KELCHNER, SCOT A. Centre for Plant Biodiversity Research, CSIRO Plant Industry, G.P.O. Box 1600, Canberra, ACT 2601, AUSTRALIA; Division of Botany and Zoology, The Australian National University, AUSTRALIA. - Chloroplast introns in plant systematics.
Group II introns constitute the majority of noncoding sequence in many
plant chloroplast genomes and include the commonly sequenced regions
trnK/matK, the rps16 intron, and the rpl16
intron. As demand increases for nucleotide characters at lower
taxonomic levels, chloroplast introns may come to provide the bulk of
plastome sequence data for assessment of evolutionary relationships in
intrageneric, intergeneric, and interfamilial studies. Group II
introns have many attractive properties for the molecular systematist:
they are usually confined to organellar genomes in eukaryotes and the
majority are single-copy; they all share a well-defined and
empirically tested secondary and tertiary structure; and, they are
easily amplified due to highly conserved sequence in flanking exons.
Functional importance of structural conformations may be the key to
understanding intron sequence evolution and enhancing their
phylogenetic utility. A disparity of mutation rates among structural
features of a group II intron can be exploited to recover phylogenetic
signal at multiple taxonomic levels within a single intron, even
between subclasses of flowering plants. Structure-linked mutational
phenomena have important implications for the treatment of intron
sequence data when aligning nucleotides, assessing mutational biases
in the data, and selecting appropriate models of character evolution
for phylogenetic analysis. A description of group II intron function
and structure will be followed by a discussion of simple strategies to
accomodate observed mutational biases and enhance the accuracy of
phylogenies derived from intron sequence data.
Key words: group II introns, phylogenetic methods, phylogenetic tools, RNA secondary structure, rpl16 intron, trnK/matK