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
Vvi2g872 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g873 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g874 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g875 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g876 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g877 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g878 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g879 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g880 . . . . . . Bma07g00966 Bma14g00111 Cmo06g00611 Cmo16g00575 . . . . . Cpe14g00445 . . . . . . . . Cla10g00110 Cam10g0105 Cec10g0114 Cco10g0115 Clacu10g0111 Cmu10g0958 Cre10g0368 . . . . Lsi07g01139 . . Cme06g02415 Blo03g00840 . Bda07g00139 . Bpe08g01075 . . . . . . Cma06g00604 Cma16g00526 Car06g00539 Car16g01140 . . . . . . . . . . . . . . . . . Csa03g00109 Chy06g02196 .
Vvi2g881 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
7 1727290 1734115 + Bda025204.1 Bda07g00139 139
3 34120859 34135932 - BLOR12021 Blo03g00840 840
7 37095505 37102101 + Bma026107.1 Bma07g00966 966
14 1479448 1486654 - Bma010516.1 Bma14g00111 111
8 12890205 12893650 - Bpe023200.1 Bpe08g01075 1075
10 2630150 2635915 + CaPI482276_10g001050.1 Cam10g0105 105
6 3028724 3032678 + Carg16291-RA Car06g00539 539
16 9738891 9742902 - Carg23569-RA Car16g01140 1140
10 1042883 1048648 + CcPI632755_10g001150.1 Cco10g0115 115
10 1058275 1061920 + CePI673135_10g001140.1 Cec10g0114 114
6 26189382 26193760 - Chy6G127240.1 Chy06g02196 2196
10 1359409 1363052 + ClG42_10g0011100.10 Clacu10g0111 111
10 1086073 1092038 + ClCG10G001070.1 Cla10g00110 110
6 2923248 2927781 + CmaCh06G006040.1 Cma06g00604 604
16 2682965 2687259 + CmaCh16G005260.1 Cma16g00526 526
6 31278187 31284515 + MELO3C013799.2.1 Cme06g02415 2415
6 3014576 3018488 + CmoCh06G006110.1 Cmo06g00611 611
16 2778554 2782871 + CmoCh16G005750.1 Cmo16g00575 575
10 1510455 1514098 + CmPI595203_10g009580.1 Cmu10g0958 958
14 2777314 2781734 + Cp4.1LG14g02730.1 Cpe14g00445 445
10 2470685 2476465 + CrPI670011_10g003680.1 Cre10g0368 368
3 854120 859992 + CsaV3_3G001090.1 Csa03g00109 109
7 16837804 16844465 + Lsi07G011390.1 Lsi07g01139 1139
2 16078747 16081536 - Vvi2g872 Vvi2g872 872
2 16133392 16143005 - Vvi2g873 Vvi2g873 873
2 16187440 16189151 - Vvi2g874 Vvi2g874 874
2 16236922 16237261 + Vvi2g875 Vvi2g875 875
2 16237262 16239318 - Vvi2g876 Vvi2g876 876
2 16244696 16247594 + Vvi2g877 Vvi2g877 877
2 16300906 16318428 - Vvi2g878 Vvi2g878 878
2 16323604 16326902 + Vvi2g879 Vvi2g879 879
2 16326974 16335400 + Vvi2g880 Vvi2g880 880
2 16402917 16404247 - Vvi2g881 Vvi2g881 881
       

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