SPEER, WILLIAM D.* and PAUL G. WOLF. Department of Biology, Utah State University, Logan, UT 84322. - Analysis of basal vascular plant phylogeny using chloroplast genome sequences.
There has been considerable discussion recently regarding how to align
large sets of DNA sequence data that contain regions of ambiguity. We
examine and discuss several genome-scale alignment methods, including
“fragment level” and “elision” (concatenation), focusing on sequence
data from the chloroplast inverted repeat from currently published
genomes. We also include homologous sequences from taxa that no longer
have the inverted repeat or have a highly reduced repeat. Sequences
are from several green algal groups, liverwort, fern, gymnosperm and
angiosperms. We also present an update on the status of sequencing
complete fern chloroplast genomes. Comparisons of several vascular
plant genome sequences are then presented. We show the utility of the
data for inferring deep phylogeny and for examining genome evolution.
Key words: alignment, chloroplast genome, genome evolution, plastid genome