Granule-bound starch synthase: Structure, function, and phylogenetic utility

Interest in the use of low-copy nuclear genes for phylogenetic analyses of plants has grown rapidly, because highly repetitive genes such as those com monly used are limited in number. Furthermore, because low-copy genes are s ubject to different evolutionary processes than are plastid genes or highly repetitive nuclear markers, they provide a valuable source of independent phylogenetic evidence. The gene for granule-bound starch synthase (GBSSI or waxy) exists in a single copy in nearly all plants examined so far. Our st udy of GBSSI had three parts: (1) Amino acid sequences were compared across a broad taxonomic range, including grasses, four dicotyledons, and the mic robial homologs of GBSSI. Inferred structural information was used to aid i n the alignment of these very divergent sequences. The informed alignments highlight amino acids that are conserved across all sequences, and demonstr ate that structural motifs can be highly conserved in spite of marked diver gence in amino acid sequence. (2) Maximum-likelihood (ML) analyses were use d to examine exon sequence evolution throughout grasses. Differences in pro babilities among substitution types and marked among-site rate variation co ntributed to the observed pattern of variation. Of the parameters examined in our set of likelihood models, the inclusion of among-site rate variation following a gamma distribution caused the greatest improvement in likeliho od score. (3) We performed cladistic parsimony analyses of GBSSI sequences throughout grasses, within tribes, and within genera to examine the phyloge netic utility of the gene. Introns provide useful information among very cl osely related species, but quickly become difficult to align among more div ergent taxa. Exons are variable enough to provide extensive resolution with in the family, but with low bootstrap support. The combined results of amin o acid sequence comparisons, maximum-likelihood analyses, and phylogenetic studies underscore factors that might affect phylogenetic reconstruction. I n this case, accommodation of the variable rate of evolution among sites mi ght be the first step in maximizing the phylogenetic utility of GBSSI.