The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes
暂无分享,去创建一个
J. Matese | R. Wilson | R. Fulton | E. Mardis | S. Eddy | T. A. Jones | S. McGrath | L. Landweber | J. Bracht | V. Magrini | P. Minx | Yi Zhou | Lance L. Parsons | M. Nowacki | D. Storton | Amy Ly | N. A. Stover | Jaspreet S. Khurana | E. Swart | T. Doak | A. Goldman | Seolkyoung Jung | Klaas Schotanus | Xiao Chen | K. Haub | J. L. Wiggins | Wei-Jen Chang | Michael S. Bowen | G. Herrick | R. Wilson | K. Schotanus
[1] C. Price,et al. Tetrahymena POT1a Regulates Telomere Length and Prevents Activation of a Cell CycleCheckpoint , 2006, Molecular and Cellular Biology.
[2] M. Yao,et al. A Domesticated piggyBac Transposase Plays Key Roles in Heterochromatin Dynamics and DNA Cleavage during Programmed DNA Deletion in Tetrahymena thermophila , 2010, Molecular biology of the cell.
[3] D. L. Nanney,et al. An Analysis of Nuclear Differentiation in the Selfers of Tetrahymena , 1958, The American Naturalist.
[4] P. Quail,et al. The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway. , 2003, The Plant journal : for cell and molecular biology.
[5] C. Price,et al. Euplotes crassus has genes encoding telomere-binding proteins and telomere-binding protein homologs. , 1992, Nucleic acids research.
[6] L. Hillier,et al. PCAP: a whole-genome assembly program. , 2003, Genome research.
[7] Laura F. Landweber,et al. RNA-mediated epigenetic programming of a genome-rearrangement pathway , 2008, Nature.
[8] E. Shakirov,et al. POT1 proteins in green algae and land plants: DNA-binding properties and evidence of co-evolution with telomeric DNA , 2009, Nucleic acids research.
[9] A. Nock. RNA and Macronuclear transcription in the ciliate Stylonychia mytilus , 2004, Chromosoma.
[10] M. Lynch,et al. Large global effective population sizes in Paramecium. , 2006, Molecular biology and evolution.
[11] Michael Lynch,et al. Genetic diversity in the Paramecium aurelia species complex. , 2009, Molecular biology and evolution.
[12] D M Prescott,et al. Reordering of nine exons is necessary to form a functional actin gene in Oxytricha nova. , 1989, Proceedings of the National Academy of Sciences of the United States of America.
[13] D M Prescott,et al. Scrambling of the actin I gene in two Oxytricha species. , 1995, Proceedings of the National Academy of Sciences of the United States of America.
[14] L. Katz,et al. Patterns of protein evolution in Tetrahymena thermophila: implications for estimates of effective population size. , 2006, Molecular biology and evolution.
[15] T. Lange,et al. Recent Expansion of the Telomeric Complex in Rodents: Two Distinct POT1 Proteins Protect Mouse Telomeres , 2006, Cell.
[16] John M. Heumann,et al. Gene-sized DNA molecules of the macronuclei in three species of hypotrichs: Size distributions and absence of nicks , 1980, Chromosoma.
[17] J. Lief,et al. Rate of phenotypic assortment in Tetrahymena thermophila. , 1992, Developmental genetics.
[18] I. Skovorodkin,et al. Minichromosomal DNA replication in the macronucleus of the hypotrichous ciliate Stylonychia lemnae is independent of chromosome-internal sequences , 2001, Chromosoma.
[19] I. Schensted. Appendix Model of Subnuclear Segregation in the Macronucleus of Ciliates , 1958, The American Naturalist.
[20] M. Huynen,et al. Macronuclear genome structure of the ciliate Nyctotherus ovalis: Single-gene chromosomes and tiny introns , 2008, BMC Genomics.
[21] Lucian Ilie,et al. SHRiMP2: Sensitive yet Practical Short Read Mapping , 2011, Bioinform..
[22] S. Cartinhour,et al. Multiple sequence versions of the Oxytricha fallax 81-MAC alternate processing family. , 1987, The Journal of protozoology.
[23] W. J. Kent,et al. BLAT--the BLAST-like alignment tool. , 2002, Genome research.
[24] W. Hennig,et al. The development of the macronucleus in the ciliated protozoan Stylonychia mytilus , 1974, Chromosoma.
[25] W. Miao,et al. Whole genome studies of Tetrahymena. , 2012, Methods in cell biology.
[26] F. Legeai,et al. Predotar: A tool for rapidly screening proteomes for N‐terminal targeting sequences , 2004, Proteomics.
[27] F. Jönsson,et al. Association of the telomere-telomere-binding protein complex of hypotrichous ciliates with the nuclear matrix and dissociation during replication. , 2001, Journal of cell science.
