Chloroplast tRNA Leu (UAA) intron sequences provide phylogenetic resolution of seagrass relationships

Abstract

Recent molecular studies have indicated that seagrasses comprise three convergent angiosperm clades. Although seagrass polyphyly has been demonstrated persuasively, other details of their phylogenetic relationships remain uncertain or weakly supported. To further assess seagrass relationships, we explored the potential of chloroplast trnL (UAA) intron sequences for phylogenetic reconstruction in the Alismatidae. Sequence analysis revealed considerable length variation of the trnL intron among the eight species of the subclass Alismatidae examined. These regions (representing large insertions/deletions in loops) were difficult to align and too variable to use reliably in phylogenetic analysis. However, conserved regions of the intron were readily aligned and were characterized by levels of divergence comparable to coding rbcL sequences. When analyzed phylogenetically, conserved trnL intron sequences recovered the same phylogenetic relationships among seagrass clades that were obtained using rbcL data. Combined analysis of trnL intron and rbcL coding sequences yielded a single most parsimonious tree with levels of nodal support higher than those obtained independently for either of the datasets. Analyses of conserved intron and coding chloroplast DNA sequences provide continued support for the polyphyly of seagrasses, the monophyly of Zosteraceae and a clade comprising Ruppiaceae, Posidoniaceae and Cymodoceaceae. Conserved trnL intron should be useful for evaluating other phylogenetic relationships in subclass Alismatidae.