Plastid genome sequences of Gymnochlora stellata, Lotharella vacuolata, and Partenskyella glossopodia reveal remarkable structural conservation among chlorarachniophyte species

[1]  Monique Turmel,et al.  Dynamic Evolution of the Chloroplast Genome in the Green Algal Classes Pedinophyceae and Trebouxiophyceae , 2015, Genome biology and evolution.

[2]  Gangman Yi,et al.  The Plastid Genome of the Cryptomonad Teleaulax amphioxeia , 2015, PloS one.

[3]  K. Ishida,et al.  Nucleomorph Genome Sequences of Two Chlorarachniophytes, Amorphochlora amoebiformis and Lotharella vacuolata , 2015, Genome biology and evolution.

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

[5]  F. Leliaert,et al.  The chloroplast genomes of Bryopsis plumosa and Tydemania expeditiones (Bryopsidales, Chlorophyta): compact genomes and genes of bacterial origin , 2015, BMC Genomics.

[6]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

[7]  J. D. Vries,et al.  YCF 1 : A Green TIC ? , 2015 .

[8]  Y. Hirakawa.  Complex plastids of chlorarachniophyte algae , 2014 .

[9]  C. Lemieux,et al.  Six newly sequenced chloroplast genomes from prasinophyte green algae provide insights into the relationships among prasinophyte lineages and the diversity of streamlined genome architecture in picoplanktonic species , 2014, BMC Genomics.

[10]  S. Gould,et al.  Plastid survival in the cytosol of animal cells. , 2014, Trends in plant science.

[11]  Matthew W. Brown,et al.  Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae , 2014, BMC Genomics.

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

[13]  Masato Nakai,et al.  Uncovering the Protein Translocon at the Chloroplast Inner Envelope Membrane , 2013, Science.

[14]  A. Salamov,et al.  Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs , 2012, Nature.

[15]  Jens Stoye,et al.  UniMoG—a unifying framework for genomic distance calculation and sorting based on DCJ , 2012, Bioinform..

[16]  Maxim Teslenko,et al.  MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space , 2012, Systematic biology.

[17]  H. Doddapaneni,et al.  Cyanophora paradoxa Genome Elucidates Origin of Photosynthesis in Algae and Plants , 2012, Science.

[18]  C. Lemieux,et al.  The Chloroplast Genome of the Green Alga Schizomeris leibleinii (Chlorophyceae) Provides Evidence for Bidirectional DNA Replication from a Single Origin in the Chaetophorales , 2011, Genome biology and evolution.

[19]  K. Ishida,et al.  Partenskyella glossopodia (Chlorarachniophyceae) possesses a nucleomorph genome of approximately 1 Mbp , 2011 .

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

[21]  Songnian Hu,et al.  The Bryopsis hypnoides Plastid Genome: Multimeric Forms and Complete Nucleotide Sequence , 2011, PloS one.

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

[23]  C. Lemieux,et al.  The chloroplast genomes of the green algae Pedinomonas minor, Parachlorella kessleri, and Oocystis solitaria reveal a shared ancestry between the Pedinomonadales and Chlorellales. , 2009, Molecular biology and evolution.

[24]  J. Archibald,et al.  Going, going, not quite gone: nucleomorphs as a case study in nuclear genome reduction. , 2009, The Journal of heredity.

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

[26]  Kazutaka Katoh,et al.  Recent developments in the MAFFT multiple sequence alignment program , 2008, Briefings Bioinform..

[27]  G. McFadden,et al.  Plastid evolution. , 2008, Annual review of plant biology.

[28]  Motomi Ito,et al.  Origins of the secondary plastids of Euglenophyta and Chlorarachniophyta as revealed by an analysis of the plastid‐targeting, nuclear‐encoded gene psbO 1 , 2007 .

[29]  Peter F. Hallin,et al.  RNAmmer: consistent and rapid annotation of ribosomal RNA genes , 2007, Nucleic acids research.

[30]  B. Lang,et al.  Mitochondrial introns: a critical view. , 2007, Trends in genetics : TIG.

[31]  G. McFadden,et al.  The complete chloroplast genome of the chlorarachniophyte Bigelowiella natans: evidence for independent origins of chlorarachniophyte and euglenid secondary endosymbionts. , 2007, Molecular biology and evolution.

[32]  G. McFadden,et al.  Complete nucleotide sequence of the chlorarachniophyte nucleomorph: nature's smallest nucleus. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[33]  Richard Friedberg,et al.  Efficient sorting of genomic permutations by translocation, inversion and block interchange , 2005, Bioinform..

[34]  K. Ishida.  Protein targeting into plastids: a key to understanding the symbiogenetic acquisitions of plastids , 2005, Journal of Plant Research.

[35]  Naiara Rodríguez-Ezpeleta,et al.  Monophyly of Primary Photosynthetic Eukaryotes: Green Plants, Red Algae, and Glaucophytes , 2005, Current Biology.

[36]  Peter Schattner,et al.  The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs , 2005, Nucleic Acids Res..

[37]  A. Lambowitz,et al.  Mobile group II introns. , 2004, Annual review of genetics.

[38]  W. Martin,et al.  Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes , 2004, Nature Reviews Genetics.

[39]  R. Schnetter,et al.  Morphology, biology, and systematics ofCryptochlora perforans (Chlorarachniophyta), a phagotrophic marine alga , 1989, Plant Systematics and Evolution.

[40]  R. Schnetter,et al.  Cryptochlora perforans, a new genus and species of algae (Chlorarachniophyta), capable of penetrating dead algal filaments , 1987, Plant Systematics and Evolution.

[41]  Kim Rutherford,et al.  Artemis: sequence visualization and annotation , 2000, Bioinform..

[42]  J. Palmer,et al.  The cyanobacterial origin and vertical transmission of the plastid tRNALeu group-I intron , 2000, Current Genetics.

[43]  T. Cavalier-smith,et al.  Diversification of a Chimaeric Algal Group, the Chlorarachniophytes: Phylogeny of Nuclear and Nucleomorph Small-Subunit rRNA Genes , 1999 .

[44]  M. Hasegawa,et al.  The Origin of Chlorarachniophyte Plastids, as Inferred from Phylogenetic Comparisons of Amino Acid Sequences of EF-Tu , 1997, Journal of Molecular Evolution.

[45]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[46]  Y Van de Peer,et al.  Substitution rate calibration of small subunit ribosomal RNA identifies chlorarachniophyte endosymbionts as remnants of green algae. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[47]  J. Palmer,et al.  An ancient group I intron shared by eubacteria and chloroplasts , 1990, Science.

[48]  K. Clark,et al.  SURVEY FOR FUNCTIONAL KLEPTOPLASTY AMONG WEST ATLANTIC ASCOGLOSSA (= SACOGLOSSA) (MOLLUSCA, OPISTHOBRANCHIA) , 1990 .