WALL, DENNIS P.* AND JOSH T. HERBECK. Department of Integrative Biology &, University and Jepson Herbaria, University of California, Berkeley, Berkeley, CA 94720, Phone: (510) 643-9556 LAB, (510) 666-9749 HOME, Fax: (510) 643-5390, email:email@example.com, firstname.lastname@example.org. - Codon Usage in Green Plants: an Analysis Using rbcL.
We have constructed a composite phylogeny of 92 green plant taxa with
representatives from all major clades to examine the level and degree
of codon usage for the gene rbcL and to search for potential links
between primary and secondary levels of organization. rbcL encodes
the large subunit of RUBISCO, an important enzyme in photosynthesis.
Such functional importance predicts that changes in primary genetic
substructure, and perhaps secondary structure and enzymatic efficiency
should be infrequently tolerated. Specifically, this conservation
predicts that changes in codon bias and usage should occur
infrequently, if at all. We have tested this claim and found it to be
largely false. Instead the degree of codon bias among green plant
lineages shifted in correspondence with phylogeny. One notable
finding was a major transition to decreased codon bias at the boundary
between spore plants and seed plants. The codon bias cannot be
explained by overall genome composition bias, and must have other
explanations, related to selection. Codon preference also changed
among green plant lineages, but these changes were most often
homoplasious. However, the shifts in preference were predominantly to
G or C ending codons, indicating possible biochemical canalization.
To search for mechanisms that may explain these changes, we examined
the relationship between the degree of bias and rates of Kn/Ks
substitutions in rbcL. Lower Kn/Ks ratios were correlated with higher
codon bias, indicating tracking of preferred codons within amino acid
families. These data support the hypothesis that codon bias and usage
are under selective pressure. In general, our study identifies how
comparative analyses of genetic organization may help clarify the
mechanisms linking genes, proteins, and patterns of microevolution.
Our study also indicates that usage of nucleotide sequence alone for
phylogenetic reconstruction may be overly simple; consideration of how
the selective environment may effect phylogenetic results is critical.
Key words: Chloroplast, Codon Bias, Green Plants, rbcL