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
Vvi19g1014 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1015 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1016 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme11g01584 . . . . . . . . Sed01g0744 . . . . . . . . Bhi10g00975 Tan05g0615 Cmetu11g2544 . Hepe08g0625 . . . . . . . . . . Csa06g01176 Chy11g01016 .
Vvi19g1017 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1018 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g1019 . . . . . . . . . . . . . . . . . . . . . . . . Cla02g01811 . . . . . . Cone6ag0270 Cone9ag0304 . . . Csa07g01184 . . . . . . . . . . . . . . . . . . . Bhi10g00974 . . . . . . . . . . . . . . Csa06g01174 . .
Vvi19g1020 . . . . . . . . . . . . . . . Cpe04g00855 . . . . . . . . . . . . . . . . . . . . . . Cme11g01586 . . . . . . . . . . . . . . . . . Bhi10g00973 . . . . . . . . . . . . . . . Chy11g01019 .
Vvi19g1021 . . . . . . . . . . . . . . . . Cpe02g00615 . . . . . . . Cla02g01812 . . . . . Cre02g2161 . . . . . . . . . . . . . . . . . . . . . . . . . Bhi10g00972 . . . . . . . . . . . . . . Csa06g01172 . .
Vvi19g1022 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cme11g01588 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chy11g01021 Cme01g01536
Vvi19g1023 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
10 19863740 19866678 + XM_039046395.1 Bhi10g00972 972
10 19883345 19885335 + XM_039046668.1 Bhi10g00973 973
10 19894042 19895797 + XM_039046939.1 Bhi10g00974 974
10 19911123 19915618 + XM_039046867.1 Bhi10g00975 975
11 14340912 14348944 - Chy11G195960.1 Chy11g01016 1016
11 14377202 14378496 - Chy11G195990.1 Chy11g01019 1019
11 14390437 14392872 - Chy11G196010.1 Chy11g01021 1021
2 33150331 33162733 - ClCG02G018510.1 Cla02g01811 1811
2 33175407 33178541 - ClCG02G018520.1 Cla02g01812 1812
1 20397808 20398359 + MELO3C000922.2.1 Cme01g01536 1536
11 23501127 23505435 - MELO3C019667.2.1 Cme11g01584 1584
11 23531394 23533290 - MELO3C019666.2.1 Cme11g01586 1586
11 23564132 23565720 - MELO3C019665.2.1 Cme11g01588 1588
11 9125075 9129636 + PI0018418.1 Cmetu11g2544 2544
6 1254316 1255658 + Conep06aG0027200.1 Cone6ag0270 270
9 1325588 1327115 + Conep09aG0030700.1 Cone9ag0304 304
2 3731600 3733897 + Cp4.1LG02g02670.1 Cpe02g00615 615
4 7883661 7885146 - Cp4.1LG04g02190.1 Cpe04g00855 855
2 35184226 35187377 - CrPI670011_02g021610.1 Cre02g2161 2161
6 9901956 9903554 + CsaV3_6G013700.1 Csa06g01172 1172
6 9919247 9921289 + CsaV3_6G013720.1 Csa06g01174 1174
6 9934994 9939521 + CsaV3_6G013740.1 Csa06g01176 1176
7 11620620 11622574 - CsaV3_7G022730.1 Csa07g01184 1184
8 5529556 5533833 - Hsped.08g06250.1 Hepe08g0625 625
1 5480737 5485059 - Sed0022249.1 Sed01g0744 744
5 4537183 4540859 + Tan0019246.3 Tan05g0615 615
19 20026271 20062932 + Vvi19g1014 Vvi19g1014 1014
19 20068744 20107437 + Vvi19g1015 Vvi19g1015 1015
19 20132822 20140511 - Vvi19g1016 Vvi19g1016 1016
19 20150485 20152848 + Vvi19g1017 Vvi19g1017 1017
19 20163016 20164139 + Vvi19g1018 Vvi19g1018 1018
19 20170737 20172333 + Vvi19g1019 Vvi19g1019 1019
19 20226010 20227553 + Vvi19g1020 Vvi19g1020 1020
19 20230674 20232220 + Vvi19g1021 Vvi19g1021 1021
19 20238194 20240748 + Vvi19g1022 Vvi19g1022 1022
19 20274020 20274296 - Vvi19g1023 Vvi19g1023 1023
       

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