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
Vvi16g814 . . . . . . . . . . . . . . . . . Bhi01g01426 . . . . . . . . . . . . . Cone1ag1203 Cone5ag0905 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Csa03g02176 . .
Vvi16g815 . . . . . . . . . . . . . . . . . Bhi01g01563 Tan01g0803 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g816 . . . . . . . . . Cmo18g01317 . . . . . . . Bhi01g01427 . . . . . . . . . . . . . . . . . . . . Cme06g01057 . . . . . . . . . . . . Cma18g01288 . Car18g01206 . . . . . . . . . Cla05g00933 . . . . . . . . . .
Vvi16g817 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g818 . . . . . . . . . . . . . . . . . Bhi01g01428 . . . . Mch10g0108 . . . . . . . . . . . . . . . . . Blo09g00049 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g819 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g820 . . . . . . . . . . . . . . . . . Bhi01g01429 . . . . . . . . . . . . . . . . . Lsi05g01175 . . . . . . . . . . . . . . . . . . Cpe09g00053 . . . . . . . . . . . . . . . . . Chy06g01280 .
Vvi16g821 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g822 . . . . . . . . . . . . . . Sed01g3718 . . Bhi01g01562 Tan01g0804 Cmetu09g0373 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g823 . . Bda05g00106 . Bpe03g00248 . Bma10g01272 . Cmo16g00090 . . . . . Sed13g0100 . Cpe14g00070 Bhi01g01430 Tan01g0171 Cmetu06g1598 . Hepe07g0105 Mch10g0107 . . . . . . . . . . Cone14ag0043 . Lsi05g01174 . . Cme06g01058 Blo07g00355 . . . . . . . . . . . . Car16g00076 . . . . . . . . . . Cla05g00934 Cam05g1021 Cec05g1025 Cco05g1021 Clacu05g1010 Cmu05g0963 Cre05g1044 . Csa03g02177 Chy06g01279 .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 5222975 5227659 + Bda020715.2 Bda05g00106 106
1 29097358 29103678 + XM_039046219.1 Bhi01g01426 1426
1 29097359 29103678 + XM_039044716.1 Bhi01g01427 1427
1 29097359 29103510 + XM_039045452.1 Bhi01g01428 1428
1 29097564 29103678 + XM_039046691.1 Bhi01g01429 1429
1 29108177 29115923 + XM_039044939.1 Bhi01g01430 1430
1 32087186 32096206 - XM_039023083.1 Bhi01g01562 1562
1 32092124 32096206 - XM_039023057.1 Bhi01g01563 1563
7 5665891 5670662 - BLOR18287 Blo07g00355 355
9 771731 774906 - BLOR20964 Blo09g00049 49
10 45268527 45273201 + Bma005373.2 Bma10g01272 1272
3 3288185 3292806 - Bpe012101.2 Bpe03g00248 248
5 9215976 9222682 + CaPI482276_05g010210.1 Cam05g1021 1021
16 483375 489736 - Carg15095-RA Car16g00076 76
18 11640558 11644430 + Carg20364-RA Car18g01206 1206
5 8975835 8982568 + CcPI632755_05g010210.1 Cco05g1021 1021
5 8956421 8963135 + CePI673135_05g010250.1 Cec05g1025 1025
6 11743407 11750639 - Chy6G118070.1 Chy06g01279 1279
6 11752691 11758246 - Chy6G118080.1 Chy06g01280 1280
5 8931759 8939141 + ClG42_05g0101000.10 Clacu05g1010 1010
5 9233073 9240945 + ClCG05G008550.2 Cla05g00933 933
5 9240985 9247700 + ClCG05G008560.2 Cla05g00934 934
18 9934233 9938423 + CmaCh18G012880.1 Cma18g01288 1288
6 7684990 7690810 + MELO3C006961.2.1 Cme06g01057 1057
6 7691533 7699920 + MELO3C006963.2.1 Cme06g01058 1058
6 7677506 7685147 + PI0016860.1 Cmetu06g1598 1598
9 3724514 3751951 + PI0027571.1 Cmetu09g0373 373
16 414689 421597 - CmoCh16G000900.1 Cmo16g00090 90
18 12550001 12553941 + CmoCh18G013170.1 Cmo18g01317 1317
5 8776942 8784322 + CmPI595203_05g009630.1 Cmu05g0963 963
1 55909891 55913003 + Conep01aG0125200.1 Cone1ag1203 1203
5 3880989 3883924 + Conep05aG0093100.1 Cone5ag0905 905
14 281868 285548 + Conep14aG0004500.1 Cone14ag0043 43
9 323089 327382 - Cp4.1LG09g00610.1 Cpe09g00053 53
14 386312 392368 - Cp4.1LG14g06390.1 Cpe14g00070 70
5 9659135 9665822 + CrPI670011_05g010440.1 Cre05g1044 1044
3 18890047 18895816 + CsaV3_3G021760.1 Csa03g02176 2176
3 18898856 18907268 + CsaV3_3G021770.1 Csa03g02177 2177
7 988937 997135 - Hsped.07g01050.1 Hepe07g0105 105
5 19662866 19670708 - Lsi05G011740.1 Lsi05g01174 1174
5 19671667 19678161 - Lsi05G011750.1 Lsi05g01175 1175
10 627885 635080 - MC10g_new0015 Mch10g0107 107
10 636424 641883 - MC10g0093 Mch10g0108 108
1 66270811 66273105 - Sed0019618.1 Sed01g3718 3718
13 661251 669661 - Sed0015140.3 Sed13g0100 100
1 1581951 1588656 - Tan0012811.1 Tan01g0171 171
1 7782046 7787188 + Tan0004304.1 Tan01g0803 803
1 7782046 7787188 + Tan0004304.2 Tan01g0804 804
16 18826204 18834557 + Vvi16g814 Vvi16g814 814
16 18849597 18853350 + Vvi16g815 Vvi16g815 815
16 18853684 18860368 + Vvi16g816 Vvi16g816 816
16 18879626 18886900 + Vvi16g817 Vvi16g817 817
16 18887040 18887384 + Vvi16g818 Vvi16g818 818
16 18902672 18905654 + Vvi16g819 Vvi16g819 819
16 18906218 18911407 + Vvi16g820 Vvi16g820 820
16 18911454 18912023 + Vvi16g821 Vvi16g821 821
16 18945411 18951829 + Vvi16g822 Vvi16g822 822
16 18969067 18978429 + Vvi16g823 Vvi16g823 823
       

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