - Vvi3g226 Vvi3g226 226
3 2213051 2224945 - Vvi3g227 Vvi3g227 227
3 2225336 2228568 + Vvi3g228 Vvi3g228 228
3 2231718 2242474 + Vvi3g229 Vvi3g229 229
3 2246283 2248846 + Vvi3g230 Vvi3g230 230
3 2253366 2255550 + Vvi3g231 Vvi3g231 231
3 2267330 2269351 + Vvi3g232 Vvi3g232 232
3 2281235 2297938 + Vvi3g233 Vvi3g233 233
3 2298504 2300506 + Vvi3g234 Vvi3g234 234
3 2307661 2312585 + Vvi3g235 Vvi3g235 235
       

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