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
Vvi16g944 . Blo15g00005 . . . Bpe07g01104 . . . . . . . . . . Cpe14g00010 . . . . . . . . . . . . . . . Cone5ag0743 . . . . . . . . . . . . . . . . . Cma16g00010 . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g945 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g946 . Blo15g00038 . . . Bpe07g01070 . . . . . . . . . . Cpe14g00011 . . . . . . . . . . . . . . . Cone5ag0741 . . . . . . . . . . . . . . . . . Cma16g00011 Cma18g01347 . . . . . . . . . . . Cla05g01002 . . . . . . . . . .
Vvi16g947 . . Bda05g00152 Bda07g01963 . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone1ag1032 Cone5ag0740 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g948 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g949 . . . . . . . . Cmo16g00013 Cmo18g01380 . . . . . . Cpe14g00012 . . . . . . . . . . . . . . Cone1ag1031 Cone5ag0738 . . . . . . . . . . . . . . . . . Cma16g00012 Cma18g01346 Car16g00010 Car18g01258 Cpe09g00006 . . . . . . . . . . . . . . . . . . .
Vvi16g950 . . . . . . . . . Cmo18g01379 . . . . . . . . . . . . . . . . . . . . . Cone1ag1030 Cone5ag0737 . . . . . . . . . . . . . . . . . . Cma18g01345 . Car18g01257 Cpe09g00007 . . . . . . . . . . . . . . . . . . .
Vvi16g951 . . Bda05g00147 . . . . . Cmo16g00015 Cmo18g01377 . . . . . . Cpe14g00013 . . . . . . . . . . . . . . Cone1ag1029 Cone5ag0736 . . . . . . . . . . . . . . . . . Cma16g00013 Cma18g01344 Car16g00012 Car18g01256 Cpe09g00008 . . . . . . . . . . . . . . . . . . .
Vvi16g952 . . Bda05g00146 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Blo07g00310 . Bda06g00800 . . . . Bma12g01250 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g953 . . . . . . . . . . Cma02g01148 . Car02g00953 . . Cpe05g00575 . . . . . . . . Cla01g00001 . . . Clacu01g0001 Cmu01g0001 Cre09g2503 Cone1ag1027 Cone5ag0734 . . . . . . . . . Bda15g00799 . . . . . Cmo02g01184 . . . . . . . Bhi12g00740 . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
5 6260633 6261706 - Bda020773.1 Bda05g00146 146
5 6262623 6267033 - Bda020774.1 Bda05g00147 147
5 6374711 6381346 - Bda020779.1 Bda05g00152 152
6 11142117 11143576 - Bda024125.1 Bda06g00800 800
7 37060626 37062160 + Bda028949.1 Bda07g01963 1963
15 11866943 11876858 - Bda012659.1 Bda15g00799 799
12 21269135 21270904 + XM_039018902.1 Bhi12g00740 740
7 3907945 3909212 + BLOR18242 Blo07g00310 310
15 43478 47690 + BLOR06399 Blo15g00005 5
15 305071 307635 - BLOR06432 Blo15g00038 38
12 45522214 45522978 - Bma008614.1 Bma12g01250 1250
7 16105150 16107837 + Bpe021913.1 Bpe07g01070 1070
7 16329132 16333188 - Bpe021942.1 Bpe07g01104 1104
2 6716188 6718124 + Carg13988-RA Car02g00953 953
16 184381 185698 + Carg15029-RA Car16g00010 10
16 188816 192793 + Carg15031-RA Car16g00012 12
18 11916871 11920663 - Carg20313-RA Car18g01256 1256