[28] J. Bender,et al. The telomere binding protein of Euplotes crassus prevents non-specific transcription initiation but has no role in positioning transcription initiation complexes. , 1997, Nucleic acids research.
[29] Ning Ma,et al. BLAST+: architecture and applications , 2009, BMC Bioinformatics.
[30] Sean R Eddy,et al. A new generation of homology search tools based on probabilistic inference. , 2009, Genome informatics. International Conference on Genome Informatics.
[31] Dan Liu,et al. TPP1 is a homologue of ciliate TEBP-β and interacts with POT1 to recruit telomerase , 2007, Nature.
[32] Kazutaka Katoh,et al. Recent developments in the MAFFT multiple sequence alignment program , 2008, Briefings Bioinform..
[33] Steven J. M. Jones,et al. Abyss: a Parallel Assembler for Short Read Sequence Data Material Supplemental Open Access , 2022 .
[34] J. Lin,et al. The Saccharomyces CDC13 protein is a single-strand TG1-3 telomeric DNA-binding protein in vitro that affects telomere behavior in vivo. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[35] L. Lehmann,et al. Molecular epidemiology of clonal diploids: a quick overview and a short DIY (do it yourself) notice. , 2006, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.
[36] T. Cech,et al. Oxytricha telomere-binding protein: separable DNA-binding and dimerization domains of the alpha-subunit. , 1993, Genes & development.
[37] Siu-Ming Yiu,et al. IDBA - A Practical Iterative de Bruijn Graph De Novo Assembler , 2010, RECOMB.
[38] Daniel J. G. Lahr,et al. Estimating the timing of early eukaryotic diversification with multigene molecular clocks , 2011, Proceedings of the National Academy of Sciences.
[39] D. Prescott,et al. DNA of ciliated protozoa , 1971, Chromosoma.
[40] Hiroyuki Ogata,et al. KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..
[41] L. Lehmann,et al. The population genetics of clonal and partially clonal diploids. , 2003, Genetics.
[42] Ujjwal Kumar,et al. Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control , 2011, Genome Biology.
[43] M. Horvath. Evolution of Telomere Binding Proteins , 2013 .
[44] Shuai Weng,et al. Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research , 2005, Nucleic Acids Res..
[45] L. Katz,et al. Widespread distribution of extensive chromosomal fragmentation in ciliates. , 2001, Molecular biology and evolution.
[46] G. Crooks,et al. WebLogo: a sequence logo generator. , 2004, Genome research.
[47] P. Keeling,et al. Multiple protein phylogenies show that Oxyrrhis marina and Perkinsus marinus are early branches of the dinoflagellate lineage. , 2003, International journal of systematic and evolutionary microbiology.
[48] T. Cech,et al. Telomeric DNA-protein interactions of Oxytricha macronuclear DNA. , 1987, Genes & development.
[49] Mario Stanke,et al. Gene prediction with a hidden Markov model and a new intron submodel , 2003, ECCB.
[50] M. Summers,et al. Acquisition of Host Cell DNA Sequences by Baculoviruses: Relationship Between Host DNA Insertions and FP Mutants of Autographa californica and Galleria mellonella Nuclear Polyhedrosis Viruses , 1983, Journal of virology.
[51] R. Guigó,et al. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia , 2006, Nature.
[52] J. Vermeesch,et al. Accumulation of Telomerase RNA and Telomere Protein Transcripts during Telomere Synthesis in Euplotes , 1994, The Journal of eukaryotic microbiology.
[53] G. A. Leng. ON POPULATION. , 1963, Singapore medical journal.
[54] Keith Bradnam,et al. Assessing the gene space in draft genomes , 2008, Nucleic acids research.
[55] Matthew M. Hill,et al. Extreme genomic variation in a natural population , 2007, Proceedings of the National Academy of Sciences.
[56] William H. Majoros,et al. Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote , 2006, PLoS biology.
[57] Benjamin E. Lauderdale,et al. The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences , 2012, PLoS genetics.
[58] A. Klein,et al. Timing of differential amplification of macronucleus-destined sequences during macronuclear development in the hypotrichous ciliateEuplotes crassus , 1996, Chromosoma.
[59] D. Witherspoon,et al. Internal eliminated sequences interrupting the Oxytricha 81 locus: allelic divergence, conservation, conversions, and possible transposon origins. , 1996, Molecular biology and evolution.
[60] Modeling senescence in hypotrichous ciliates. , 2004, Protist.
[61] M. Nowacki,et al. Nowa1p and Nowa2p: Novel Putative RNA Binding Proteins Involved in trans-Nuclear Crosstalk in Paramecium tetraurelia , 2005, Current Biology.
