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
Vvi1g1341 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00159 . . . . . . Cone14ag0652 Cone15ag0664 . . . Csa04g00228 Chy11g01830 Cme11g02366 . . . . . . . Bma06g01329 . . . . . . . . Cpe03g01179 Bhi12g02390 . . . . . . . . . . . . . Lsi09g01767 . Chy07g01542 Cme07g01988
Vvi1g1342 . . . Bda11g00373 Bpe13g00827 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00226 . . Blo02g00208 . . Bda11g00373 Bpe14g00814 . . Bma06g01328 . . . . . . . . Cpe03g01178 . . . . . . . . . . . . . . . . Chy07g01544 Cme07g01989
Vvi1g1343 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1344 . . . . . . . . . . . . . . . . . . . . . . . . Cla06g00158 Cam06g0057 Cec06g0175 Cco06g0169 Clacu06g0169 Cmu06g0165 Cre06g0940 . . . . . . Chy11g01831 Cme11g02367 . Blo12g00294 . . . . . . Sed06g0273 . . . . . . Cpe17g00943 . Bhi12g02389 Tan06g1441 Cmetu10g1400 . Hepe03g1174 . . . . . . . . . Lsi09g01768 . . .
Vvi1g1345 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1346 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1347 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1348 Blo01g00156 . . . . . . . . . . . . . . . . . . . . . . . Cla06g00157 Cam06g0059 Cec06g0173 Cco06g0168 Clacu06g0167 Cmu06g0163 Cre06g0939 Cone14ag0649 Cone15ag0659 . . . . Chy11g01832 Cme11g02368 . . . . . . . . Sed09g0339 . . . . . . Cpe17g00944 . Bhi12g02387 Tan06g1439 Cmetu11g1451 . Hepe03g1175 . . . . . . . . . Lsi09g01769 . . .
Vvi1g1349 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa04g00225 . . . . . . . . . . . . . . . . . . Cpe03g01177 . . . . . . . . . . . . . . . . Chy07g01545 Cme07g01990
Vvi1g1350 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone15ag0657 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
11 4099611 4110556 + Bda005111.1 Bda11g00373 373
12 75414632 75423882 - XM_039020357.1 Bhi12g02387 2387
12 75464016 75466809 + XM_039020164.1 Bhi12g02389 2389
12 75489427 75491522 + XM_039050857.1 Bhi12g02390 2390
1 2129098 2135884 + BLOR00156 Blo01g00156 156
2 1905689 1916927 - BLOR09938 Blo02g00208 208
12 17360239 17361916 + BLOR04313 Blo12g00294 294
6 50248891 50260398 + Bma024439.1 Bma06g01328 1328
6 50262148 50269595 + Bma024440.1 Bma06g01329 1329
13 14547461 14558117 - Bpe025249 Bpe13g00827 827
14 6138522 6148741 - Bpe014191.1 Bpe14g00814 814
6 2425891 2428024 - CaPI482276_06g000570.1 Cam06g0057 57
6 2446525 2453912 + CaPI482276_06g000590.1 Cam06g0059 59
6 1719877 1727197 - CcPI632755_06g001680.1 Cco06g0168 168
6 1745410 1747544 + CcPI632755_06g001690.1 Cco06g0169 169
6 1746653 1754038 - CePI673135_06g001730.1 Cec06g0173 173
6 1772642 1774776 + CePI673135_06g001750.1 Cec06g0175 175
7 19666562 19668437 - Chy7G143720.1 Chy07g01542 1542
7 19670257 19683659 - Chy7G143740.1 Chy07g01544 1544
7 19694621 19698960 - Chy7G143750.1 Chy07g01545 1545
