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Purifying selection detected in the plastid gene matK and flanking ribozyme regions within a group II intron of nonphotosynthetic plants.

In a striking contrast, matK is one of the most rapidly evolving plastid genes and also one of the few plastid genes to be retained in all nonphotosynthetic plants examined to date. DNA sequences of this region were obtained from photosynthetic and nonphotosynthetic plants of Orobanchaceae and their relatives. The resulting plastid DNA phylogeny was congruent with that recently obtained from analyses of rps2 and provided much better resolution. This phylogeny was then used to examine the relative degrees of evolutionary constraint of both the matK gene and the non-protein-coding regions that flank it inside the trnK intron. The method of subtree contrasts was introduced to compare levels of constraint. matK has evolved with a low but significant level of constraint on its amino acid sequence in both photosynthetic and nonphotosynthetic plants. Constraint is greater in photosynthetic than in nonphotosynthetic plants of this group. Domain X, thought to contain the active site of the protein, is not significantly more constrained than the rest of the protein. The portions of the flanking regions that are thought to form paired stem structures also show constraint, but in this case, there is no significant difference in degree of constraint between photosynthetic and nonphotosynthetic plants.