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
Vvi16g844 . . . Bda07g01914 Bpe03g00166 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo09g00047 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g845 . . . . Bpe03g00247 . Bma10g01273 . Cmo16g00087 . . . . . Sed07g0970 . Cpe14g00067 Bhi01g01433 Tan01g0167 Cmetu06g1299 . Hepe07g0102 Mch10g0104 . . . . . . . . . . Cone14ag0040 Cone15ag0041 Lsi05g01170 . . Cme06g01063 Blo07g00354 . . . . . . . . . . Cma16g00084 . Car16g00073 . . . . . . . . . . . . . . . . . . . Chy06g01274 .
Vvi16g846 . . . Bda07g01915 Bpe03g00167 . . . Cmo16g00086 Cmo18g01320 . . . . . . Cpe14g00066 Bhi01g01434 . . . Hepe07g0101 Mch10g0103 . . . . . . . . Cone1ag0952 Cone5ag0661 . . Lsi05g01169 . . Cme06g01064 . Blo09g00046 . . . . . . . . . Cma16g00082 Cma18g01291 Car16g00072 Car18g01208 Cpe09g00051 . . . . . . . . Cla05g00937 Cam05g1026 Cec05g1030 Cco05g1026 Clacu05g1015 Cmu05g0968 Cre05g1049 . Csa03g02180 Chy06g01273 .
Vvi16g847 . . . . . . . Bma14g01994 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g848 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g849 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g850 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g851 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g852 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g853 . . . . . . . . . . . Cma15g01041 . Car15g00971 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe12g00370 . . . . Cmo15g01101 . . . . . . Bhi12g00610 . . . . . . . . . . . . . Lsi09g00041 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 36595903 36599348 - Bda028890.1 Bda07g01914 1914
7 36601765 36607599 - Bda028891.3 Bda07g01915 1915
1 29186917 29189418 + XM_039024359.1 Bhi01g01433 1433
1 29189509 29196695 - XM_039024245.1 Bhi01g01434 1434
12 18855893 18861720 + XM_039019808.1 Bhi12g00610 610
7 5642461 5644002 - BLOR18286 Blo07g00354 354
9 728929 734414 + BLOR20961 Blo09g00046 46
9 736722 749305 + BLOR20962 Blo09g00047 47
10 45293454 45295457 + Bma005375.1 Bma10g01273 1273
14 43253140 43255561 - Bma012802.1 Bma14g01994 1994
3 2107620 2111053 - Bpe012012.1 Bpe03g00166 166
3 2125108 2130901 - Bpe012013.1 Bpe03g00167 167
3 3265250 3267277 - Bpe012100.1 Bpe03g00247 247
12 8973396 8977705 + Bpe005626.1 Bpe12g00370 370
5 9245968 9251889 - CaPI482276_05g010260.1 Cam05g1026 1026
15 7182153 7186782 - Carg26220-RA Car15g00971 971
16 466092 471951 + Carg15091-RA Car16g00072 72
16 472389 474494 - Carg15092-RA Car16g00073 73
18 11653283 11660170 - Carg20362-RA Car18g01208 1208
5 9005286 9012476 - CcPI632755_05g010260.1 Cco05g1026 1026
5 8986056 8991995 - CePI673135_05g010300.1 Cec05g1030 1030
6 11713822 11720454 + Chy6G118010.1 Chy06g01273 1273
6 11720901 11722636 - Chy6G118020.1 Chy06g01274 1274
5 8962415 8969457 - ClG42_05g0101500.10 Clacu05g1015 1015
5 9276181 9284828 - ClCG05G008600.1 Cla05g00937 937
15 6513733 6518328 - CmaCh15G010410.1 Cma15g01041 1041
16 358537 364265 + CmaCh16G000820.1 Cma16g00082 82
16 364484 366858 - CmaCh16G000840.1 Cma16g00084 84
18 9946556 9953369 - CmaCh18G012910.1 Cma18g01291 1291
6 7740244 7742225 + MELO3C006968.2.1 Cme06g01063 1063
6 7742288 7749403 - MELO3C006969.2.1 Cme06g01064 1064
6 7701055 7704055 + PI0017792.1 Cmetu06g1299 1299
15 7382873 7387301 - CmoCh15G011010.1 Cmo15g01101 1101
16 397796 404009 + CmoCh16G000860.1 Cmo16g00086 86
16 403770 405968 - CmoCh16G000870.1 Cmo16g00087 87
18 12565352 12572185 - CmoCh18G013200.1 Cmo18g01320 1320
5 8807484 8813405 - CmPI595203_05g009680.1 Cmu05g0968 968
1 54766348 54771526 - Conep01aG0099500.1 Cone1ag0952 952
5 2821233 2826863 + Conep05aG0068500.1 Cone5ag0661 661
14 274454 276308 - Conep14aG0004200.1 Cone14ag0040 40
15 270194 272018 - Conep15aG0004300.1 Cone15ag0041 41
9 309560 316168 + Cp4.1LG09g00520.1 Cpe09g00051 51
14 368740 375222 + Cp4.1LG14g06450.1 Cpe14g00066 66
14 373509 377087 - Cp4.1LG14g06340.1 Cpe14g00067 67
5 9688930 9696017 - CrPI670011_05g010490.1 Cre05g1049 1049
3 18917683 18927344 - CsaV3_3G021800.1 Csa03g02180 2180
7 964916 971725 + Hsped.07g01010.1 Hepe07g0101 101
7 972143 973980 - Hsped.07g01020.1 Hepe07g0102 102
5 19635764 19643335 + Lsi05G011690.1 Lsi05g01169 1169
5 19643303 19645175 - Lsi05G011700.1 Lsi05g01170 1170
9 364863 371314 - Lsi09G000410.1 Lsi09g00041 41
10 607679 614752 + MC10g0092 Mch10g0103 103
10 614652 616322 - MC10g_new0012 Mch10g0104 104
7 7135572 7137362 - Sed0009140.1 Sed07g0970 970
1 1542203 1544232 - Tan0012449.1 Tan01g0167 167
16 19207201 19213829 - Vvi16g844 Vvi16g844 844
16 19214733 19218905 + Vvi16g845 Vvi16g845 845
16 19218946 19224345 - Vvi16g846 Vvi16g846 846
16 19230434 19234443 + Vvi16g847 Vvi16g847 847
16 19238716 19239864 + Vvi16g848 Vvi16g848 848
16 19240224 19246621 - Vvi16g849 Vvi16g849 849
16 19246765 19251841 - Vvi16g850 Vvi16g850 850
16 19252973 19259256 - Vvi16g851 Vvi16g851 851
16 19262280 19270069 - Vvi16g852 Vvi16g852 852
16 19277663 19288859 - Vvi16g853 Vvi16g853 853
       

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