18 11922712 11923229 - Carg20312-RA Car18g01257 1257
18 11924208 11926129 - Carg20311-RA Car18g01258 1258
1 105201 106525 + ClG42_01g0000100.10 Clacu01g0001 1
1 12480 14267 + ClCG01G000010.2 Cla01g00001 1
5 10080430 10083600 - ClCG05G009270.1 Cla05g01002 1002
2 6786034 6788096 + CmaCh02G011480.1 Cma02g01148 1148
16 67066 70707 + CmaCh16G000100.1 Cma16g00010 10
16 71399 74784 + CmaCh16G000110.1 Cma16g00011 11
16 75525 77478 + CmaCh16G000120.1 Cma16g00012 12
16 80600 84932 + CmaCh16G000130.1 Cma16g00013 13
18 10213286 10217456 - CmaCh18G013440.1 Cma18g01344 1344
18 10220303 10221073 - CmaCh18G013450.1 Cma18g01345 1345
18 10222326 10224070 - CmaCh18G013460.1 Cma18g01346 1346
18 10224735 10228266 - CmaCh18G013470.1 Cma18g01347 1347
2 7095862 7097719 + CmoCh02G011840.1 Cmo02g01184 1184
16 89520 91417 + CmoCh16G000130.1 Cmo16g00013 13
16 95071 98997 + CmoCh16G000150.1 Cmo16g00015 15
18 12848882 12852582 - CmoCh18G013770.1 Cmo18g01377 1377
18 12854805 12855318 - CmoCh18G013790.1 Cmo18g01379 1379
18 12856335 12858056 - CmoCh18G013800.1 Cmo18g01380 1380
1 50194 51518 + CmPI595203_01g000010.1 Cmu01g0001 1
1 55142430 55143697 + Conep01aG0107500.1 Cone1ag1027 1027
1 55148977 55152982 - Conep01aG0107700.1 Cone1ag1029 1029
1 55159728 55160359 - Conep01aG0107800.1 Cone1ag1030 1030
1 55162315 55163958 - Conep01aG0107900.1 Cone1ag1031 1031
1 55166478 55173460 - Conep01aG0108000.1 Cone1ag1032 1032
5 3161042 3162841 + Conep05aG0075900.1 Cone5ag0734 734
5 3165647 3169689 - Conep05aG0076100.1 Cone5ag0736 736
5 3174116 3174846 - Conep05aG0076200.1 Cone5ag0737 737
5 3176854 3178929 - Conep05aG0076300.1 Cone5ag0738 738
5 3189171 3191174 - Conep05aG0076500.1 Cone5ag0740 740
5 3191485 3194492 - Conep05aG0076600.1 Cone5ag0741 741
5 3197642 3200562 - Conep05aG0076800.1 Cone5ag0743 743
5 3484620 3486420 - Cp4.1LG05g05740.1 Cpe05g00575 575
9 27301 33194 + Cp4.1LG09g00080.1 Cpe09g00006 6
9 33843 34519 + Cp4.1LG09g00020.1 Cpe09g00007 7
9 36343 40454 + Cp4.1LG09g00030.1 Cpe09g00008 8
14 66539 70475 + Cp4.1LG14g07140.1 Cpe14g00010 10
14 70892 74352 + Cp4.1LG14g07100.1 Cpe14g00011 11
14 75150 76995 + Cp4.1LG14g07080.1 Cpe14g00012 12
14 80169 87274 + Cp4.1LG14g07060.1 Cpe14g00013 13
9 44266660 44275178 - CrPI670011_09g025030.1 Cre09g2503 2503
16 21102337 21105009 + Vvi16g944 Vvi16g944 944
16 21105155 21105374 - Vvi16g945 Vvi16g945 945
16 21111940 21114958 + Vvi16g946 Vvi16g946 946
16 21116338 21124894 + Vvi16g947 Vvi16g947 947
16 21124894 21126512 + Vvi16g948 Vvi16g948 948
16 21130942 21133170 + Vvi16g949 Vvi16g949 949
16 21140126 21142774 + Vvi16g950 Vvi16g950 950
16 21144713 21150818 + Vvi16g951 Vvi16g951 951
16 21152034 21155500 + Vvi16g952 Vvi16g952 952
16 21156214 21158377 - Vvi16g953 Vvi16g953 953
       

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