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
Vvi17g986 . . Bda06g00849 . . . . . . . . . . . . Cpe20g00040 . . . . . . . . . . . . . . . . . Cone13ag0357 . Lsi02g00045 Csa01g00520 . Cme12g02021 . Blo15g00038 . . Bpe07g01070 . . . . . . Cma13g01112 . Car13g00946 . . . . . . . . . . . . . . . . . . . . .
Vvi17g987 . . . . . . . . . . . . . . . Cpe20g00039 . . . . . . . . . . . . . . . . . . . Lsi02g00046 Csa01g00521 Chy12g01564 Cme12g02020 . . . . . . . Bma08g00119 . . . Cma13g01113 . Car13g00947 . . . . . . . . . . . . . . . . . . . . .
Vvi17g988 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi02g00047 Csa01g00522 Chy12g01563 Cme12g02019 Blo13g00083 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g989 . . Bda06g00850 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo15g00036 . . Bpe07g01071 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g990 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g991 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g992 . . . . . . . . Cmo13g01147 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo15g00035 . . . . . Bma08g00117 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g993 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g994 . . Bda06g00851 . Bpe12g00588 . . Bma12g01208 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo13g00053 . . . Bpe07g01072 . . . . . . . . Car13g00932 . . . . . . . . . . . . . . . . . . . . .
Vvi17g995 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 11745377 11748149 + Bda024186.1 Bda06g00849 849
6 11749222 11757476 - Bda024187.1 Bda06g00850 850
6 11759153 11764578 - Bda024188.1 Bda06g00851 851
13 779490 782661 + BLOR05334 Blo13g00053 53
13 1299725 1305956 - BLOR05364 Blo13g00083 83
15 280556 286235 + BLOR06429 Blo15g00035 35
15 291196 294105 + BLOR06430 Blo15g00036 36
15 305071 307635 - BLOR06432 Blo15g00038 38
8 1454981 1460025 + Bma027121.1 Bma08g00117 117
8 1473576 1476414 + Bma027123.1 Bma08g00119 119
12 45032197 45043368 - Bma008569.1 Bma12g01208 1208
7 16105150 16107837 + Bpe021913.1 Bpe07g01070 1070
7 16117872 16120757 - Bpe026089 Bpe07g01071 1071
7 16122315 16126069 - Bpe021914.1 Bpe07g01072 1072
12 11659486 11662643 + Bpe005851.1 Bpe12g00588 588
13 9556231 9569271 - Carg04739-RA Car13g00932 932
13 9625176 9626528 + Carg04725-RA Car13g00946 946
13 9626578 9630173 - Carg04724-RA Car13g00947 947
12 19217305 19218895 - Chy12G221630.1 Chy12g01563 1563
12 19219515 19222542 + Chy12G221640.1 Chy12g01564 1564
13 8320215 8324077 + CmaCh13G011120.1 Cma13g01112 1112
13 8323927 8327016 - CmaCh13G011130.1 Cma13g01113 1113
12 25767579 25770467 - MELO3C001961.2.1 Cme12g02019 2019
12 25771018 25775732 + MELO3C001960.2.1 Cme12g02020 2020
12 25774584 25777874 - MELO3C001959.2.1 Cme12g02021 2021
13 9272262 9285659 - CmoCh13G011470.1 Cmo13g01147 1147
13 3229542 3232227 - Conep13aG0037700.1 Cone13ag0357 357
20 178993 182887 + Cp4.1LG20g00120.1 Cpe20g00039 39
20 181170 184005 - Cp4.1LG20g00280.1 Cpe20g00040 40
1 3452533 3455302 + CsaV3_1G005200.1 Csa01g00520 520
1 3455062 3459182 - CsaV3_1G005210.1 Csa01g00521 521
1 3459467 3462888 + CsaV3_1G005220.1 Csa01g00522 522
2 430791 435027 + Lsi02G000450.1 Lsi02g00045 45
2 435190 438928 - Lsi02G000460.1 Lsi02g00046 46
2 444584 447809 + Lsi02G000470.1 Lsi02g00047 47
17 16114327 16117505 + Vvi17g986 Vvi17g986 986
17 16119130 16147753 - Vvi17g987 Vvi17g987 987
17 16178828 16197202 + Vvi17g988 Vvi17g988 988
17 16227030 16230509 - Vvi17g989 Vvi17g989 989
17 16245899 16246154 + Vvi17g990 Vvi17g990 990
17 16310723 16311002 + Vvi17g991 Vvi17g991 991
17 16330181 16454350 - Vvi17g992 Vvi17g992 992
17 16520371 16521511 + Vvi17g993 Vvi17g993 993
17 16524938 16681799 - Vvi17g994 Vvi17g994 994
17 16699889 16705592 - Vvi17g995 Vvi17g995 995
       

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