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
Vvi4g552 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi04g02103 . . . . . . . . . . . Sed13g1999 . . . . . . . . Bhi09g02957 Tan01g3609 Cmetu07g1126 . Hepe01g1994 . . . . . . . . . . . . Cme07g00089
Vvi4g553 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g554 . . . . . . . . . . Cma01g01489 . . . . . . . . . . . . . Cla05g01710 Cam05g1825 Cec05g1837 Cco05g1895 Clacu05g1810 Cmu05g1696 Cre05g1825 . . . . Lsi04g02102 . . . . . . Bda13g01251 . . . . Sed13g1998 Cmo01g01543 . . . . . . . Bhi09g02959 Tan01g3607 Cmetu07g2079 . Hepe01g1993 . . . . . . . . . . . . Cme07g00090
Vvi4g555 . . . . . . . . . . . . . . . . . Bhi04g00020 . . . Hepe10g0239 . Lcy13g1802 . . . . . . . . . . . . . . . . Blo18g00017 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g556 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme07g00085
Vvi4g557 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g558 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g559 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g560 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bhi09g02944 Tan01g3613 Cmetu07g2096 . Hepe01g1997 Mch11g0532 . . . . . . . . . . . .
Vvi4g561 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
13 34939734 34941767 + Bda000058.3 Bda13g01251 1251
4 376082 380528 - XM_039028090.1 Bhi04g00020 20
9 76793018 76796689 + XM_039040919.1 Bhi09g02944 2944
9 76996176 77000722 + XM_039042794.1 Bhi09g02957 2957
9 77031397 77035208 + XM_039042003.1 Bhi09g02959 2959
18 152663 156375 + BLOR08505 Blo18g00017 17
5 27180215 27182485 - CaPI482276_05g018250.1 Cam05g1825 1825
5 28023903 28028178 - CcPI632755_05g018950.1 Cco05g1895 1895
5 30400434 30404600 - CePI673135_05g018370.1 Cec05g1837 1837
5 27389093 27391363 - ClG42_05g0181000.10 Clacu05g1810 1810
5 28924616 28928192 - ClCG05G016630.1 Cla05g01710 1710
1 10466794 10470332 - CmaCh01G014890.1 Cma01g01489 1489
7 530028 531314 + MELO3C016997.2.1 Cme07g00085 85
7 547704 551366 + MELO3C016993.2.1 Cme07g00089 89
7 553799 557689 + MELO3C016991.2.1 Cme07g00090 90
7 24230385 24234334 - PI0013969.1 Cmetu07g1126 1126
7 24222750 24226449 - PI0011173.1 Cmetu07g2079 2079
7 24252536 24254173 - PI0015583.2 Cmetu07g2096 2096
1 11901795 11904318 - CmoCh01G015430.1 Cmo01g01543 1543
5 27108172 27110442 - CmPI595203_05g016960.1 Cmu05g1696 1696
5 30412395 30416951 - CrPI670011_05g018250.1 Cre05g1825 1825
1 84724458 84728204 - Hsped.01g19930.1 Hepe01g1993 1993
1 84732028 84735548 - Hsped.01g19940.1 Hepe01g1994 1994
1 84758181 84761828 - Hsped.01g19970.1 Hepe01g1997 1997
10 2527208 2536692 + Hsped.10g02390.1 Hepe10g0239 239
13 36995303 37000271 - Maker00033910 Lcy13g1802 1802
4 28185193 28188772 - Lsi04G021020.1 Lsi04g02102 2102
4 28194516 28196284 - Lsi04G021030.1 Lsi04g02103 2103
11 3427230 3428738 - MC11g0435 Mch11g0532 532
13 24892880 24896661 - Sed0016854.1 Sed13g1998 1998
13 24904081 24909228 - Sed0015380.1 Sed13g1999 1999
1 101063302 101066971 - Tan0009989.1 Tan01g3607 3607
1 101072580 101080161 - Tan0012999.1 Tan01g3609 3609
1 101117198 101119274 - Tan0001252.1 Tan01g3613 3613
4 6129270 6138162 + Vvi4g552 Vvi4g552 552
4 6145586 6149666 + Vvi4g553 Vvi4g553 553
4 6153540 6159242 + Vvi4g554 Vvi4g554 554
4 6187948 6199288 + Vvi4g555 Vvi4g555 555
4 6200585 6211153 - Vvi4g556 Vvi4g556 556
4 6237414 6238065 + Vvi4g557 Vvi4g557 557
4 6257827 6258502 + Vvi4g558 Vvi4g558 558
4 6258506 6261202 + Vvi4g559 Vvi4g559 559
4 6271230 6277645 + Vvi4g560 Vvi4g560 560
4 6279732 6280638 + Vvi4g561 Vvi4g561 561
       

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