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
Vvi4g402 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bma01g01328 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g403 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g404 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g405 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone4ag0697 Cone7ag0657 . . . . . Blo18g00037 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy03g01152 .
Vvi4g406 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g407 . . . . . . . . Cmo05g00705 . . Cma05g00672 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe11g00597 . . . . . . . . . . . . . . . . . . .
Vvi4g408 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g409 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g410 . . . . . Bpe02g00578 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cpe02g00464 Bhi09g02274 . . . . . . . . . . . . . . . . .
Vvi4g411 . Blo12g01086 . . . . . . . . . . . . . . . . . . . . . . Cla05g01760 Cam05g1875 Cec05g1887 Cco05g1951 Clacu05g1867 Cmu05g1748 Cre05g1877 Cone4ag1815 Cone7ag1724 . . . . . . . . . . . . . . . . . . . . . . Cpe02g00465 . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
9 63535396 63546203 - XM_039042037.1 Bhi09g02274 2274
12 28530262 28531437 + BLOR05105 Blo12g01086 1086
18 255200 255523 + BLOR08525 Blo18g00037 37
1 18173621 18175072 - Bma001647.1 Bma01g01328 1328
2 3730633 3737414 - Bpe008420.1 Bpe02g00578 578
5 27679117 27681204 - CaPI482276_05g018750.1 Cam05g1875 1875
5 28561458 28577367 - CcPI632755_05g019510.1 Cco05g1951 1951
5 30916354 30920873 - CePI673135_05g018870.1 Cec05g1887 1887
3 14761814 14762354 + Chy3G061320.1 Chy03g01152 1152
5 27875752 27877838 - ClG42_05g0186700.10 Clacu05g1867 1867
5 29424675 29429488 - ClCG05G017170.2 Cla05g01760 1760
5 3457860 3461191 - CmaCh05G006720.1 Cma05g00672 672
5 3620563 3623533 - CmoCh05G007050.1 Cmo05g00705 705
5 27593973 27596059 - CmPI595203_05g017480.1 Cmu05g1748 1748
4 3559985 3560797 - Conep04aG0072600.1 Cone4ag0697 697
4 13133731 13135069 + Conep04aG0187400.1 Cone4ag1815 1815
7 3438176 3438955 - Conep07aG0068000.1 Cone7ag0657 657
7 11428078 11429588 + Conep07aG0177700.1 Cone7ag1724 1724
2 2627065 2635615 - Cp4.1LG02g04150.1 Cpe02g00464 464
2 2637304 2640032 + Cp4.1LG02g04060.1 Cpe02g00465 465
11 3575328 3579319 - Cp4.1LG11g05970.1 Cpe11g00597 597
5 30912125 30916611 - CrPI670011_05g018770.1 Cre05g1877 1877
4 4067248 4076646 - Vvi4g402 Vvi4g402 402
4 4078392 4085329 + Vvi4g403 Vvi4g403 403
4 4085349 4088042 + Vvi4g404 Vvi4g404 404
4 4123086 4132649 + Vvi4g405 Vvi4g405 405
4 4133780 4133891 + Vvi4g406 Vvi4g406 406
4 4133939 4146561 - Vvi4g407 Vvi4g407 407
4 4149580 4155798 + Vvi4g408 Vvi4g408 408
4 4157701 4159725 - Vvi4g409 Vvi4g409 409
4 4166327 4177492 - Vvi4g410 Vvi4g410 410
4 4177696 4184300 + Vvi4g411 Vvi4g411 411
       

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