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

Interest in the use of low-copy nuclear genes for phylogenetic analyses ofplants has grown rapidly, because highly repetitive genes such as thosecommonly used are limited in number. Furthermore, because low- copy genesare subject to different evolutionary processes than are plastid genes orhighly repetitive nuclear markers, they provide a valuable source ofindependent phylogenetic evidence. The gene for granule-bound starchsynthase (GBSSI or waxy) exists in a single copy in nearly all plantsexamined so far. Our study of GBSSI had three parts: (1) Amino acidsequences were compared across a broad taxonomic range, including grasses,four dicotyledons, and the microbial homologs of GBSSI. Inferred structuralinformation was used to aid in the alignment of these very divergentsequences. The informed alignments highlight amino acids that are conservedacross all sequences, and demonstrate that structural motifs can be highlyconserved in spite of marked divergence in amino acid sequence. (2)Maximum-likelihood (ML) analyses were used to examine exon sequenceevolution throughout grasses. Differences in probabilities amongsubstitution types and marked among-site rate variation contributed to theobserved pattern of variation. Of the parameters examined in our set oflikelihood models, the inclusion of among-site rate variation following agamma distribution caused the greatest improvement in likelihood score. (3)We performed cladistic parsimony analyses of GBSSI sequences throughoutgrasses, within tribes, and within genera to examine the phylogeneticutility of the gene. Introns provide useful information among very closelyrelated species, but quickly become difficult to align among more divergenttaxa. Exons are variable enough to provide extensive resolution within thefamily, but with low bootstrap support. The combined results of amino acidsequence comparisons, maximum-likelihood analyses, and phylogenetic studiesunderscore factors that might affect phylogenetic reconstruction. In thiscase, accommodation of the variable rate of evolution among sites might bethe first step in maximizing the phylogenetic utility of GBSSI.