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.

Rensing et al. BMC Genomics 2005 6:43   doi:10.1186/1471-2164-6-43