The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes (Q21145727)

April 2022 Public Data File from Crossref

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The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes

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Telomere formation on macronuclear chromosomes of Oxytricha trifallax and O. fallax: alternatively processed regions have multiple telomere addition sites.

19 March 2017

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19 March 2017

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19 March 2017

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A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

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Consed: a graphical tool for sequence finishing

19 March 2017

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Base-calling of automated sequencer traces using phred. I. Accuracy assessment

19 March 2017

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The Saccharomyces CDC13 protein is a single-strand TG1-3 telomeric DNA-binding protein in vitro that affects telomere behavior in vivo

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Cdc13p: a single-strand telomeric DNA-binding protein with a dual role in yeast telomere maintenance

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Feedback control of mitosis in budding yeast

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MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons

19 March 2017

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SHRiMP2: sensitive yet practical SHort Read Mapping

19 March 2017

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ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia

19 March 2017

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A domesticated piggyBac transposase plays key roles in heterochromatin dynamics and DNA cleavage during programmed DNA deletion in Tetrahymena thermophila

19 March 2017

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Assessing the gene space in draft genomes

19 March 2017

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KEGG for integration and interpretation of large-scale molecular data sets

19 March 2017

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Search and clustering orders of magnitude faster than BLAST

7 April 2017

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7 April 2017

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7 April 2017

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7 April 2017

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Computational method to predict mitochondrially imported proteins and their targeting sequences

7 April 2017

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A new generation of homology search tools based on probabilistic inference

7 April 2017

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tRNAdb 2009: compilation of tRNA sequences and tRNA genes

7 April 2017

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Gene prediction with a hidden Markov model and a new intron submodel

7 April 2017

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Codon usage and tRNA content in unicellular and multicellular organisms

7 April 2017

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The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences

7 April 2017

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Characterization and taxonomic validity of the ciliate Oxytricha trifallax (Class Spirotrichea) based on multiple gene sequences: limitations in identifying genera solely by morphology

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

The Oxytricha trifallax mitochondrial genome

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

The Pot1a-associated proteins Tpt1 and Pat1 coordinate telomere protection and length regulation in Tetrahymena.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Targeted assembly of short sequence reads

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

RNA-mediated epigenetic regulation of DNA copy number

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

RNA-dependent control of gene amplification

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Assembly of large genomes using second-generation sequencing

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

POT1 proteins in green algae and land plants: DNA-binding properties and evidence of co-evolution with telomeric DNA

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Genetic diversity in the Paramecium aurelia species complex.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

RNA-mediated epigenetic programming of a genome-rearrangement pathway

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Extreme genomic variation in a natural population

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Tetrahymena POT1a regulates telomere length and prevents activation of a cell cycle checkpoint

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Recent expansion of the telomeric complex in rodents: Two distinct POT1 proteins protect mouse telomeres

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Nowa1p and Nowa2p: novel putative RNA binding proteins involved in trans-nuclear crosstalk in Paramecium tetraurelia

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

The effective size of mixed sexually and asexually reproducing populations

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Developmentally regulated chromosome fragmentation linked to imprecise elimination of repeated sequences in paramecia.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

The population genetics of clonal and partially clonal diploids.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Multiple protein phylogenies show that Oxyrrhis marina and Perkinsus marinus are early branches of the dinoflagellate lineage

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Organization of the macronuclear gene-sized pieces of stichotrichous ciliates into a higher order structure via telomere-matrix interactions

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Oxytricha telomere-binding protein: separable DNA-binding and dimerization domains of the alpha-subunit

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Macronuclear gene-sized molecules of hypotrichs

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Scrambling of the actin I gene in two Oxytricha species

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Three different macronuclear DNAs in Oxytricha fallax share a common sequence block

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Sequence structures of two developmentally regulated, alternative DNA deletion junctions in Tetrahymena thermophila

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Telomeric DNA-protein interactions of Oxytricha macronuclear DNA.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Reordering of nine exons is necessary to form a functional actin gene in Oxytricha nova

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Overamplification of macronuclear linear DNA molecules during prolonged vegetative growth of Oxytricha nova

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

A high degree of macronuclear chromosome polymorphism is generated by variable DNA rearrangements in Paramecium primaurelia during macronuclear differentiation

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Euplotes crassus has genes encoding telomere-binding proteins and telomere-binding protein homologs

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Whole genome studies of Tetrahymena

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

PCAP: a whole-genome assembly program

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

A unique pattern of intrastrand anomalies in base composition of the DNA in hypotrichs

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

The telomere binding protein of Euplotes crassus prevents non-specific transcription initiation but has no role in positioning transcription initiation complexes

