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

Abstract

Interest in the use of low-copy nuclear genes for phylogenetic analyses of plants has grown rapidly, because highly repetitive genes such as those commonly used are limited in number. Furthermore, because low-copy genes are subject 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 study of GBSSI had three parts: (1) Amino acid sequences were compared across a broad taxonomic range, including grasses, four dicotyledons, and the microbial homologs of GBSSI. Inferred structural information was used to aid in the alignment of these very divergent sequences. The informed alignments highlight amino acids that are conserved across all sequences, and demonstrate that structural motifs can be highly conserved in spite of marked divergence in amino acid sequence. (2) Maximum-likelihood (ML) analyses were used to examine exon sequence evolution throughout grasses. Differences in probabilities among substitution types and marked among-site rate variation contributed 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 likelihood score. (3) We performed cladistic parsimony analyses of GBSSI sequences throughout grasses, within tribes, and within genera to examine the phylogenetic utility of the gene. Introns provide useful information among very closely related species, but quickly become difficult to align among more divergent taxa. Exons are variable enough to provide extensive resolution within the family, but with low bootstrap support. The combined results of amino acid sequence comparisons, maximum-likelihood analyses, and phylogenetic studies underscore factors that might affect phylogenetic reconstruction. In this case, accommodation of the variable rate of evolution among sites might be the first step in maximizing the phylogenetic utility of GBSSI.

Phylogenetics of Andropogoneae (Poaceae: Panicoideae) Based on Nuclear Ribosomal Internal Transcribed Spacer and Chloroplast trnL–F Sequences

“…The low resolution and support for clades in the ITS, trnL-F, and combined trees are consistent with previous studies and may reflect a rapid radiation or slowdown in molecular evolution as these lineages arose (Mason-Gamer et al 1998;Spangler et al 1999). Low rates of nucleotide substitution among members of Andropogoneae have been reported by Mason-Gamer et al (1998) for GBSSI, Spangler et al (1999) for ndhF, Lukens and Doebley (2001) for tb1, and Mathews et al (2002) for PHYB.…”

“…Low rates of nucleotide substitution among members of Andropogoneae have been reported by Mason-Gamer et al (1998) for GBSSI, Spangler et al (1999) for ndhF, Lukens and Doebley (2001) for tb1, and Mathews et al (2002) for PHYB.…”

“…Arundinella is strongly supported as sister to Andropogoneae in analyses of GBSSI (Mason-Gamer et al 1998), ndhF (Spangler et al 1999;Giussani et al 2001;Mathews et al 2002), tb1 (Lukens and Doebley 2001), ITS ALISO Skendzic, Columbus, and Cerros-Tlatilpa Clayton and Renvoize (1986). The subtribes are from Clayton and Renvoize (1986).…”

“…recommended Arundinella to be included in Andropogoneae. Likewise, phylogenetic trees from all four markers show a similar pattern-internal branches are short and poorly supported, suggesting that the tribe resulted from a rapid radiation or that molecular evolution was relatively slow as these lineages arose (Mason-Gamer et al 1998;Spangler et al 1999). Despite much phylogenetic uncertainty, these studies cast doubt on the monophyly of Maydeae (Watson and Dallwitz 1992) and most of Clayton and Ren- Table 1.…”

“…DNA sequence data (chloroplast gene NADH dehydrogenase [ndhF]; nuclear genes granule-bound starch synthase [GBSSI or waxy], phytochrome B [PHYB], and teosinte branched 1 [tb1]) have also been used to investigate the phylogeny of Andropogoneae (Mason-Gamer et al 1998;Spangler et al 1999;Spangler 2000;Lukens and Doebley 2001;Giussani et al 2001;Mathews et al 2002). The largest number of genera and species of Andropogoneae in these studies is 23 and 41, respectively.…”