[62] T R Hughes,et al. Cdc13p: A Single-Strand Telomeric DNA-Binding Protein with a Dual Role in Yeast Telomere Maintenance , 1996, Science.
[63] L. Landweber,et al. A Functional Role for Transposases in a Large Eukaryotic Genome , 2009, Science.
[64] Thomas G Doak,et al. Telomere formation on macronuclear chromosomes of Oxytricha trifallax and O. fallax: alternatively processed regions have multiple telomere addition sites , 2002, BMC Genetics.
[65] G. Steinbrück,et al. Characterization of macronuclear DNA in five species of ciliates , 2004, Chromosoma.
[66] G. Herrick,et al. Alternative processing during development of a macronuclear chromosome family in Oxytricha fallax. , 1987, Genes & development.
[67] D. Prescott,et al. A unique pattern of intrastrand anomalies in base composition of the DNA in hypotrichs. , 2000, Nucleic acids research.
[68] Susumu Goto,et al. KEGG for integration and interpretation of large-scale molecular data sets , 2011, Nucleic Acids Res..
[69] T. C. White,et al. Alternative processing of sequences during macronuclear development in Tetrahymena thermophila. , 1986, The Journal of protozoology.
[70] P. Green,et al. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.
[71] T. Doak,et al. A proposed superfamily of transposase genes: transposon-like elements in ciliated protozoa and a common "D35E" motif. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[72] Serena Heyse. Functional divergence between Tetrahymena telomere proteins: Potential role for POT1b in chromosome breakage and new telomere synthesis , 2011 .
[73] T. Nagamine,et al. The Effective Size of Mixed Sexually and Asexually Reproducing Populations , 2004, Genetics.
[74] L. Klobutcher,et al. Developmental genome reorganization in ciliated protozoa: the transposon link. , 1997, Progress in nucleic acid research and molecular biology.
[75] J. Dawson. An experimental study of an amicronucleate Oxytricha. I. Study of the normal animal, with an account of cannibalism , 1919 .
[76] L. Landweber,et al. RNA-mediated epigenetic regulation of DNA copy number , 2010, Proceedings of the National Academy of Sciences.
[77] D. Prescott,et al. Topological organization of DNA molecules in the macronucleus of hypotrichous ciliated protozoa , 2004, Chromosome Research.
[78] Jonathan A Eisen,et al. Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure , 2008, BMC Genomics.
[79] Toni Gabaldón,et al. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..
[80] Rongcheng Lin,et al. Transposase-Derived Transcription Factors Regulate Light Signaling in Arabidopsis , 2007, Science.
[81] H. Lipps,et al. Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax. , 2012, Gene.
[82] Wing-Kin Sung,et al. PE-Assembler: de novo assembler using short paired-end reads , 2011, Bioinform..
[83] F. Jönsson,et al. RNA-dependent control of gene amplification , 2010, Proceedings of the National Academy of Sciences.
[84] P. Capy,et al. Analysis of the DDE Motif in the Mutator Superfamily , 2008, Journal of Molecular Evolution.
[85] Darren A. Natale,et al. The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.
[86] S. Cartinhour,et al. Three different macronuclear DNAs in Oxytricha fallax share a common sequence block , 1984, Molecular and cellular biology.
[87] Frédéric Delsuc,et al. MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons , 2011, PloS one.
[88] K. Song,et al. Overamplification of macronuclear linear DNA molecules during prolonged vegetative growth of Oxytricha nova. , 1991, Gene.
[89] G. Morin,et al. The Pot1a-associated proteins Tpt1 and Pat1 coordinate telomere protection and length regulation in Tetrahymena , 2011, Molecular biology of the cell.
[90] F. Jönsson,et al. Organization of the macronuclear gene-sized pieces of stichotrichous ciliates into a higher order structure via telomere–matrix interactions , 2004, Chromosome Research.
[91] John C. Marioni,et al. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data , 2009, Bioinform..
[92] R. Holt,et al. Targeted Assembly of Short Sequence Reads , 2011, PloS one.
[93] M. Schatz,et al. Assembly of large genomes using second-generation sequencing. , 2010, Genome research.
[94] D. Prescott,et al. Macronuclear gene-sized molecules of hypotrichs. , 1995, Nucleic acids research.
[95] Olivier Arnaiz,et al. ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia , 2010, Nucleic Acids Res..
[96] Jonathan E. Allen,et al. Genome sequence of the human malaria parasite Plasmodium falciparum , 2002, Nature.
[97] Andrew W. Murray,et al. Feedback control of mitosis in budding yeast , 1991, Cell.
[98] Lorenzo Orecchia,et al. Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project , 2004, Chromosoma.
[99] E. Mardis,et al. Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes , 2011, Nucleic acids research.
