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
Vvi4g442 . . Bda01g00732 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag1808 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g443 Blo01g01376 . Bda01g00733 . . Bpe02g00573 . . Cmo05g00414 Cmo12g00274 . Cma05g00403 . Car12g00304 Sed03g1593 Cpe07g00283 . Bhi04g01000 Tan02g2700 Cmetu03g2157 . Hepe10g0271 . Lcy13g1761 . . . . . . . Cone4ag1807 Cone7ag1715 . . . . . Cme03g01643 . . . . . . . . . . . . . . Car05g00337 Cpe11g00343 . . . . . . . . Cla08g01311 Cam08g1771 Cec08g1352 Cco08g1473 Clacu08g1467 . Cre08g1254 Lsi08g01175 . Chy03g01145 .
Vvi4g444 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g445 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1035 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g446 . . . . Bpe02g01238 . . . Cmo05g00413 Cmo12g00276 . Cma05g00402 . Car12g00307 . Cpe07g00284 . Bhi04g00994 . . . Hepe10g0270 . . . . . . . . . Cone4ag1806 Cone7ag1714 . . . . . Cme03g01642 Blo17g00026 Blo18g00035 Bda01g00993 . . . Bma01g01285 Bma02g00030 . . . . Cma12g00325 . Car05g00336 Cpe11g00342 . . . . . . . . Cla08g01312 Cam08g1772 Cec08g1354 Cco08g1474 Clacu08g1468 . Cre08g1255 Lsi08g01176 . Chy03g01144 .
Vvi4g447 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g448 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g449 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g450 . . . . . . . . Cmo05g00411 . . Cma05g00401 . Car12g00308 . Cpe07g00285 . Bhi04g00988 . . . . . . . . . . . . . Cone4ag1805 Cone7ag1713 Cone17ag1033 Cone20ag0662 . . . Cme03g01641 . . . Bda13g01269 Bpe14g00574 . . . . . . . Cma12g00326 . Car05g00335 Cpe11g00341 . . . . . . . . Cla08g01313 Cam08g1773 Cec08g1355 Cco08g1475 Clacu08g1469 . Cre08g1256 Lsi08g01177 . Chy03g01142 .
Vvi4g451 . . . . . . . . . . . Cma05g00400 . . . . . . . . . . . . . . . . . . . . . Cone17ag1032 Cone20ag0663 . . . . . . . . . . . . . . . . . . Car05g00334 . . . . . . . . . Cla08g01314 Cam08g1774 Cec08g1356 Cco08g1476 Clacu08g1470 . Cre08g1257 Lsi08g01178 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 34626310 34628841 - Bda002771.1 Bda01g00732 732
1 34629894 34634929 - Bda002772.1 Bda01g00733 733
1 43561205 43567688 + Bda003153.1 Bda01g00993 993
13 35054111 35056210 - Bda032809 Bda13g01269 1269
4 25135602 25141907 - XM_039030169.1 Bhi04g00988 988
4 25158357 25166969 - XM_039029806.1 Bhi04g00994 994
4 25194207 25202086 + XM_039028712.1 Bhi04g01000 1000
1 52018332 52022937 - BLOR01376 Blo01g01376 1376
17 138784 155800 - BLOR15847 Blo17g00026 26
18 229690 239721 - BLOR08523 Blo18g00035 35
1 17326086 17332225 - Bma001600.1 Bma01g01285 1285
2 323718 334667 - Bma014486.1 Bma02g00030 30
2 3699221 3704013 + Bpe008415.2 Bpe02g00573 573
2 15970800 15976833 + Bpe009097.1 Bpe02g01238 1238
14 4880325 4882368 + Bpe024986 Bpe14g00574 574
8 23938917 23945418 - CaPI482276_08g017710.1 Cam08g1771 1771
8 23953334 23960963 + CaPI482276_08g017720.1 Cam08g1772 1772
8 23969145 23973581 + CaPI482276_08g017730.1 Cam08g1773 1773
8 23974490 23979776 - CaPI482276_08g017740.1 Cam08g1774 1774
5 1915958 1921224 + Carg09325-RA Car05g00334 334
5 1921787 1925253 - Carg09324-RA Car05g00335 335
5 1928178 1934456 - Carg09323-RA Car05g00336 336
5 1935735 1944569 + Carg09322-RA Car05g00337 337
12 1987601 1990753 - Carg03911-RA Car12g00304 304
12 1995781 2002358 + Carg03914-RA Car12g00307 307
12 2006467 2010701 + Carg03915-RA Car12g00308 308
8 26584361 26590802 - CcPI632755_08g014730.1 Cco08g1473 1473
8 26599483 26606955 + CcPI632755_08g014740.1 Cco08g1474 1474
8 26614596 26619008 + CcPI632755_08g014750.1 Cco08g1475 1475
8 26619917 26625101 - CcPI632755_08g014760.1 Cco08g1476 1476
8 25449533 25461276 - CePI673135_08g013520.1 Cec08g1352 1352
8 25472549 25480270 + CePI673135_08g013540.1 Cec08g1354 1354
