Mode and Tempo of matK: Gene Evolution and Phylogenetic Implications

Abstract

The matK gene is approximately 1,500 base pairs in length, located in the large single copy region of the chloroplast genome, nested in the trnK intron. The protein product of the gene is proposed to function as a group II intron maturase. Evolutionary, molecular, and bioinformatic evidence supports this proposed function. The open reading frame of this protein-coding gene, however, has a high proportion of substitutions at the nucleotide and amino acid levels and has accumulated substantial numbers of insertions/deletions. These features have rendered matK as a valuable source of phylogenetic signal in resolving relationships in plants at various historic levels but have also raised questions about the functionality of the gene. We discuss in this chapter how the unique combination of high substitution rates and mode of evolution that approach neutrality results in high phylogenetic signal and preservation of protein function in matK.