Rampant Gene Loss in the Underground Orchid Rhizanthella gardneri Highlights Evolutionary Constraints on Plastid Genomes

Since the endosymbiotic origin of chloroplasts from cyanobacteria 2 billion years ago, the evolution of plastids has been characterized by massive loss of genes. Most plants and algae depend on photosynthesis for energy and have retained ∼110 genes in their chloroplast genome that encode components of the gene expression machinery and subunits of the photosystems. However, nonphotosynthetic parasitic plants have retained a reduced plastid genome, showing that plastids have other essential functions besides photosynthesis. We sequenced the complete plastid genome of the underground orchid, Rhizanthella gardneri. This remarkable parasitic subterranean orchid possesses the smallest organelle genome yet described in land plants. With only 20 proteins, 4 rRNAs, and 9 tRNAs encoded in 59,190 bp, it is the least gene-rich plastid genome known to date apart from the fragmented plastid genome of some dinoflagellates. Despite numerous differences, striking similarities with plastid genomes from unrelated parasitic plants identify a minimal set of protein-encoding and tRNA genes required to reside in plant plastids. This prime example of convergent evolution implies shared selective constraints on gene loss or transfer.

[1]  M. Chase,et al.  A phylogenetic analysis of Diurideae (Orchidaceae) based on plastid DNA sequence data. , 2001, American journal of botany.

[2]  Debashish Bhattacharya,et al.  A single origin of the peridinin- and fucoxanthin-containing plastids in dinoflagellates through tertiary endosymbiosis , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[3]  R. Tanaka,et al.  Tetrapyrrole biosynthesis in higher plants. , 2007, Annual review of plant biology.

[4]  K. Awai,et al.  Non-vesicular and vesicular lipid trafficking involving plastids. , 2006, Current opinion in plant biology.

[5]  Y. Asakura,et al.  Arabidopsis Orthologs of Maize Chloroplast Splicing Factors Promote Splicing of Orthologous and Species-Specific Group II Introns1[W] , 2006, Plant Physiology.

[6]  C. dePamphilis,et al.  Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function , 2005, BMC Evolutionary Biology.

[7]  M. Sugiura,et al.  An organellar maturase associates with multiple group II introns , 2010, Proceedings of the National Academy of Sciences.

[8]  C. dePamphilis,et al.  Functional gene losses occur with minimal size reduction in the plastid genome of the parasitic liverwort Aneura mirabilis. , 2008, Molecular biology and evolution.

[9]  Jeffrey P. Mower,et al.  The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. , 2006, Molecular biology and evolution.

[10]  Dean Laslett,et al.  ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. , 2004, Nucleic acids research.

[11]  A. Barbrook,et al.  Comparative analysis of dinoflagellate chloroplast genomes reveals rRNA and tRNA genes , 2006, BMC Genomics.

[12]  T. Börner,et al.  High diversity of plastidial promoters in Arabidopsis thaliana , 2007, Molecular Genetics and Genomics.

[13]  J. Leebens-Mack,et al.  Parallel Loss of Plastid Introns and Their Maturase in the Genus Cuscuta , 2009, PloS one.

[14]  Monika J. Madej,et al.  Identification of small non-coding RNAs from mitochondria and chloroplasts , 2006, Nucleic acids research.

[15]  G. Friso,et al.  Large Scale Comparative Proteomics of a Chloroplast Clp Protease Mutant Reveals Folding Stress, Altered Protein Homeostasis, and Feedback Regulation of Metabolism* , 2009, Molecular & Cellular Proteomics.

[16]  F. Wollman,et al.  Biogenesis of PSI involves a cascade of translational autoregulation in the chloroplast of Chlamydomonas , 2004, The EMBO journal.

[17]  D. Karcher,et al.  Superwobbling facilitates translation with reduced tRNA sets , 2008, Nature Structural &Molecular Biology.

[18]  Ralph Bock,et al.  Plastid protein synthesis is required for plant development in tobacco , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[19]  P. Maliga,et al.  The plastid clpP1 protease gene is essential for plant development , 2003, Nature.