11 24658353 24661333 - Chy11G204100.1 Chy11g01830 1830
11 24665080 24667119 - Chy11G204110.1 Chy11g01831 1831
11 24676839 24685756 + Chy11G204120.1 Chy11g01832 1832
6 1892160 1899554 - ClG42_06g0016700.10 Clacu06g0167 167
6 1917979 1920112 + ClG42_06g0016900.10 Clacu06g0169 169
6 1762811 1771522 - ClCG06G001730.2 Cla06g00157 157
6 1791448 1794235 + ClCG06G001740.1 Cla06g00158 158
6 1797604 1802801 + ClCG06G001750.2 Cla06g00159 159
7 24985937 24988587 - MELO3C017812.2.1 Cme07g01988 1988
7 24989258 25003409 - MELO3C017813.2.1 Cme07g01989 1989
7 25014630 25020678 - MELO3C017814.2.1 Cme07g01990 1990
11 30645231 30646819 - MELO3C022355.2.1 Cme11g02366 2366
11 30650125 30652863 - MELO3C022356.2.1 Cme11g02367 2367
11 30664878 30673374 + MELO3C022357.2.1 Cme11g02368 2368
10 10397613 10408158 + PI0004704.1 Cmetu10g1400 1400
11 1374601 1381485 - PI0003852.1 Cmetu11g1451 1451
6 1687517 1694908 - CmPI595203_06g001630.1 Cmu06g0163 163
6 1713341 1715474 + CmPI595203_06g001650.1 Cmu06g0165 165
14 3252699 3260201 - Conep14aG0066300.1 Cone14ag0649 649
14 3277702 3279205 + Conep14aG0066600.1 Cone14ag0652 652
15 3445803 3448178 - Conep15aG0067000.1 Cone15ag0657 657
15 3452258 3458796 - Conep15aG0067200.1 Cone15ag0659 659
15 3482693 3485581 + Conep15aG0067700.1 Cone15ag0664 664
3 9637966 9643350 + Cp4.1LG03g13380.1 Cpe03g01177 1177
3 9646363 9656771 + Cp4.1LG03g13390.1 Cpe03g01178 1178
3 9656983 9660521 + Cp4.1LG03g13400.1 Cpe03g01179 1179
17 7242980 7245727 - Cp4.1LG17g09540.1 Cpe17g00943 943
17 7250975 7259758 + Cp4.1LG17g09420.1 Cpe17g00944 944
6 2789913 2797289 - CrPI670011_06g009390.1 Cre06g0939 939
6 2815622 2817756 + CrPI670011_06g009400.1 Cre06g0940 940
4 1342718 1349059 + CsaV3_4G002250.1 Csa04g00225 225
4 1357655 1371168 + CsaV3_4G002260.1 Csa04g00226 226
4 1372960 1374834 + CsaV3_4G002280.1 Csa04g00228 228
3 65350949 65353571 - Hsped.03g11740.1 Hepe03g1174 1174
3 65401378 65409459 + Hsped.03g11750.1 Hepe03g1175 1175
9 26417938 26420376 - Lsi09G017670.1 Lsi09g01767 1767
9 26424891 26427809 - Lsi09G017680.1 Lsi09g01768 1768
9 26445413 26454528 + Lsi09G017690.1 Lsi09g01769 1769
6 2297785 2304325 + Sed0022566.1 Sed06g0273 273
9 3071159 3080277 + Sed0023962.2 Sed09g0339 339
6 19271257 19280228 - Tan0016414.2 Tan06g1439 1439
6 19306930 19309839 + Tan0020024.2 Tan06g1441 1441
1 22414828 22417602 - Vvi1g1341 Vvi1g1341 1341
1 22419937 22442311 - Vvi1g1342 Vvi1g1342 1342
1 22452108 22456182 + Vvi1g1343 Vvi1g1343 1343
1 22456616 22459058 - Vvi1g1344 Vvi1g1344 1344
1 22467217 22468254 + Vvi1g1345 Vvi1g1345 1345
1 22469074 22482650 - Vvi1g1346 Vvi1g1346 1346
1 22490169 22493936 - Vvi1g1347 Vvi1g1347 1347
1 22510169 22524870 + Vvi1g1348 Vvi1g1348 1348
1 22527462 22544554 - Vvi1g1349 Vvi1g1349 1349
1 22547028 22561957 + Vvi1g1350 Vvi1g1350 1350
       

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