Table 3.

Codon usage of Physcomitrella retained genes, orthologs and paralogs

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

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.