[20]  Aaron M. Duffy,et al.  Conservation of selection on matK following an ancient loss of its flanking intron. , 2009, Gene.

[21]  K. H. Wolfe,et al.  Nucleotide Substitution Rates in Legume Chloroplast DNA Depend on the Presence of the Inverted Repeat , 2002, Journal of Molecular Evolution.

[22]  A. Clarke,et al.  Identification of new protein substrates for the chloroplast ATP-dependent Clp protease supports its constitutive role in Arabidopsis. , 2009, The Biochemical journal.

[23]  Chung-Yen Lin,et al.  The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications. , 2006, Molecular biology and evolution.

[24]  John W. Stiller,et al.  A SINGLE ORIGIN OF PLASTIDS REVISITED: CONVERGENT EVOLUTION IN ORGANELLAR GENOME CONTENT 1 , 2003 .

[25]  R. Bock,et al.  The two largest chloroplast genome-encoded open reading frames of higher plants are essential genes. , 2000, The Plant journal : for cell and molecular biology.

[26]  P. Grierson,et al.  Carbon and nitrogen supply to the underground orchid, Rhizanthella gardneri. , 2010, The New phytologist.

[27]  M. Strath,et al.  Complete gene map of the plastid-like DNA of the malaria parasite Plasmodium falciparum. , 1996, Journal of molecular biology.

[28]  M. Press,et al.  Localization of photosynthetic metabolism in the parasitic angiosperm Cuscuta reflexa , 1998, Planta.

[29]  S. Malfatti,et al.  The Complete Plastid Genome Sequence of the Secondarily Nonphotosynthetic Alga Cryptomonas paramecium: Reduction, Compaction, and Accelerated Evolutionary Rate , 2009, Genome biology and evolution.

[30]  Linda A. Raubeson,et al.  Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus , 2007, BMC Genomics.

[31]  D. Morrison,et al.  Monocots: Systematics and Evolution , 2000 .

[32]  D. Knowles,et al.  Babesia bovis: a comprehensive phylogenetic analysis of plastid-encoded genes supports green algal origin of apicoplasts. , 2009, Experimental parasitology.

[33]  A. Millar,et al.  The pentatricopeptide repeat gene OTP51 with two LAGLIDADG motifs is required for the cis-splicing of plastid ycf3 intron 2 in Arabidopsis thaliana. , 2008, The Plant journal : for cell and molecular biology.

[34]  J. Palmer,et al.  Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[35]  J. Palmer,et al.  Chloroplast genomes of two conifers lack a large inverted repeat and are extensively rearranged. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[36]  P. Maliga,et al.  The two RNA polymerases encoded by the nuclear and the plastid compartments transcribe distinct groups of genes in tobacco plastids , 1997, The EMBO journal.

[37]  W. Hess,et al.  Comparative analysis of splicing of the complete set of chloroplast group II introns in three higher plant mutants. , 1999, Nucleic acids research.

[38]  Aubrey D N J de Grey,et al.  Forces maintaining organellar genomes: is any as strong as genetic code disparity or hydrophobicity? , 2005, BioEssays : news and reviews in molecular, cellular and developmental biology.

[39]  Robert C. Edgar,et al.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.

[40]  M. Hasegawa,et al.  Gene transfer to the nucleus and the evolution of chloroplasts , 1998, Nature.

[41]  M. Kearney,et al.  Birth of a biome: insights into the assembly and maintenance of the Australian arid zone biota , 2008, Molecular ecology.

[42]  Uwe G Maier,et al.  Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii , 2007, BMC Plant Biology.

[43]  Aubrey D.N.J. de Grey,et al.  Forces maintaining organellar genomes: is any as strong as genetic code disparity or hydrophobicity? , 2005 .

[44]  I. Small,et al.  Pentatricopeptide repeat proteins: a socket set for organelle gene expression. , 2008, Trends in plant science.

[45]  J. Palmer,et al.  The chloroplast genome arrangement ofLobelia thuliniana (Lobeliaceae): Expansion of the inverted repeat in an ancestor of theCampanulales , 1999, Plant Systematics and Evolution.