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Multiple sequence versions of the Oxytricha fallax 81-MAC alternate processing family

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Alternative use of chromosome fragmentation sites in the ciliated protozoan Oxytricha nova.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Chromatin structure in the macronucleus of the ciliate Stylonychia mytilus

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

A functional role for transposases in a large eukaryotic genome

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Developmental genome reorganization in ciliated protozoa: the transposon link

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements in the ciliate Paramecium tetraurelia

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Transposase-derived transcription factors regulate light signaling in Arabidopsis

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Internal eliminated sequences interrupting the Oxytricha 81 locus: allelic divergence, conservation, conversions, and possible transposon origins.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Gene-sized DNA molecules of the macronuclei in three species of hypotrichs: size distributions and absence of nicks. DNA of ciliated protozoa. VIII.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Control of rDNA replication in Tetrahymena involves a cis-acting upstream repeat of a promoter element.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Mobile elements bounded by C4A4 telomeric repeats in Oxytricha fallax.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3558436

Modeling senescence in hypotrichous ciliates.

30 May 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1001473

A weak germ-line excision mutation blocks developmentally controlled amplification of the rDNA minichromosome of Tetrahymena thermophila.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1001473

IDBA – A Practical Iterative de Bruijn Graph De Novo Assembler

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1001473

Assembling millions of short DNA sequences using SSAKE.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1001473

Patterns of protein evolution in Tetrahymena thermophila: implications for estimates of effective population size.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1001473

Large global effective population sizes in Paramecium

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1001473

Nucleotide sequence of a macronuclear gene for actin in Oxytricha fallax.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1001473

The FHY3 and FAR1 genes encode transposase‐related proteins involved in regulation of gene expression by the phytochrome A‐signaling pathway

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1001473

Analysis of the DDE motif in the Mutator superfamily.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1001473

Accumulation of telomerase RNA and telomere protein transcripts during telomere synthesis in Euplotes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1001473

Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1001473

21 January 2018

DNA of ciliated protozoa

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1001473

Using native and syntenically mapped cDNA alignments to improve de novo gene finding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1001473

Alternative processing of sequences during macronuclear development in Tetrahymena thermophila

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1001473

Alternative processing during development of a macronuclear chromosome family in Oxytricha fallax

21 January 2018

1 reference

12 December 2020

PE-Assembler: de novo assembler using short paired-end reads

1 reference

12 December 2020

Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project

1 reference

12 December 2020

The development of the macronucleus in the ciliated protozoan Stylonychia mytilus

1 reference

12 December 2020

Widespread distribution of extensive chromosomal fragmentation in ciliates

1 reference

12 December 2020

Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax

1 reference

12 December 2020

DNA of ciliated protozoa: DNA sequence diminution during macronuclear development of Oxytricha

1 reference

12 December 2020

A micronuclear locus containing three protein-coding genes remains linked during macronuclear development in the spirotrichous ciliate Holosticha

1 reference

12 December 2020

Telomeric properties of C4A4-homologous sequences in micronuclear DNA of Oxytricha fallax

1 reference

12 December 2020

Rate of phenotypic assortment in Tetrahymena thermophila

1 reference

12 December 2020

Timing of differential amplification of macronucleus-destined sequences during macronuclear development in the hypotrichous ciliate Euplotes crassus

1 reference

12 December 2020

Characterization of macronuclear DNA in five species of ciliates

1 reference

12 December 2020

RNA and macronuclear transcription in the ciliate Stylonychia mytilus

1 reference

12 December 2020

Morphology and development of the macronuclei of the ciliates Stylonychia mytilus and Euplotes aediculatus

1 reference

12 December 2020

Arrangement of coding and non-coding sequences in the DNA molecules coding for rRNAs in Oxytricha sp. DNA of ciliated protozoa. VII

1 reference

12 December 2020

Topological organization of DNA molecules in the macronucleus of hypotrichous ciliated protozoa

1 reference

12 December 2020

Minichromosomal DNA replication in the macronucleus of the hypotrichous ciliate Stylonychia lemnae is independent of chromosome-internal sequences

1 reference

12 December 2020

Association of the telomere-telomere-binding protein complex of hypotrichous ciliates with the nuclear matrix and dissociation during replication

1 reference

12 December 2020

Telomere proteins: specific recognition and protection of the natural termini of Oxytricha macronuclear DNA

1 reference

12 December 2020

10.1371/JOURNAL.PBIO.1001473

Identifiers

DOI

1 reference

1981104

1981104

1 reference

1 reference

1 reference