Gene loss and genome rearrangement in the plastids of five Hemiparasites in the family Orobanchaceae

[1]  G. Serino,et al.  Plastid transformation in Arabidopsis thaliana , 2019, Plant Cell Reports.

[2]  K. Han,et al.  Complete chloroplast genome sequence of Pedicularis cheilanthifolia, an alpine plant in China , 2017, Conservation Genetics Resources.

[3]  P. Taberlet,et al.  Understanding the evolution of holoparasitic plants: the complete plastid genome of the holoparasite Cytinus hypocistis (Cytinaceae). , 2016, Annals of botany.

[4]  M. Logacheva,et al.  Comparative analysis of plastid genomes of non-photosynthetic Ericaceae and their photosynthetic relatives , 2016, Scientific Reports.

[5]  C. dePamphilis,et al.  Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants , 2016, Proceedings of the National Academy of Sciences.

[6]  Sudhir Kumar,et al.  MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. , 2016, Molecular biology and evolution.

[7]  M. Logacheva,et al.  Complete Plastid Genome of the Recent Holoparasite Lathraea squamaria Reveals Earliest Stages of Plastome Reduction in Orobanchaceae , 2016, PloS one.

[8]  Jeffrey P. Mower,et al.  Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates. , 2016, The New phytologist.

[9]  Sarah T. Wagner,et al.  Detecting and Characterizing the Highly Divergent Plastid Genome of the Nonphotosynthetic Parasitic Plant Hydnora visseri (Hydnoraceae) , 2016, Genome biology and evolution.

[10]  Susanne S. Renner,et al.  The Plastomes of Two Species in the Endoparasite Genus Pilostyles (Apodanthaceae) Each Retain Just Five or Six Possibly Functional Genes , 2015, Genome biology and evolution.

[11]  Robert K. Jansen,et al.  Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP , 2015, Scientific Reports.

[12]  Filipa L. Sousa,et al.  YCF1: A Green TIC? , 2015, Plant Cell.

[13]  S. Downie,et al.  A Comparative Analysis of Whole Plastid Genomes from the Apiales: Expansion and Contraction of the Inverted Repeat, Mitochondrial to Plastid Transfer of DNA, and Identification of Highly Divergent Noncoding Regions , 2015 .

[14]  Timothy B Sackton,et al.  Investigating the path of plastid genome degradation in an early-transitional clade of heterotrophic orchids, and implications for heterotrophic angiosperms. , 2014, Molecular biology and evolution.

[15]  Justin N. Vaughn,et al.  Whole Plastome Sequences from Five Ginger Species Facilitate Marker Development and Define Limits to Barcode Methodology , 2014, PloS one.

[16]  Jeffrey P. Mower,et al.  Predominant and Substoichiometric Isomers of the Plastid Genome Coexist within Juniperus Plants and Have Shifted Multiple Times during Cupressophyte Evolution , 2014, Genome biology and evolution.

[17]  Rachel S. Meyer,et al.  Possible Loss of the Chloroplast Genome in the Parasitic Flowering Plant Rafflesia lagascae (Rafflesiaceae) , 2014, Molecular biology and evolution.

[18]  Koichiro Tamura,et al.  MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. , 2013, Molecular biology and evolution.

[19]  C. Neinhuis,et al.  Single-Copy Nuclear Genes Place Haustorial Hydnoraceae within Piperales and Reveal a Cretaceous Origin of Multiple Parasitic Angiosperm Lineages , 2013, PloS one.

[20]  Yan Zhang,et al.  Mechanisms of Functional and Physical Genome Reduction in Photosynthetic and Nonphotosynthetic Parasitic Plants of the Broomrape Family[W][OPEN] , 2013, Plant Cell.

[21]  S. Mathews,et al.  Phylogeny and origins of holoparasitism in Orobanchaceae. , 2013, American journal of botany.

[22]  Shane S. Sturrock,et al.  Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data , 2012, Bioinform..

[23]  J. Bennetzen,et al.  Genomic Characterization for Parasitic Weeds of the Genus Striga by Sample Sequence Analysis , 2012 .

[24]  Kai F. Müller,et al.  The evolution of the plastid chromosome in land plants: gene content, gene order, gene function , 2011, Plant Molecular Biology.

[25]  J. B. Davidson,et al.  The evolution of chloroplast genes and genomes in ferns , 2011, Plant Molecular Biology.

[26]  S. H. Wani,et al.  Plant Plastid Engineering , 2010, Current genomics.

[27]  Aaron M. Duffy,et al.  The evolution of chloroplast genome structure in ferns. , 2010, Genome.

[28]  Bartolomé Sabater,et al.  Plastid ndh genes in plant evolution. , 2010, Plant physiology and biochemistry : PPB.

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

[30]  P. Keeling The endosymbiotic origin, diversification and fate of plastids , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.

[31]  H. Daniell,et al.  Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae , 2010, BMC Plant Biology.

[32]  Aaron M. Duffy,et al.  Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes , 2010, BMC Genomics.

[33]  R. Jansen,et al.  Implications of the Plastid Genome Sequence of Typha (Typhaceae, Poales) for Understanding Genome Evolution in Poaceae , 2010, Journal of Molecular Evolution.

[34]  B. Lang,et al.  Whirly proteins maintain plastid genome stability in Arabidopsis , 2009, Proceedings of the National Academy of Sciences.

[35]  Ching-Ping Lin,et al.  Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: selection toward a lower-cost strategy. , 2009, Molecular phylogenetics and evolution.

