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
Vvi1g971 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g972 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g973 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g974 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00731 Cam01g0759 Cec01g0759 Cco01g0785 Clacu01g0751 Cmu01g0720 Cre09g1785 . . . .
Vvi1g975 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g976 . . . . . . . . . . . . . . . . Cpe01g01907 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo04g02298 . Cma04g02197 . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g977 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car04g02124 . . . . . . . . . . . . . . . . . . Csa05g01397 . .
Vvi1g978 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g979 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g980 . . . . . . . . . Cmo18g00243 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 8435561 8436295 + CaPI482276_01g007590.1 Cam01g0759 759
4 17295013 17296000 + Carg17731-RA Car04g02124 2124
1 8246308 8247043 + CcPI632755_01g007850.1 Cco01g0785 785
1 8308253 8308989 + CePI673135_01g007590.1 Cec01g0759 759
1 8107677 8108412 + ClG42_01g0075100.10 Clacu01g0751 751
1 8525172 8525907 + ClCG01G007500.2 Cla01g00731 731
4 15337097 15338436 + CmaCh04G021970.1 Cma04g02197 2197
4 17099257 17100562 + CmoCh04G022980.1 Cmo04g02298 2298
18 1606394 1610176 + CmoCh18G002430.1 Cmo18g00243 243
1 8075246 8075981 + CmPI595203_01g007200.1 Cmu01g0720 720
1 16277394 16278797 + Cp4.1LG01g18980.1 Cpe01g01907 1907
9 36276213 36276950 - CrPI670011_09g017850.1 Cre09g1785 1785
5 14937232 14943388 + CsaV3_5G020180.1 Csa05g01397 1397
1 14402384 14405941 + Vvi1g971 Vvi1g971 971
1 14497778 14497910 - Vvi1g972 Vvi1g972 972
1 14534079 14534298 + Vvi1g973 Vvi1g973 973
1 14669980 14678135 + Vvi1g974 Vvi1g974 974
1 14794022 14795637 + Vvi1g975 Vvi1g975 975
1 14811851 14816337 - Vvi1g976 Vvi1g976 976
1 14854162 14859888 - Vvi1g977 Vvi1g977 977
1 14903167 14903422 + Vvi1g978 Vvi1g978 978
1 14954684 14959548 - Vvi1g979 Vvi1g979 979
1 14982722 14984281 + Vvi1g980 Vvi1g980 980
       

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