[100] F. Caron. A high degree of macronuclear chromosome polymorphism is generated by variable DNA rearrangements in Paramecium primaurelia during macronuclear differentiation. , 1992, Journal of molecular biology.
[101] D. Lisch. Mutator transposons. , 2002, Trends in plant science.
[102] David Haussler,et al. Using native and syntenically mapped cDNA alignments to improve de novo gene finding , 2008, Bioinform..
[103] A. Butler,et al. Developmentally Regulated Chromosome Fragmentation Linked to Imprecise Elimination of Repeated Sequences in Paramecia , 2003, Eukaryotic Cell.
[104] L. Landweber,et al. A micronuclear locus containing three protein-coding genes remains linked during macronuclear development in the spirotrichous ciliate Holosticha. , 2004, Protist.
[105] O. Gascuel,et al. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.
[106] D. Prescott,et al. DNA of ciliated protozoa: DNA sequence diminution during macronuclear development of oxytricha , 1976, Cell.
[107] P Vincens,et al. Computational method to predict mitochondrially imported proteins and their targeting sequences. , 1996, European journal of biochemistry.
[108] Lawrence A. Klobutcher,et al. Alternative use of chromosome fragmentation sites in the ciliated protozoan Oxytricha nova , 1988, Nucleic Acids Res..
[109] M. Yao,et al. Sequence structures of two developmentally regulated, alternative DNA deletion junctions in Tetrahymena thermophila , 1988, Molecular and cellular biology.
[110] R. Grosberg,et al. Muller's Ratchet. (Book Reviews: Sex and Death in Protozoa. The History of an Obsession.) , 1989 .
[111] Philippe Dessen,et al. Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline. , 2008, Genome research.
[112] C. Desmarais,et al. Automated finishing with autofinish. , 2001, Genome research.
[113] Robert C. Edgar,et al. BIOINFORMATICS APPLICATIONS NOTE , 2001 .
[114] René L. Warren,et al. Assembling millions of short DNA sequences using SSAKE , 2006, Bioinform..
[115] D. Dawson,et al. Telomeric properties of C4A4-homologous sequences in micronuclear DNA of Oxytricha fallax , 1984, Cell.
[116] B. Kaine,et al. Nucleotide sequence of a macronuclear gene for actin in Oxytricha fallax , 1982, Nature.
[117] E. Blackburn,et al. Control of rDNA replication in Tetrahymena involves a cis-acting upstream repeat of a promoter element , 1986, Cell.
[118] D. Ang,et al. Mobile elements bounded by C4A4 telomeric repeats in oxytricha fallax , 1985, Cell.
[119] Jason Wolfe. Structural aspects of amitosis: a light and electron microscope study of the isolated macronuclei of Paramecium aurelia and Tetrahymena pyriformis , 1967, Chromosoma.
[120] D. Ammermann. Morphology and development of the macronuclei of the ciliates Stylonychia mytilus and Euplotes aediculatus , 2004, Chromosoma.
[121] Aurélie Kapusta,et al. PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements in the ciliate Paramecium tetraurelia. , 2009, Genes & development.
[122] L. Landweber,et al. Characterization and taxonomic validity of the ciliate Oxytricha trifallax (Class Spirotrichea) based on multiple gene sequences: limitations in identifying genera solely by morphology. , 2012, Protist.
[123] D. Gottschling,et al. Telomere proteins: Specific recognition and protection of the natural termini of Oxytricha macronuclear DNA , 1986, Cell.
[124] E. Mardis,et al. The Oxytricha trifallax Mitochondrial Genome , 2011, Genome biology and evolution.
[125] E. Blackburn,et al. A weak germ-line excision mutation blocks developmentally controlled amplification of the rDNA minichromosome of Tetrahymena thermophila. , 1994, Genes & development.
[126] X. Huang,et al. CAP3: A DNA sequence assembly program. , 1999, Genome research.
[127] P. Green,et al. Consed: a graphical tool for sequence finishing. , 1998, Genome research.
[128] H. Lipps,et al. Chromatin structure in the macronucleus of the ciliate Stylonychia mytilus. , 1978, Nucleic acids research.
[129] Peter F. Stadler,et al. tRNAdb 2009: compilation of tRNA sequences and tRNA genes , 2008, Nucleic Acids Res..
[130] Ken Chen,et al. VarScan: variant detection in massively parallel sequencing of individual and pooled samples , 2009, Bioinform..
[131] T. Ikemura. Codon usage and tRNA content in unicellular and multicellular organisms. , 1985, Molecular biology and evolution.
[132] D. Prescott,et al. Arrangement of coding and non-coding sequences in the DNA molecules coding for rRNAs in Oxytricha sp. , 1980, Chromosoma.