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
Vvi4g22 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g23 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g24 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g25 . . . . . . . . . . . . . . . Cpe07g00506 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma12g00230 . . . . . . . . . . . . . . . . . . . . . .
Vvi4g26 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g27 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g28 . . . . . . . . . . . . . . . Cpe07g00201 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla08g01205 . . . . . . . . . .
Vvi4g29 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g30 . . . . . . . . . . . . Car09g00553 . . . Cpe06g00482 . . . . . . . . . . . . . . . . . . Lsi04g02320 Csa03g04539 Chy04g00164 . . . . . . . . . Sed12g1384 . . Cma09g00626 . . . . . Bhi09g02561 Tan01g3910 Cmetu04g0733 . Hepe01g2210 Mch11g0758 . . . . . . . . . . . Cme04g00188
Vvi4g31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
9 69484919 69492193 - XM_039043921.1 Bhi09g02561 2561
9 3125463 3132007 - Carg03035-RA Car09g00553 553
4 1451356 1458597 + Chy4G068820.1 Chy04g00164 164
8 24958351 24962693 - ClCG08G012090.2 Cla08g01205 1205
9 2935584 2946842 - CmaCh09G006260.1 Cma09g00626 626
12 1131420 1134780 + CmaCh12G002300.1 Cma12g00230 230
4 1417543 1426284 + MELO3C003474.2.1 Cme04g00188 188
4 31980210 31989436 - PI0015159.1 Cmetu04g0733 733
6 2837392 2844398 - Cp4.1LG06g03760.1 Cpe06g00482 482
7 1285539 1291308 - Cp4.1LG07g02410.1 Cpe07g00201 201
7 3323608 3326734 - Cp4.1LG07g04960.1 Cpe07g00506 506
3 39555701 39562968 - CsaV3_3G048450.1 Csa03g04539 4539
1 86787875 86794756 - Hsped.01g22100.1 Hepe01g2210 2210
4 30394260 30408133 - Lsi04G023200.1 Lsi04g02320 2320
11 5102939 5111224 - MC11g0637 Mch11g0758 758
12 11075290 11083356 - Sed0005675.1 Sed12g1384 1384
1 104054319 104062787 - Tan0016244.1 Tan01g3910 3910
4 258002 279395 + Vvi4g22 Vvi4g22 22
4 279750 299210 + Vvi4g23 Vvi4g23 23
4 299265 314682 + Vvi4g24 Vvi4g24 24
4 314871 324465 + Vvi4g25 Vvi4g25 25
4 324759 362232 + Vvi4g26 Vvi4g26 26
4 366544 381751 + Vvi4g27 Vvi4g27 27
4 397121 399004 + Vvi4g28 Vvi4g28 28
4 399138 400374 + Vvi4g29 Vvi4g29 29
4 401318 408009 + Vvi4g30 Vvi4g30 30
4 408259 409072 - Vvi4g31 Vvi4g31 31
       

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