Detecting and Characterizing the Highly Divergent Plastid Genome of the Nonphotosynthetic Parasitic Plant Hydnora visseri (Hydnoraceae).

Autor:	Naumann J; Institut für Botanik, Technische Universität Dresden, Germany Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University jxn25@psu.edu., Der JP; Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University Department of Biological Science, California State University Fullerton., Wafula EK; Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University., Jones SS; Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University Intercollege Graduate Program in Plant Biology, The Pennsylvania State University., Wagner ST; Institut für Botanik, Technische Universität Dresden, Germany., Honaas LA; Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University., Ralph PE; Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University., Bolin JF; Department of Biology, Catawba College., Maass E; Department of Biological Sciences, University of Namibia, Windhoek, Namibia., Neinhuis C; Institut für Botanik, Technische Universität Dresden, Germany., Wanke S; Institut für Botanik, Technische Universität Dresden, Germany., dePamphilis CW; Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University Intercollege Graduate Program in Plant Biology, The Pennsylvania State University.
Jazyk:	angličtina
Zdroj:	Genome biology and evolution [Genome Biol Evol] 2016 Jan 06; Vol. 8 (2), pp. 345-63. Date of Electronic Publication: 2016 Jan 06.
DOI:	10.1093/gbe/evv256
Abstrakt:	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. (© The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
Databáze:	MEDLINE
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