title: The plastid genome of the mycoheterotrophic Corallorhiza striata (Orchidaceae) is in the relatively early stages of degradation.
abstract: OBJECTIVE
  Plastid genomes of nonphotosynthetic, mycoheterotrophic plants represent apt systems in which to study effects of relaxed evolutionary constraints. The few mycoheterotrophic angiosperm plastomes sequenced to date display drastic patterns of degradation/reduction relative to those of photosynthetic relatives. The goal of this study was to focus on a mycoheterotrophic orchid hypothesized to be in the "early" stages of plastome degradation, to provide perspective on this process.
  
  
  METHODS
  Short-read sequencing was used to generate a complete plastome sequence for Corallorhiza striata var. vreelandii, a mycoheterotrophic orchid, to investigate the extent of plastome degradation. Patterns of nonsynonymous/synonymous mutations were also assessed, and comparisons were made between Corallorhiza and other heterotrophic plant lineages.
  
  
  RESULTS
  Corallorhiza yielded a plastome of 137505 bp, with several photosynthesis-related genes either lost or pseudogenized. Members of all major photosynthesis complexes, except ATP-synthase genes, were affected. "Housekeeping" genes were intact, despite the loss of a single tRNA. Intact photosynthesis genes (excluding atp genes) together displayed elevated nonsynonymous changes, while housekeeping genes did not.
  
  
  CONCLUSIONS
  The Corallorhiza plastome is not drastically reduced in overall size (∼6% reduction relative to that of photosynthetic Oncidium), but displays a pattern congruent with a loss of photosynthetic function. Comparing Corallorhiza with other heterotrophs allows some emergent evolutionary patterns to be inferred, but these remain as hypotheses to be tested, especially at lower taxonomic levels, and in lineages illustrating transitions from autotrophy to heterotrophy. The independent, unique processes of plastome modification among mycoheterotrophic lineages illustrate the urgency of their conservation.
authors.affiliation: Department of Plant Biology and L.H. Bailey Hortorium, 412 Mann Library, Cornell University, Ithaca, New York 14853, USA. cfb66@cornell.edu
authors.forename: Craig F
authors.initials: CF
authors.lastname: Barrett
authors.forename: Jerrold I
authors.initials: JI
authors.lastname: Davis
mesh_terms: D019943:Amino Acid Substitution / Q000235:genetics; D017353:Gene Deletion; D017343:Genes, Plant / Q000235:genetics; D054627:Genome, Plastid / Q000235:genetics*; D052836:Heterotrophic Processes / Q000235:genetics*; D029595:Orchidaceae / Q000235:genetics*; D011544:Pseudogenes / Q000235:genetics