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
Vvi16g964 . . . Bda07g01958 . . . Bma14g02029 Cmo16g00020 . . . . . . . Cpe14g00016 . . . . . . . . . . . . . . Cone1ag1020 Cone5ag0727 . . . . . . . Blo09g00002 . . . . . . . . . . . Car16g00017 . . . . . . . . . . . . . . . . . . . . .
Vvi16g965 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cma16g00017 . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g966 . . . . . . . . Cmo16g00021 . . . . . . . Cpe14g00017 . . . . . . . . . . . . . . . . . . . . . . . . . Bda15g00798 . . . . . . . . . Car16g00018 . . . . . . . . . . . . . . . . . . . . .
Vvi16g967 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag1019 Cone5ag0726 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g968 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g969 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g970 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g971 . . Bda05g00142 . . . Bma10g01319 . . . . . Car02g00950 . . Cpe05g00577 . . . . . . . . Cla01g00010 Cam01g0010 Cec01g0009 Cco01g0011 Clacu01g0011 Cmu01g0011 Cre09g2494 Cone1ag1018 . . . . Csa05g00007 Chy09g01474 . Blo07g00317 . . . . . . . . Cmo02g01181 Cmo15g01056 . . . . . Cpe13g00338 Bhi12g00700 . . . . . . . . . . . . . . . . Cme09g02022
Vvi16g972 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g973 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag1017 Cone5ag0725 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 6221925 6224096 + Bda020768.2 Bda05g00142 142
7 36959422 36961170 - Bda028937.1 Bda07g01958 1958
15 11856134 11857402 + Bda012658.1 Bda15g00798 798
12 20401498 20408168 + XM_039051303.1 Bhi12g00700 700
7 4001181 4002570 - BLOR18249 Blo07g00317 317
9 39140 40898 + BLOR20917 Blo09g00002 2
10 46828428 46830677 + Bma005435.1 Bma10g01319 1319
14 43601440 43603297 - Bma012837.1 Bma14g02029 2029
1 564567 569433 - CaPI482276_01g000100.1 Cam01g0010 10
2 6700510 6705217 + Carg13991-RA Car02g00950 950
16 203126 208669 + Carg15036-RA Car16g00017 17
16 203184 212568 - Carg15037-RA Car16g00018 18
1 75923 80779 - CcPI632755_01g000110.1 Cco01g0011 11
1 96605 102063 - CePI673135_01g000090.1 Cec01g0009 9
9 16155610 16161326 - Chy9G171900.1 Chy09g01474 1474
1 166705 173320 - ClG42_01g0001100.10 Clacu01g0011 11
1 82795 89757 - ClCG01G000100.2 Cla01g00010 10
16 100925 104680 - CmaCh16G000170.1 Cma16g00017 17
9 23900559 23912043 - MELO3C033837.2.1 Cme09g02022 2022
2 7082299 7084992 + CmoCh02G011810.1 Cmo02g01181 1181
15 6850601 6859326 - CmoCh15G010560.1 Cmo15g01056 1056
16 109316 114736 + CmoCh16G000200.1 Cmo16g00020 20
16 116359 120087 - CmoCh16G000210.1 Cmo16g00021 21
1 111685 118300 - CmPI595203_01g000110.1 Cmu01g0011 11
1 55099894 55103814 - Conep01aG0106500.1 Cone1ag1017 1017
1 55105300 55109445 + Conep01aG0106600.1 Cone1ag1018 1018
1 55110268 55111919 + Conep01aG0106700.1 Cone1ag1019 1019
1 55112143 55113520 - Conep01aG0106800.1 Cone1ag1020 1020
5 3119691 3123599 - Conep05aG0075000.1 Cone5ag0725 725
5 3127659 3132540 + Conep05aG0075100.1 Cone5ag0726 726
5 3132623 3134434 - Conep05aG0075200.1 Cone5ag0727 727
5 3498066 3502930 - Cp4.1LG05g05770.1 Cpe05g00577 577
13 3044268 3051828 + Cp4.1LG13g03390.1 Cpe13g00338 338
14 93670 100349 + Cp4.1LG14g07130.1 Cpe14g00016 16
14 98846 109110 - Cp4.1LG14g06970.1 Cpe14g00017 17
9 44205366 44210256 + CrPI670011_09g024940.1 Cre09g2494 2494
5 42567 51326 + CsaV3_5G000070.1 Csa05g00007 7
16 21255004 21256990 + Vvi16g964 Vvi16g964 964
16 21257360 21269242 - Vvi16g965 Vvi16g965 965
16 21269850 21283495 - Vvi16g966 Vvi16g966 966
16 21283941 21286566 - Vvi16g967 Vvi16g967 967
16 21288394 21289333 - Vvi16g968 Vvi16g968 968
16 21290995 21291719 - Vvi16g969 Vvi16g969 969
16 21294628 21295918 - Vvi16g970 Vvi16g970 970
16 21297785 21301549 - Vvi16g971 Vvi16g971 971
16 21301556 21303346 - Vvi16g972 Vvi16g972 972
16 21304767 21311485 + Vvi16g973 Vvi16g973 973
       

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