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
Vvi1g141 . . Bda01g02180 . . . . . . Cmo18g00542 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00952 . Cec01g0977 Cco01g1024 Clacu01g0983 Cmu01g0936 Cre01g0865 . . . .
Vvi1g142 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00951 . Cec01g0976 Cco01g1023 Clacu01g0982 Cmu01g0935 Cre01g0864 . . . .
Vvi1g143 . . . . . . . . . Cmo18g00540 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00950 . Cec01g0975 Cco01g1022 Clacu01g0981 Cmu01g0934 Cre01g0863 . . . .
Vvi1g144 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00949 . Cec01g0974 Cco01g1021 Clacu01g0980 Cmu01g0933 Cre01g0862 . . . .
Vvi1g145 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g146 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g147 Blo01g00904 . . . . . . . . Cmo18g00528 . Cma18g00548 . . . Cpe09g00690 . . . . . . . . . . . . . . . . . . . . . . . . . Bda07g00890 . . . . . . . . . . . . . . . . . . . . . Cla01g00931 . . . . . . . . . .
Vvi1g148 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda07g00896 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g149 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g150 Blo01g00905 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00928 . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57789746 57791735 - Bda004522.1 Bda01g02180 2180
7 10404755 10409568 - Bda026030.1 Bda07g00890 890
7 10502506 10506148 + Bda026036.1 Bda07g00896 896
1 18753578 18759958 - BLOR00904 Blo01g00904 904
1 18938528 18946470 + BLOR00905 Blo01g00905 905
1 13039266 13058686 + CcPI632755_01g010210.1 Cco01g1021 1021
1 13060437 13063460 - CcPI632755_01g010220.1 Cco01g1022 1022
1 13063739 13068101 + CcPI632755_01g010230.1 Cco01g1023 1023
1 13072609 13076820 - CcPI632755_01g010240.1 Cco01g1024 1024
1 13129676 13149011 + CePI673135_01g009740.1 Cec01g0974 974
1 13149686 13153762 - CePI673135_01g009750.1 Cec01g0975 975
1 13154031 13158397 + CePI673135_01g009760.1 Cec01g0976 976
1 13162547 13166653 - CePI673135_01g009770.1 Cec01g0977 977
1 12791500 12815712 + ClG42_01g0098000.10 Clacu01g0980 980
1 12817278 12820241 - ClG42_01g0098100.10 Clacu01g0981 981
1 12820519 12824860 + ClG42_01g0098200.10 Clacu01g0982 982
1 12829335 12833429 - ClG42_01g0098300.10 Clacu01g0983 983
1 12840615 12864439 - ClCG01G009340.2 Cla01g00928 928
1 12902156 12913102 + ClCG01G009380.2 Cla01g00931 931
1 13403681 13429120 + ClCG01G009560.1 Cla01g00949 949
1 13430310 13434002 - ClCG01G009570.1 Cla01g00950 950
1 13433705 13438302 + ClCG01G009580.1 Cla01g00951 951
1 13442589 13446683 - ClCG01G009590.2 Cla01g00952 952
18 3551057 3558806 - CmaCh18G005480.1 Cma18g00548 548
18 3870046 3878875 - CmoCh18G005280.1 Cmo18g00528 528
18 4109986 4113113 - CmoCh18G005400.1 Cmo18g00540 540
18 4119526 4121949 - CmoCh18G005420.1 Cmo18g00542 542
1 12791400 12815609 + CmPI595203_01g009330.1 Cmu01g0933 933
1 12817175 12820145 - CmPI595203_01g009340.1 Cmu01g0934 934
1 12820425 12824767 + CmPI595203_01g009350.1 Cmu01g0935 935
1 12829243 12833337 - CmPI595203_01g009360.1 Cmu01g0936 936
9 6077498 6085087 + Cp4.1LG09g06860.1 Cpe09g00690 690
1 11521779 11541110 + CrPI670011_01g008620.1 Cre01g0862 862
1 11542875 11545839 - CrPI670011_01g008630.1 Cre01g0863 863
1 11546122 11550467 + CrPI670011_01g008640.1 Cre01g0864 864
1 11555008 11559110 - CrPI670011_01g008650.1 Cre01g0865 865
1 1418371 1422376 + Vvi1g141 Vvi1g141 141
1 1422451 1425224 - Vvi1g142 Vvi1g142 142
1 1425249 1426536 + Vvi1g143 Vvi1g143 143
1 1426625 1460682 - Vvi1g144 Vvi1g144 144
1 1466984 1495349 + Vvi1g145 Vvi1g145 145
1 1495866 1499100 + Vvi1g146 Vvi1g146 146
1 1500585 1504450 + Vvi1g147 Vvi1g147 147
1 1508153 1513345 + Vvi1g148 Vvi1g148 148
1 1513378 1514013 + Vvi1g149 Vvi1g149 149
1 1515089 1528970 + Vvi1g150 Vvi1g150 150
       

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