title: Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): Loss of the ndh gene suite and inverted repeat.
abstract: •
  
  
  OBJECTIVE
  Land-plant plastid genomes have only rarely undergone significant changes in gene content and order. Thus, discovery of additional examples adds power to tests for causes of such genome-scale structural changes.•
  
  
  METHODS
  Using next-generation sequence data, we assembled the plastid genome of saguaro cactus and probed the nuclear genome for transferred plastid genes and functionally related nuclear genes. We combined these results with available data across Cactaceae and seed plants more broadly to infer the history of gene loss and to assess the strength of phylogenetic association between gene loss and loss of the inverted repeat (IR).•
  
  
  RESULTS
  The saguaro plastid genome is the smallest known for an obligately photosynthetic angiosperm (∼113 kb), having lost the IR and plastid ndh genes. This loss supports a statistically strong association across seed plants between the loss of ndh genes and the loss of the IR. Many nonplastid copies of plastid ndh genes were found in the nuclear genome, but none had intact reading frames; nor did three related nuclear-encoded subunits. However, nuclear pgr5, which functions in a partially redundant pathway, was intact.•
  
  
  CONCLUSIONS
  The existence of an alternative pathway redundant with the function of the plastid NADH dehydrogenase-like complex (NDH) complex may permit loss of the plastid ndh gene suite in photoautotrophs like saguaro. Loss of these genes may be a recurring mechanism for overall plastid genome size reduction, especially in combination with loss of the IR.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Sanderson
authors.affiliation: School of Plant Sciences, University of Arizona, Tucson, Arizona 85721 USA International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines.
authors.forename: Dario
authors.initials: D
authors.lastname: Copetti
authors.affiliation: Instituto de Ecologia, Unidad Hermosillo, UNAM, Hermosillo, Sonora, Mexico.
authors.forename: Alberto
authors.initials: A
authors.lastname: Búrquez
authors.affiliation: Instituto de Ecologia, Unidad Hermosillo, UNAM, Hermosillo, Sonora, Mexico.
authors.forename: Enriquena
authors.initials: E
authors.lastname: Bustamante
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 USA.
authors.forename: Joseph L M
authors.initials: JL
authors.lastname: Charboneau
authors.affiliation: Instituto de Ecologia, UNAM Mexico D.F., Mexico.
authors.forename: Luis E
authors.initials: LE
authors.lastname: Eguiarte
authors.affiliation: Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania 19122 USA.
authors.forename: Sudhir
authors.initials: S
authors.lastname: Kumar
authors.affiliation: Phyzen Genomics Institute, 501-1, Gwanak Century Tower, Gwanak-gu, Seoul, 151-836, Republic of Korea.
authors.forename: Hyun Oh
authors.initials: HO
authors.lastname: Lee
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
authors.forename: Junki
authors.initials: J
authors.lastname: Lee
authors.affiliation: School of Plant Sciences, University of Arizona, Tucson, Arizona 85721 USA.
authors.forename: Michelle
authors.initials: M
authors.lastname: McMahon
authors.affiliation: Faculty of Science and Mathematics, College of Letters and Sciences, Arizona State University, Mesa, Arizona 85212 USA.
authors.forename: Kelly
authors.initials: K
authors.lastname: Steele
authors.affiliation: School of Plant Sciences, University of Arizona, Tucson, Arizona 85721 USA International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines.
authors.forename: Rod
authors.initials: R
authors.lastname: Wing
authors.affiliation: Faculty of Science and Mathematics, College of Letters and Sciences, Arizona State University, Mesa, Arizona 85212 USA.
authors.forename: Tae-Jin
authors.initials: TJ
authors.lastname: Yang
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 USA.
authors.forename: Derrick
authors.initials: D
authors.lastname: Zwickl
authors.affiliation: School of Life Sciences, Arizona State University, Tempe, Arizona 85287 USA.
authors.forename: Martin F
authors.initials: MF
authors.lastname: Wojciechowski
mesh_terms: D029421:Cactaceae / Q000235:genetics*; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D015723:Gene Library; D054627:Genome, Plastid / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D055029:Inverted Repeat Sequences / Q000235:genetics*; D058977:Molecular Sequence Annotation; D009245:NADH Dehydrogenase / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D018087:Plastids / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant; D010940:Plant Proteins; D009245:NADH Dehydrogenase
keywords: Cactaceae; Carnegiea gigantea; cacti; inverted repeat; ndh genes; phylogenomics; saguaro