The matK gene: sequence variation and application in plant systematics.

Although the matK gene has been used in addressing systematic questions in four families, its potential application to plant systematics above the family level has not been investigated. This paper examines the rates, patterns, and types of nucleotide substitutions in the gene and addresses its utility in constructing phylogenies above the family level. Eleven complete sequences from the GenBank representing seed plants and liverworts and nine partial sequences generated for genera representing the monocot families Poaceae, Joinvilleaceae, Cyperaceae, and Smilacaceae were analyzed. The study underscored the high rate of substitution in the gene and the presence of mutationally conserved sectors. The use of different sectors of the gene and the cumulative inclusion of informative sites showed that the 3' region was most useful in resolving phylogeny, and that the topology and robustness of the tree reached a plateau after the inclusion of 100 informative sites from that region for the taxa used. The impact of using partial sequencing on sample size is addressed. The presence of a relatively conserved 3' region and the less conserved 5' region provides two sets of characters that can be used at different taxonomic levels from the tribal to the division levels.