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
Vvi4g382 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g383 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g384 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy04g00335 . . . . . . Bpe04g00038 . . . . . Cma09g00486 . . . . . . . . . . . . . . . . . . . . . . Cme04g00374
Vvi4g385 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g386 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g387 . . . . . . . . . Cmo12g00252 . . . Car12g00283 . Cpe07g00259 . . . . . . . . . . . . . . . . . Cone17ag1059 . . . . . Blo17g00037 Blo18g00048 Bda01g00977 . Bpe14g00562 . . Bma02g00044 . . . . Cma12g00301 . . . . . . . . . . . . . . . . . . . . . .
Vvi4g388 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme04g00373
Vvi4g389 Blo01g01360 . Bda01g00720 . . . . Bma01g02148 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy04g00331 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme04g00372
Vvi4g390 . . Bda01g00719 . . . . Bma01g02147 . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag1741 . . . . Chy04g00329 Cme03g01673 . . . . . . . . . . . . . . . . . . . . . . . . Cla08g01282 Cam08g1740 Cec08g1322 Cco08g1443 Clacu08g1437 . Cre08g1224 Lsi08g01145 . . Cme04g00370
Vvi4g391 Blo01g01358 . Bda01g00718 . . . . Bma01g02146 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy04g00328 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme04g00369
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 34453723 34454453 - Bda002756.1 Bda01g00718 718
1 34477925 34479109 + Bda002757.1 Bda01g00719 719
1 34480854 34483136 - Bda002758.2 Bda01g00720 720
1 43368414 43369799 + Bda003135.1 Bda01g00977 977
1 51547884 51549889 - BLOR01358 Blo01g01358 1358
1 51674407 51678992 - BLOR01360 Blo01g01360 1360
17 220725 225359 - BLOR15858 Blo17g00037 37
18 320271 321767 - BLOR08536 Blo18g00048 48
1 77966553 77967294 - Bma002988.1 Bma01g02146 2146
1 77975415 77976599 + Bma002989.1 Bma01g02147 2147
1 77978920 77981190 - Bma002990.2 Bma01g02148 2148
2 405104 411011 - Bma014500.1 Bma02g00044 44
4 373898 379479 - Bpe014763.2 Bpe04g00038 38
14 4797051 4801557 + Bpe007211.1 Bpe14g00562 562
8 23673720 23675967 + CaPI482276_08g017400.1 Cam08g1740 1740
12 1866759 1868280 + Carg03890-RA Car12g00283 283
8 26313644 26315892 + CcPI632755_08g014430.1 Cco08g1443 1443
8 25174168 25176698 + CePI673135_08g013220.1 Cec08g1322 1322
4 2920908 2922663 - Chy4G070460.1 Chy04g00328 328
4 2939851 2941113 + Chy4G070470.1 Chy04g00329 329
4 2953836 2956754 - Chy4G070490.1 Chy04g00331 331
4 2974920 2980872 - Chy4G070530.1 Chy04g00335 335
8 24423858 24426123 + ClG42_08g0143700.10 Clacu08g1437 1437
8 25726252 25728806 + ClCG08G012840.1 Cla08g01282 1282
9 2176848 2183194 + CmaCh09G004860.1 Cma09g00486 486
12 1537773 1546539 + CmaCh12G003010.1 Cma12g00301 301
3 25466676 25469265 - MELO3C011209.2.1 Cme03g01673 1673
4 2923222 2925056 - MELO3C003657.2.1 Cme04g00369 369
4 2937116 2939975 + MELO3C003658.2.1 Cme04g00370 370
4 2948953 2954071 - MELO3C003660.2.1 Cme04g00372 372
4 2967029 2971196 - MELO3C003661.2.1 Cme04g00373 373
4 2972903 2979989 - MELO3C003662.2.1 Cme04g00374 374
12 1636967 1646578 + CmoCh12G002520.1 Cmo12g00252 252
7 11519548 11523938 - Conep07aG0179400.1 Cone7ag1741 1741
17 7954761 7956518 - Conep17aG0108700.1 Cone17ag1059 1059
7 1680996 1682336 + Cp4.1LG07g01890.1 Cpe07g00259 259
8 25467112 25469327 + CrPI670011_08g012240.1 Cre08g1224 1224
8 20091980 20094553 + Lsi08G011450.1 Lsi08g01145 1145
4 3796709 3800733 - Vvi4g382 Vvi4g382 382
4 3800994 3812258 - Vvi4g383 Vvi4g383 383
4 3814570 3816956 + Vvi4g384 Vvi4g384 384
4 3819307 3820674 + Vvi4g385 Vvi4g385 385
4 3829576 3830913 + Vvi4g386 Vvi4g386 386
4 3830984 3835172 - Vvi4g387 Vvi4g387 387
4 3843672 3850303 + Vvi4g388 Vvi4g388 388
4 3855436 3861860 + Vvi4g389 Vvi4g389 389
4 3865121 3866244 - Vvi4g390 Vvi4g390 390
4 3873221 3875153 + Vvi4g391 Vvi4g391 391
       

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