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
Vvi3g336 Blo02g00838 Blo15g00710 . Bda08g00946 Bpe07g00415 . Bma05g00435 Bma12g00496 . . Cma02g00376 Cma20g00825 Car02g00243 Car20g00711 . . . . . . . . . . . . . . . . . . . . . Lsi10g00399 . Chy11g00352 . . . . . . . . . Sed01g0281 Cmo02g00383 Cmo20g00836 . . . . Cpe16g00263 Cpe05g01278 Bhi10g01969 Tan05g1264 Cmetu11g1045 . Hepe08g0992 . . . . . . . . . . Csa02g01289 . Cme11g00143
Vvi3g337 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g338 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g339 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g340 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g341 . . . . . . . . . . . Cma20g00827 . Car20g00712 . . . . . . . . . . . . . . . . . Cone12ag1167 Cone8ag1215 . . Lsi10g00398 . Chy11g00353 . Blo04g00524 . . . . . . . Sed01g0282 . Cmo20g00837 . . . . Cpe16g00262 . Bhi10g01970 Tan05g1265 Cmetu11g1211 . Hepe08g0993 . . . . . . . . . . Csa02g01288 . Cme11g00142
Vvi3g342 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g343 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g344 . . . . Bpe07g00416 . . Bma12g00499 . . Cma02g00378 Cma20g00829 Car02g00245 Car20g00714 Sed05g2310 . . Bhi05g01247 Tan02g0782 Cmetu01g1358 . . . . . . . . . . . . . . . Lsi10g00395 . Chy11g00356 . Blo04g00522 . Bda15g00059 . . . . . Sed01g0284 Cmo02g00384 . . . . . Cpe16g00260 Cpe05g01277 Bhi10g01975 Tan05g1268 Cmetu11g0620 . Hepe08g0995 . . . . . . . . . . Csa02g01285 . Cme11g00139
Vvi3g345 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 17754969 17759703 - Bda029592.1 Bda08g00946 946
15 2153339 2155112 - Bda011826.2 Bda15g00059 59
5 45295517 45298752 + XM_039031764.1 Bhi05g01247 1247
10 49027716 49036038 + XM_039044388.1 Bhi10g01969 1969
10 49037377 49043303 - XM_039044389.1 Bhi10g01970 1970
10 49076202 49080903 - XM_039045816.1 Bhi10g01975 1975
2 30947685 30948403 + BLOR10568 Blo02g00838 838
4 4520810 4522957 + BLOR13434 Blo04g00522 522
4 4526238 4528626 + BLOR13436 Blo04g00524 524
15 22998955 23003653 - BLOR07104 Blo15g00710 710
5 14516402 14521151 + Bma021285.1 Bma05g00435 435
12 14904169 14906252 + Bma007543.1 Bma12g00496 496
12 14993381 14995052 - Bma007547.1 Bma12g00499 499
7 4184478 4189170 + Bpe021237.3 Bpe07g00415 415
7 4242597 4244292 - Bpe021238.1 Bpe07g00416 416
2 1646489 1654082 + Carg24147-RA Car02g00243 243
2 1655022 1658153 - Carg24149-RA Car02g00245 245
20 4104139 4111988 + Carg26793-RA Car20g00711 711
20 4112482 4117083 - Carg26792-RA Car20g00712 712
20 4120384 4124132 - Carg26790-RA Car20g00714 714
11 3222199 3230762 + Chy11G189320.1 Chy11g00352 352
11 3231400 3235833 - Chy11G189330.1 Chy11g00353 353
11 3255038 3258056 - Chy11G189360.1 Chy11g00356 356
2 1895077 1901889 + CmaCh02G003760.1 Cma02g00376 376
2 1903314 1910319 - CmaCh02G003780.1 Cma02g00378 378
20 3926872 3934851 + CmaCh20G008250.1 Cma20g00825 825
20 3935895 3940840 - CmaCh20G008270.1 Cma20g00827 827
20 3943916 3948897 - CmaCh20G008290.1 Cma20g00829 829
11 1426924 1431573 + MELO3C023321.2.1 Cme11g00139 139
11 1445054 1450754 + MELO3C023324.2.1 Cme11g00142 142
11 1449739 1459209 - MELO3C023325.2.1 Cme11g00143 143
1 5914174 5916236 - PI0016059.1 Cmetu01g1358 1358
11 27715942 27720605 + PI0003751.1 Cmetu11g0620 620
11 27736767 27746797 - PI0022821.1 Cmetu11g1045 1045
11 27731341 27736120 + PI0008580.1 Cmetu11g1211 1211
2 1960185 1968384 + CmoCh02G003830.1 Cmo02g00383 383
2 1969171 1972690 - CmoCh02G003840.1 Cmo02g00384 384
20 4169755 4177633 + CmoCh20G008360.1 Cmo20g00836 836
20 4178136 4187836 - CmoCh20G008370.1 Cmo20g00837 837
8 10304042 10306455 + Conep08aG0125200.1 Cone8ag1215 1215
12 9272080 9274132 + Conep12aG0120600.1 Cone12ag1167 1167
5 8914985 8918267 + Cp4.1LG05g12740.1 Cpe05g01277 1277
5 8919056 8926276 - Cp4.1LG05g12780.1 Cpe05g01278 1278
16 4619644 4624816 + Cp4.1LG16g02610.1 Cpe16g00260 260
16 4628618 4633515 + Cp4.1LG16g02650.1 Cpe16g00262 262
16 4633855 4641709 - Cp4.1LG16g02700.1 Cpe16g00263 263
2 12524603 12529607 + CsaV3_2G015010.1 Csa02g01285 1285
2 12540497 12546100 + CsaV3_2G015040.1 Csa02g01288 1288
2 12545593 12555095 - CsaV3_2G015050.1 Csa02g01289 1289
8 9401718 9408567 + Hsped.08g09920.1 Hepe08g0992 992
8 9409599 9414601 - Hsped.08g09930.1 Hepe08g0993 993
8 9420579 9425593 - Hsped.08g09950.1 Hepe08g0995 995
10 6045914 6048893 + Lsi10G003950.1 Lsi10g00395 395
10 6062696 6068050 + Lsi10G003980.1 Lsi10g00398 398
10 6069494 6084679 - Lsi10G003990.1 Lsi10g00399 399
1 2155271 2162956 + Sed0019695.3 Sed01g0281 281
1 2163553 2169692 - Sed0009940.1 Sed01g0282 282
1 2173225 2177744 - Sed0002025.1 Sed01g0284 284
5 35567154 35569268 - Sed0016001.1 Sed05g2310 2310
2 7444629 7449096 - Tan0021793.4 Tan02g0782 782
5 13741849 13748084 + Tan0014584.3 Tan05g1264 1264
5 13750724 13754613 - Tan0020831.1 Tan05g1265 1265
5 13927380 13931550 - Tan0003158.1 Tan05g1268 1268
3 3142871 3151289 + Vvi3g336 Vvi3g336 336
3 3151786 3152495 - Vvi3g337 Vvi3g337 337
3 3154243 3156674 + Vvi3g338 Vvi3g338 338
3 3158671 3165038 + Vvi3g339 Vvi3g339 339
3 3165258 3173838 - Vvi3g340 Vvi3g340 340
3 3176214 3181195 - Vvi3g341 Vvi3g341 341
3 3181820 3183254 + Vvi3g342 Vvi3g342 342
3 3186255 3187245 - Vvi3g343 Vvi3g343 343
3 3189940 3193848 - Vvi3g344 Vvi3g344 344
3 3201264 3203036 - Vvi3g345 Vvi3g345 345
       

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