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Table 3 Codon usage of Physcomitrella retained genes, orthologs and paralogs

From: Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens

sequence set # bases mean # of each triplet G/C content # significant codon usage changes codon usage towards At codon usage away from At codon over represented codon under represented significant changes per aa
At mRNAs 10,755,859 56,020 43.32 n.a. n.a. n.a. n.a. n.a. n.a.
Pp ORFs 7,638,122 39,782 49.94 n.a. n.a. n.a. n.a. n.a. n.a.
retained genes 77,998 406 50.30 7 1 6 2 5 Phe under represented
paralogs 1,115,937 5,812 50.07 3 1 2 1 2 none
orthologs 953,293 4,965 49.04 10 8 2 4 6 Pro under reprensented
     sum 10 10 7 13  
  1. The predicted Physcomitrella ORF were used as background to check for significant changes in percentage codon fraction usage in the orthologs, paralogs and retained genes (best BLAST hit not among plants). In case of significant deviation (two times average absolute deviation – AAD) from the total set, the direction of the change relative to the Arabidopsis codon usage was checked. Significant deviations are shown enlarged, At = Arabidopsis thaliana, Pp = Physcomitrella patens.