title: Detecting and Characterizing the Highly Divergent Plastid Genome of the Nonphotosynthetic Parasitic Plant Hydnora visseri (Hydnoraceae).
abstract: Plastid genomes of photosynthetic flowering plants are usually highly conserved in both structure and gene content. However, the plastomes of parasitic and mycoheterotrophic plants may be released from selective constraint due to the reduction or loss of photosynthetic ability. Here we present the greatly reduced and highly divergent, yet functional, plastome of the nonphotosynthetic holoparasite Hydnora visseri (Hydnoraceae, Piperales). The plastome is 27 kb in length, with 24 genes encoding ribosomal proteins, ribosomal RNAs, tRNAs, and a few nonbioenergetic genes, but no genes related to photosynthesis. The inverted repeat and the small single copy region are only approximately 1.5 kb, and intergenic regions have been drastically reduced. Despite extreme reduction, gene order and orientation are highly similar to the plastome of Piper cenocladum, a related photosynthetic plant in Piperales. Gene sequences in Hydnora are highly divergent and several complementary approaches using the highest possible sensitivity were required for identification and annotation of this plastome. Active transcription is detected for all of the protein-coding genes in the plastid genome, and one of two introns is appropriately spliced out of rps12 transcripts. The whole-genome shotgun read depth is 1,400× coverage for the plastome, whereas the mitochondrial genome is covered at 40× and the nuclear genome at 2×. Despite the extreme reduction of the genome and high sequence divergence, the presence of syntenic, long transcriptionally active open-reading frames with distant similarity to other plastid genomes and a high plastome stoichiometry relative to the mitochondrial and nuclear genomes suggests that the plastome remains functional in H. visseri. A four-stage model of gene reduction, including the potential for complete plastome loss, is proposed to account for the range of plastid genomes in nonphotosynthetic plants.
authors.affiliation: Institut für Botanik, Technische Universität Dresden, Germany Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University jxn25@psu.edu.
authors.forename: Julia
authors.initials: J
authors.lastname: Naumann
authors.affiliation: Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University Department of Biological Science, California State University Fullerton.
authors.forename: Joshua P
authors.initials: JP
authors.lastname: Der
authors.affiliation: Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University.
authors.forename: Eric K
authors.initials: EK
authors.lastname: Wafula
authors.affiliation: Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University Intercollege Graduate Program in Plant Biology, The Pennsylvania State University.
authors.forename: Samuel S
authors.initials: SS
authors.lastname: Jones
authors.affiliation: Institut für Botanik, Technische Universität Dresden, Germany.
authors.forename: Sarah T
authors.initials: ST
authors.lastname: Wagner
authors.affiliation: Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University.
authors.forename: Loren A
authors.initials: LA
authors.lastname: Honaas
authors.affiliation: Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University.
authors.forename: Paula E
authors.initials: PE
authors.lastname: Ralph
authors.affiliation: Department of Biology, Catawba College.
authors.forename: Jay F
authors.initials: JF
authors.lastname: Bolin
authors.affiliation: Department of Biological Sciences, University of Namibia, Windhoek, Namibia.
authors.forename: Erika
authors.initials: E
authors.lastname: Maass
authors.affiliation: Institut für Botanik, Technische Universität Dresden, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: Neinhuis
authors.affiliation: Institut für Botanik, Technische Universität Dresden, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Wanke
authors.affiliation: Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University Intercollege Graduate Program in Plant Biology, The Pennsylvania State University.
authors.forename: Claude W
authors.initials: CW
authors.lastname: dePamphilis
mesh_terms: D001483:Base Sequence; D021901:DNA, Intergenic / Q000235:genetics; D019143:Evolution, Molecular; D014644:Genetic Variation; D018745:Genome, Plant; D054627:Genome, Plastid; D007438:Introns; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D026321:Piperaceae / Q000235:genetics*; D012335:RNA, Ribosomal / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D012269:Ribosomal Proteins / Q000235:genetics
chemical_list: D021901:DNA, Intergenic; D012335:RNA, Ribosomal; D012269:Ribosomal Proteins; D012343:RNA, Transfer
keywords: Hydnoraceae; holoparasite; nonphotosynthetic; parasitic plants; plastid genome; plastome