[36]  H. Funk,et al.  Functional characterization of the thylakoid Ndh complex phosphorylation by site-directed mutations in the ndhF gene. , 2009, Biochimica et biophysica acta.

[37]  Felix Grewe,et al.  A trans-splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii , 2009, Nucleic acids research.

[38]  A. Phongdara,et al.  Cloning and expression of a plastid-encoded subunit, beta-carboxyltransferase gene (accD) and a nuclear-encoded subunit, biotin carboxylase of acetyl-CoA carboxylase from oil palm (Elaeis guineensis Jacq.) , 2008 .

[39]  K. Krause From chloroplasts to “cryptic” plastids: evolution of plastid genomes in parasitic plants , 2008, Current Genetics.

[40]  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.

[41]  Linda A. Raubeson,et al.  The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates , 2008, BMC Evolutionary Biology.

[42]  S. Chaw,et al.  Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots , 2008, BMC Evolutionary Biology.

[43]  C. dePamphilis,et al.  Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae) , 2007, BMC Biology.

[44]  James Leebens-Mack,et al.  Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns , 2007, Proceedings of the National Academy of Sciences.

[45]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[46]  J. Boore,et al.  Bmc Plant Biology , 2007 .

[47]  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.

[48]  R. Bock Structure, function, and inheritance of plastid genomes , 2007 .

[49]  S. Mathews,et al.  Phylogeny of the parasitic plant family Orobanchaceae inferred from phytochrome A. , 2006, American journal of botany.

[50]  J. Tomkins,et al.  Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes , 2006, Theoretical and Applied Genetics.

[51]  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.

[52]  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.

[53]  Alexander Richter,et al.  ChloroplastDB: the Chloroplast Genome Database , 2005, Nucleic Acids Res..

[54]  K. H. Wolfe,et al.  Ebb and flow of the chloroplast inverted repeat , 1996, Molecular and General Genetics MGG.

[55]  Robert K. Jansen,et al.  Chloroplast genomes of plants. , 2005 .

[56]  Robert J Henry,et al.  Plant Diversity and Evolution: Genotypic and Phenotypic Variation in Higher Plants , 2004 .

[57]  G. McFadden,et al.  Evolution: Red Algal Genome Affirms a Common Origin of All Plastids , 2004, Current Biology.

[58]  F. Blattner,et al.  Mauve: multiple alignment of conserved genomic sequence with rearrangements. , 2004, Genome research.

[59]  B. Bremer,et al.  Molecular phylogenetic dating of asterid flowering plants shows early Cretaceous diversification. , 2004, Systematic biology.

[60]  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.

[61]  C. dePamphilis,et al.  Do nonasterid holoparasitic flowering plants have plastid genomes? , 1997, Plant Molecular Biology.

[62]  J. Palmer,et al.  Structure and evolution of the largest chloroplast gene (ORF2280): internal plasticity and multiple gene loss during angiosperm evolution , 1994, Current Genetics.

[63]  M. Sugiura,et al.  Chloroplast DNA of black pine retains a residual inverted repeat lacking rRNA genes: nucleotide sequences of trnQ, trnK, psbA, trnI and trnH and the absence of rps16 , 1992, Molecular and General Genetics MGG.

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

[65]  Sabine Cornelsen,et al.  Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[66]  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.

[67]  C. dePamphilis,et al.  Disintegration of the scrophulariaceae. , 2001, American journal of botany.

[68]  J. Palmer Molecular evolution: A single birth of all plastids? , 2000, Nature.

[69]  J. Zapata,et al.  Chlororespiration and Poising of Cyclic Electron Transport , 2000, The Journal of Biological Chemistry.

[70]  S. Downie,et al.  Expansion and Contraction of the Chloroplast Inverted Repeat in Apiaceae Subfamily Apioideae , 2000 .

[71]  Kasten,et al.  Technical Advance: Stable chloroplast transformation in potato: use of green fluorescent protein as a plastid marker. , 1999, The Plant journal : for cell and molecular biology.

[72]  P. Delavault,et al.  Organization of the reduced plastid genome of Lathraea clandestina, an achlorophyllous parasitic plant. , 1996 .

[73]  T. Friedrich,et al.  The proton‐pumping respiratory complex I of bacteria and mitochondria and its homologue in chloroplasts , 1995, FEBS letters.

[74]  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.

[75]  J. Palmer,et al.  Restriction site mapping of the chloroplast DNA inverted repeat : A molecular phylogeny of the Asteridae , 1992 .

[76]  M. Sugiura,et al.  The chloroplast genome. , 1992, Plant molecular biology.

[77]  J. Palmer,et al.  CHAPTER 2 – Plastid Chromosomes: Structure and Evolution , 1991 .

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

[79]  P. Maliga,et al.  Stable transformation of plastids in higher plants. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[80]  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.

[81]  Jeffrey D. Palmer,et al.  Chloroplast DNA Evolution and Biosystematic Uses of Chloroplast DNA Variation , 1987, The American Naturalist.

[82]  J. Palmer,et al.  Comparative organization of chloroplast genomes. , 1985, Annual review of genetics.

[83]  E. Pahlich,et al.  A rapid DNA isolation procedure for small quantities of fresh leaf tissue , 1980 .

[84]  R. Kolodner,et al.  Inverted repeats in chloroplast DNA from higher plants. , 1979, Proceedings of the National Academy of Sciences of the United States of America.