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Positive Selection in Rapidly Evolving Plastid-Nuclear Enzyme Complexes.

Kate Rockenbach1, Justin C Havird1, J Grey Monroe2

  • 1Department of Biology, Colorado State University, Fort Collins, Colorado 80523.

Genetics
|October 7, 2016
PubMed
Summary
This summary is machine-generated.

Accelerated evolution in plant plastid genomes, particularly in caseinolytic protease (CLP) and acetyl-CoA carboxylase (ACCase) genes, is driven by positive selection and potential plastid-nuclear conflict, not just relaxed constraint.

Keywords:
McDonald–Kreitman testchloroplastcytonuclear interactionsplastome

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Area of Science:

  • Evolutionary Biology
  • Molecular Evolution
  • Genomics

Background:

  • Plastid genomes typically evolve slowly, but accelerated rates are observed in specific genes like clpP1 and accD across diverse angiosperms.
  • The drivers of these accelerations—adaptive change (positive selection) versus relaxed functional constraint (purifying selection)—remain debated.

Purpose of the Study:

  • To investigate the evolutionary mechanisms behind accelerated plastid genome evolution in the genus Silene.
  • To determine if rapid evolution in plastid genes is linked to rapid evolution in their nuclear-encoded counterparts.

Main Methods:

  • Phylogenetic analysis and population genetic variation were examined in nuclear genes encoding subunits of the caseinolytic protease (CLP) and acetyl-CoA carboxylase (ACCase) complexes.
  • Comparative analysis was performed between species exhibiting accelerated plastid genome evolution and those without.

Main Results:

  • Nuclear-encoded subunits of CLP and ACCase complexes also show rapid evolution in species with accelerated plastid evolution, particularly at interaction interfaces.
  • A significant excess of nonsynonymous substitutions suggests strong positive selection, especially in CLP genes.
  • Evidence suggests some species may be replacing native plastid ACCase with duplicated cytosolic versions.

Conclusions:

  • Accelerated evolution in these plastid-nuclear gene complexes is driven by strong positive selection and potentially by plastid-nuclear conflict.
  • The observed patterns challenge traditional views of molecular evolution for conserved enzymes and resemble antagonistic coevolutionary dynamics.