[46]  T. Konishi,et al.  Acetyl-CoA carboxylase in higher plants: most plants other than gramineae have both the prokaryotic and the eukaryotic forms of this enzyme. , 1996, Plant & cell physiology.

[47]  Sujith Puthiyaveetil,et al.  Energy transduction anchors genes in organelles. , 2005, BioEssays : news and reviews in molecular, cellular and developmental biology.

[48]  A. Horák,et al.  A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids , 2010, Proceedings of the National Academy of Sciences.

[49]  J. Archibald.  The Puzzle of Plastid Evolution , 2009, Current Biology.

[50]  Sergey Koren,et al.  Aggressive assembly of pyrosequencing reads with mates , 2008, Bioinform..

[51]  N. Pierce,et al.  Dating the origin of the Orchidaceae from a fossil orchid with its pollinator , 2007, Nature.

[52]  Wen-Hsiung Li,et al.  Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[53]  John P. Huelsenbeck,et al.  MrBayes 3: Bayesian phylogenetic inference under mixed models , 2003, Bioinform..

[54]  A. Barbrook,et al.  Why are plastid genomes retained in non-photosynthetic organisms? , 2006, Trends in plant science.

[55]  K. H. Wolfe,et al.  A subset of conserved tRNA genes in plastid DNA of nongreen plants. , 1998, Genetics.

[56]  A. Day,et al.  The tobacco plastid accD gene is essential and is required for leaf development. , 2005, The Plant journal : for cell and molecular biology.

[57]  B. Lang,et al.  Purification of mitochondrial and plastid DNA , 2007, Nature Protocols.

[58]  P. Grierson,et al.  Identity and specificity of the fungi forming mycorrhizas with the rare mycoheterotrophic orchid Rhizanthella gardneri. , 2009, Mycological research.

[59]  D. Daley,et al.  Why genes persist in organelle genomes , 2005, Genome Biology.

[60]  Mark C. Brundrett.  Mycorrhizal associations and other means of nutrition of vascular plants: understanding the global diversity of host plants by resolving conflicting information and developing reliable means of diagnosis , 2009, Plant and Soil.

[61]  A. Barkan,et al.  Nuclear mutations that block group II RNA splicing in maize chloroplasts reveal several intron classes with distinct requirements for splicing factors. , 1997, The Plant cell.

[62]  A. Barbrook,et al.  The remarkable chloroplast genome of dinoflagellates. , 2007, Journal of experimental botany.

[63]  J. Palmer,et al.  A Plastid of Probable Green Algal Origin in Apicomplexan Parasites , 1997, Science.

[64]  Y. Ogihara,et al.  Phylogenetic affinities of the grasses to other monocots as revealed by molecular analysis of chloroplast DNA , 1996, Current Genetics.

[65]  D. Meinke,et al.  Requirement of aminoacyl-tRNA synthetases for gametogenesis and embryo development in Arabidopsis. , 2005, The Plant journal : for cell and molecular biology.

[66]  R. Jansen,et al.  Extensive Reorganization of the Plastid Genome of Trifolium subterraneum (Fabaceae) Is Associated with Numerous Repeated Sequences and Novel DNA Insertions , 2008, Journal of Molecular Evolution.

[67]  A. Stengel,et al.  Protein import into chloroplasts: new aspects of a well-known topic , 2007, Biological chemistry.

[68]  K. V. van Wijk,et al.  Subunits of the Plastid ClpPR Protease Complex Have Differential Contributions to Embryogenesis, Plastid Biogenesis, and Plant Development in Arabidopsis[C][W] , 2009, The Plant Cell Online.

[69]  J. Palmer,et al.  Loss of photosynthetic and chlororespiratory genes from the plastid genome of a parasitic flowering plant , 1990, Nature.

[70]  W. Zerges.  Does complexity constrain organelle evolution? , 2002, Trends in plant science.

[71]  Claude W dePamphilis,et al.  The evolution of parasitism in plants. , 2010, Trends in plant science.

[72]  T. Hübschmann,et al.  Splicing and intron-internal RNA editing of trnK-matK transcripts in barley plastids: support for MatK as an essential splice factor. , 1997, Journal of molecular biology.