8 25488272 25492712 + CePI673135_08g013550.1 Cec08g1355 1355
8 25493608 25498895 - CePI673135_08g013560.1 Cec08g1356 1356
3 14685817 14690450 - Chy3G061220.1 Chy03g01142 1142
3 14700719 14704954 - Chy3G061240.1 Chy03g01144 1144
3 14707479 14714482 + Chy3G061250.1 Chy03g01145 1145
8 24689338 24695817 - ClG42_08g0146700.10 Clacu08g1467 1467
8 24704627 24712316 + ClG42_08g0146800.10 Clacu08g1468 1468
8 24720385 24724836 + ClG42_08g0146900.10 Clacu08g1469 1469
8 24725163 24731081 - ClG42_08g0147000.10 Clacu08g1470 1470
8 26013454 26020122 - ClCG08G013130.1 Cla08g01311 1311
8 26027462 26036441 + ClCG08G013140.1 Cla08g01312 1312
8 26043581 26049401 + ClCG08G013150.1 Cla08g01313 1313
8 26049978 26055291 - ClCG08G013160.2 Cla08g01314 1314
5 1738700 1744638 + CmaCh05G004000.1 Cma05g00400 400
5 1744661 1748649 - CmaCh05G004010.1 Cma05g00401 401
5 1751271 1758966 - CmaCh05G004020.1 Cma05g00402 402
5 1759613 1766935 + CmaCh05G004030.1 Cma05g00403 403
12 1661544 1668608 + CmaCh12G003250.1 Cma12g00325 325
12 1672438 1676950 + CmaCh12G003260.1 Cma12g00326 326
3 25224980 25229749 - MELO3C011237.2.1 Cme03g01641 1641
3 25236324 25243634 - MELO3C011236.2.1 Cme03g01642 1642
3 25246038 25254392 + MELO3C011235.2.1 Cme03g01643 1643
3 4160474 4167903 - PI0016280.1 Cmetu03g2157 2157
5 1883808 1887499 - CmoCh05G004110.1 Cmo05g00411 411
5 1892276 1897301 - CmoCh05G004130.1 Cmo05g00413 413
5 1898041 1905312 + CmoCh05G004140.1 Cmo05g00414 414
12 1756068 1759974 - CmoCh12G002740.1 Cmo12g00274 274
12 1764470 1780233 + CmoCh12G002760.1 Cmo12g00276 276
4 13094711 13096924 - Conep04aG0186400.1 Cone4ag1805 1805
4 13098215 13103991 - Conep04aG0186500.1 Cone4ag1806 1806
4 13104344 13107002 + Conep04aG0186600.1 Cone4ag1807 1807
4 13107601 13111071 + Conep04aG0186700.1 Cone4ag1808 1808
7 11394025 11396314 - Conep07aG0176600.1 Cone7ag1713 1713
7 11397704 11403450 - Conep07aG0176700.1 Cone7ag1714 1714
7 11403680 11406673 + Conep07aG0176800.1 Cone7ag1715 1715
17 7825791 7830179 + Conep17aG0106000.1 Cone17ag1032 1032
17 7830592 7836766 - Conep17aG0106100.1 Cone17ag1033 1033
17 7841288 7842906 - Conep17aG0106300.1 Cone17ag1035 1035
20 4041248 4043146 + Conep20aG0068300.1 Cone20ag0662 662
20 4043960 4048297 - Conep20aG0068400.1 Cone20ag0663 663
7 1864173 1870200 - Cp4.1LG07g02960.1 Cpe07g00283 283
7 1871644 1879785 + Cp4.1LG07g02870.1 Cpe07g00284 284
7 1883384 1888678 + Cp4.1LG07g02830.1 Cpe07g00285 285
11 1834494 1839138 - Cp4.1LG11g03450.1 Cpe11g00341 341
11 1842188 1849260 - Cp4.1LG11g03440.1 Cpe11g00342 342
11 1849788 1857914 + Cp4.1LG11g03360.1 Cpe11g00343 343
8 25738182 25744602 - CrPI670011_08g012540.1 Cre08g1254 1254
8 25753534 25761182 + CrPI670011_08g012550.1 Cre08g1255 1255
8 25769295 25773735 + CrPI670011_08g012560.1 Cre08g1256 1256
8 25774642 25779931 - CrPI670011_08g012570.1 Cre08g1257 1257
10 2793756 2802553 - Hsped.10g02700.1 Hepe10g0270 270
10 2805349 2810846 + Hsped.10g02710.1 Hepe10g0271 271
13 36541599 36549921 - Maker00033958 Lcy13g1761 1761
8 20362599 20371354 - Lsi08G011750.1 Lsi08g01175 1175
8 20374694 20383858 + Lsi08G011760.1 Lsi08g01176 1176
8 20392181 20396941 + Lsi08G011770.1 Lsi08g01177 1177
8 20397358 20402937 - Lsi08G011780.1 Lsi08g01178 1178
3 10118639 10125341 - Sed0010731.1 Sed03g1593 1593
2 95298252 95309893 - Tan0014121.1 Tan02g2700 2700
4 4539834 4544615 - Vvi4g442 Vvi4g442 442
4 4545233 4550231 - Vvi4g443 Vvi4g443 443
4 4553792 4556216 - Vvi4g444 Vvi4g444 444
4 4560586 4563264 + Vvi4g445 Vvi4g445 445
4 4564493 4575191 + Vvi4g446 Vvi4g446 446
4 4575191 4576673 + Vvi4g447 Vvi4g447 447
4 4580990 4585068 + Vvi4g448 Vvi4g448 448
4 4585357 4586699 - Vvi4g449 Vvi4g449 449
4 4590125 4595121 + Vvi4g450 Vvi4g450 450
4 4595143 4612704 - Vvi4g451 Vvi4g451 451
       

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