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
Vvi4g392 Blo01g01357 . Bda01g00717 . . . . Bma01g02145 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy04g00327 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme04g00367
Vvi4g393 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone7ag1743 . . . . Chy04g00326 . . . . . . Bpe04g00036 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme04g00365
Vvi4g394 Blo01g01356 . Bda01g00716 . . . . Bma01g02144 . . Cma01g01543 . Car09g00435 . . . Cpe06g00371 . . . . . . . . . . . . . . . Cone7ag1744 . . Lsi04g02172 Csa03g04378 Chy04g00324 . . . . . . . . . . Cmo01g01593 Cmo09g00497 . . Car01g01172 . . . . . . . . . . . . . . . . . . . . Cme04g00364
Vvi4g395 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g396 . . . . . . . . . . . . . . Sed03g1501 . . Bhi04g00813 Tan02g2584 Cmetu03g0483 . Hepe10g0339 . Lcy13g1384 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car05g00552 . . . . . . . . . . . . . . . . . . Chy03g01227 .
Vvi4g397 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g398 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g399 . . . . . . . . Cmo05g00419 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car05g00342 Cpe11g00347 . . . . . . . . . . . . . . . . . . .
Vvi4g400 . . . . Bpe02g01199 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma01g01329 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g401 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 34439843 34443518 - Bda002754.1 Bda01g00716 716
1 34445562 34451810 + Bda002755.1 Bda01g00717 717
4 20569730 20578652 + XM_039029650.1 Bhi04g00813 813
1 51525431 51529057 - BLOR01356 Blo01g01356 1356
1 51536529 51547663 + BLOR01357 Blo01g01357 1357
1 18192951 18194591 - Bma001648.1 Bma01g01329 1329
1 77954217 77957918 - Bma002986.1 Bma01g02144 2144
1 77959850 77966386 + Bma002987.1 Bma01g02145 2145
2 15711383 15713023 + Bpe009059.3 Bpe02g01199 1199
4 325604 354929 + Bpe014759.1 Bpe04g00036 36
1 10945730 10953529 + Carg21152-RA Car01g01172 1172
5 1969563 1970075 + Carg09317-RA Car05g00342 342
5 3242194 3244242 - Carg08295-RA Car05g00552 552
9 2435945 2441604 + Carg02916-RA Car09g00435 435
3 15355699 15357403 + Chy3G062070.1 Chy03g01227 1227
4 2854997 2860325 - Chy4G070420.1 Chy04g00324 324
4 2899541 2907751 + Chy4G070440.1 Chy04g00326 326
4 2913339 2920746 + Chy4G070450.1 Chy04g00327 327
1 10773625 10779662 + CmaCh01G015430.1 Cma01g01543 1543
4 2870061 2877100 - MELO3C003652.2.1 Cme04g00364 364
4 2879050 2911116 + MELO3C003655.2.1 Cme04g00365 365
4 2916235 2919710 + MELO3C003656.2.1 Cme04g00367 367
3 3636724 3638719 - PI0008071.1 Cmetu03g0483 483
1 12227163 12232501 + CmoCh01G015930.1 Cmo01g01593 1593
5 1930417 1932020 + CmoCh05G004190.1 Cmo05g00419 419
9 2309124 2314737 + CmoCh09G004970.1 Cmo09g00497 497
7 11531235 11549842 - Conep07aG0179600.1 Cone7ag1743 1743
7 11550622 11553753 + Conep07aG0179700.1 Cone7ag1744 1744
6 2101530 2107443 + Cp4.1LG06g03610.1 Cpe06g00371 371
11 1883599 1884693 + Cp4.1LG11g03350.1 Cpe11g00347 347
3 38242671 38248639 + CsaV3_3G046840.1 Csa03g04378 4378
10 3642697 3645973 + Hsped.10g03390.1 Hepe10g0339 339
13 31992980 31995188 + Maker00025574 Lcy13g1384 1384
4 28792004 28803730 + Lsi04G021720.1 Lsi04g02172 2172
3 9600997 9603300 - Sed0000644.2 Sed03g1501 1501
2 94510540 94512724 - Tan0010298.1 Tan02g2584 2584
4 3875332 3885838 - Vvi4g392 Vvi4g392 392
4 3888014 3967707 - Vvi4g393 Vvi4g393 393
4 3971722 3977416 + Vvi4g394 Vvi4g394 394
4 3982692 3982800 + Vvi4g395 Vvi4g395 395
4 3992667 4000655 + Vvi4g396 Vvi4g396 396
4 4015550 4016530 + Vvi4g397 Vvi4g397 397
4 4031893 4032929 + Vvi4g398 Vvi4g398 398
4 4056575 4057713 + Vvi4g399 Vvi4g399 399
4 4058297 4065804 - Vvi4g400 Vvi4g400 400
4 4066502 4066983 + Vvi4g401 Vvi4g401 401
       

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