PGI Gene Sequences and Phylogenetic Inferences in Clarkia

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Evolutionary Biology has been studied in the California annual plant Clarkia (Onagraceae) for four decades and the genus has provided a number of model systems in which to study the origin of species, genetic variation in natural populations and, more recently, molecular evolution. The molecular studies were initiated to determine the mode of origin of the duplicated cytosolic phosphoglucose isomerase (PGI) siozymes that are present in 12 Clarkia species but absent in 12 others. PGI catalyzes an essential reaction in sugar metabolism. To date, several PGI genes have been partially sequenced. They have remarkably complex structure with 19 exons (and 18 introns) so far identified encoding about 88% of the PGI protein (483/550 amino acids), the largest number of exons known for any plant gene. A gene encoding the chloroplast PGI isozyme from a different Clarkia has also been sequenced; it has a continuous open reading frame with no exons. During the current project, additional PGI genes encoding both isozymes from clarkias with and without the duplication will be cloned and sequenced. Evidence from the sequences will be used to determine whether the duplication occurred early in the evolution of genus and was retained in some lineages but lost in others or whether it arose more recently. Since duplicated PGIs characterize species in four taxonomic sections but are absent in three other sections, the evidence can be expected to resolve the phylogenetic relationships among the sections, a problem that has remained refractory even though Clarkia has been studied intensively. The sequence evidence will also be used to compare the rate and amount of divergence between the plastid and cytosolic PGIs. The analysis will contribute to understanding the mechanisms that generate molecular divergence and constitutes one of the few studies to date of the evolution of plant nuclear genes encoding proteins.