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
Vvi1g1371 . . . Bda11g00366 Bpe13g00839 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00366 . . . Bma06g01317 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1372 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1373 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00152 Cam06g0063 Cec06g0168 Cco06g0162 . Cmu06g0159 Cre06g0934 . . . . . . Chy11g01839 Cme11g02375 Blo02g00218 . . . . . . . Sed07g0982 . . . . . . Cpe17g00948 . Bhi12g02380 Tan06g1431 Cmetu06g0570 . . . . . . . . . . . Lsi09g01774 . . .
Vvi1g1374 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1375 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1376 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0637 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1377 . Blo16g00692 . Bda11g00363 Bpe13g00842 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone13ag0275 Cone19ag0259 . . . . Blo02g00221 . . Bda11g00363 Bpe14g00833 . . Bma06g01315 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1378 . Blo16g00691 . Bda11g00361 Bpe13g00844 . . . . . . . . . . . . . . . . . . . . . . . . . . Cone14ag0634 Cone15ag0646 . . . . . . . . . Bda11g00361 . . . Bma06g01313 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1379 . . . Bda11g00360 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g00360 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1380 . Blo16g00690 . . Bpe13g00845 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo02g00224 . . . . . . Bma06g01312 . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 3993448 3997517 + Bda005095.1 Bda11g00360 360
11 4004112 4006803 - Bda005096.1 Bda11g00361 361
11 4012611 4015980 - Bda005098.1 Bda11g00363 363
11 4035383 4036400 + Bda005102.1 Bda11g00366 366
12 75147820 75149198 + XM_039050556.1 Bhi12g02380 2380
2 2050192 2050607 + BLOR09948 Blo02g00218 218
2 2073955 2080449 + BLOR09951 Blo02g00221 221
2 2087145 2092305 - BLOR09954 Blo02g00224 224
16 26609407 26613473 + BLOR07938 Blo16g00690 690
16 26617404 26620327 - BLOR07939 Blo16g00691 691
16 26660089 26663393 - BLOR07940 Blo16g00692 692
6 50120991 50125000 + Bma024422.1 Bma06g01312 1312
6 50127492 50130129 - Bma024423.1 Bma06g01313 1313
6 50134955 50138949 - Bma024425.2 Bma06g01315 1315
6 50175929 50176940 + Bma024426.1 Bma06g01317 1317
13 14623360 14624368 - Bpe010529.1 Bpe13g00839 839
13 14640475 14643628 + Bpe010532.1 Bpe13g00842 842
13 14649163 14651958 + Bpe010534.1 Bpe13g00844 844
13 14655177 14659187 - Bpe010535.1 Bpe13g00845 845
14 6263114 6265609 + Bpe014210.1 Bpe14g00833 833
6 2488685 2493946 + CaPI482276_06g000630.1 Cam06g0063 63
6 1677776 1681247 - CcPI632755_06g001620.1 Cco06g0162 162
6 1706365 1708030 - CePI673135_06g001680.1 Cec06g0168 168
11 24719663 24720167 + Chy11G204190.1 Chy11g01839 1839
6 1722288 1723041 - ClCG06G001680.1 Cla06g00152 152
11 30712438 30714290 + MELO3C022364.2.1 Cme11g02375 2375
6 7496576 7497426 - PI0027682.1 Cmetu06g0570 570
6 1647520 1652856 - CmPI595203_06g001590.1 Cmu06g0159 159
13 1933697 1936681 + Conep13aG0028700.1 Cone13ag0275 275
14 3183434 3184792 - Conep14aG0064800.1 Cone14ag0634 634
14 3200945 3206343 - Conep14aG0065100.1 Cone14ag0637 637
15 3387904 3388218 - Conep15aG0065900.1 Cone15ag0646 646
19 1712830 1715861 + Conep19aG0026700.1 Cone19ag0259 259
17 7272151 7276762 + Cp4.1LG17g09470.1 Cpe17g00948 948
6 2749368 2750779 - CrPI670011_06g009340.1 Cre06g0934 934
9 26494253 26495163 + Lsi09G017740.1 Lsi09g01774 1774
7 7208273 7208900 + Sed0011159.1 Sed07g0982 982
6 18911206 18911996 - Tan0000109.1 Tan06g1431 1431
1 22724638 22728768 + Vvi1g1371 Vvi1g1371 1371
1 22732852 22736901 + Vvi1g1372 Vvi1g1372 1372
1 22737930 22739007 + Vvi1g1373 Vvi1g1373 1373
1 22739458 22746440 - Vvi1g1374 Vvi1g1374 1374
1 22748078 22755774 + Vvi1g1375 Vvi1g1375 1375
1 22756440 22763125 + Vvi1g1376 Vvi1g1376 1376
1 22768823 22774222 + Vvi1g1377 Vvi1g1377 1377
1 22777580 22797480 + Vvi1g1378 Vvi1g1378 1378
1 22798593 22814521 - Vvi1g1379 Vvi1g1379 1379
1 22815075 22819209 - Vvi1g1380 Vvi1g1380 1380
       

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