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A recently silenced, duplicate PgiC locus in Clarkia

L D Gottlieb1, V S Ford

  • 1Section of Evolution and Ecology, University of California, Davis 95616-8755, USA. ldgottlieb@ucdavis.edu

Molecular Biology and Evolution
|February 1, 1997
PubMed
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GENE DUPLICATION AND PHYLOGENY IN CLARKIA.

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The wildflower Clarkia has duplicate phosphoglucose isomerase genes (PgiC1 and PgiC2). This study found a silenced PgiC2 gene in Clarkia mildrediae, confirming previous phylogenetic predictions of gene silencing events.

Area of Science:

  • Plant genetics
  • Molecular evolution
  • Biochemistry

Background:

  • Wildflower Clarkia species exhibit variation in cytosolic phosphoglucose isomerase (PGIC) expression, with some having two isozymes and others one.
  • Electrophoretic and molecular studies indicate that two PGIC isozymes are encoded by duplicate genes (PgiC1 and PgiC2), while a single isozyme is encoded by PgiC1 alone.

Purpose of the Study:

  • To characterize a pseudogene (psi) of PgiC2 in Clarkia mildrediae, a species expressing only PgiC1.
  • To confirm phylogenetic predictions regarding the independent silencing of the PgiC2 gene in the Clarkia genus.

Main Methods:

  • Phylogenetic analysis of nucleotide sequences.
  • Description and characterization of the psi PgiC2 gene structure, including exons, introns, and the 3' non-translated region.

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Main Results:

  • A psi PgiC2 gene was identified in Clarkia mildrediae, comprising 5,039 nucleotides, 18 of 23 exons, introns, and the 3' non-translated region.
  • The absence of elevated nucleotide substitutions in the "exons" of psi PgiC2 suggests recent gene silencing.
  • This represents the first documented case of a duplicated gene locus, typically expressed in related plant species, being silenced in one species.

Conclusions:

  • The independent silencing of PgiC2 multiple times suggests it was functional but non-essential in ancestral lineages.
  • The preservation of PgiC2 might be due to selection against deleterious effects of defective PGIC1-PGIC2 heterodimers.